Collagen alpha-1(I) chain precursor - Rattus norvegicus (Rat)

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P02454 (CO1A1_RAT) Reviewed, UniProtKB/Swiss-Prot

Last modified April 3, 2013. Version 118. History...

Clusters with 100%, 90%, 50% identity |

Documents (2) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
Collagen alpha-1(I) chain

Alternative name(s):
Alpha-1 type I collagen

Gene names

Name:

Col1a1

Organism

Rattus norvegicus (Rat) [Reference proteome]

Taxonomic identifier

10116 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Glires › Rodentia › Sciurognathi › Muroidea › Muridae › Murinae › Rattus

Protein attributes

Sequence length	1453 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Type I collagen is a member of group I collagen (fibrillar forming collagen).
Subunit structure	Trimers of one alpha 2(I) and two alpha 1(I) chains. Interacts with MRC2. Interacts with TRAM2 By similarity. Ref.15
Subcellular location	Secreted › extracellular space › extracellular matrix By similarity.
Tissue specificity	Forms the fibrils of tendon, ligaments and bones. In bones the fibrils are mineralized with calcium hydroxyapatite.
Domain	The C-terminal propeptide, also known as COLFI domain, have crucial roles in tissue growth and repair by controlling both the intracellular assembly of procollagen molecules and the extracellular assembly of collagen fibrils. It binds a calcium ion which is essential for its function By similarity.
Post-translational modification	Proline residues at the third position of the tripeptide repeating unit (G-X-P) are hydroxylated in some or all of the chains. Proline residues at the second position of the tripeptide repeating unit (G-P-X) are hydroxylated in some of the chains. O-linked glycan consists of a Glc-Gal disaccharide bound to the oxygen atom of a post-translationally added hydroxyl group. Hydroxylation on proline residues within the sequence motif, GXPG, is most likely to be 4-hydroxy as this fits the requirement for 4-hydroxylation in vertebrates.
Sequence similarities	Belongs to the fibrillar collagen family. Contains 1 fibrillar collagen NC1 domain. Contains 1 VWFC domain.

Ontologies

Keywords
Cellular component	Extracellular matrix Secreted
Domain	Collagen Repeat Signal
Ligand	Calcium Metal-binding
PTM	Disulfide bond Glycoprotein Hydroxylation Pyrrolidone carboxylic acid
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	blood vessel development Inferred from electronic annotation. Source: Compara bone trabecula formation Inferred from electronic annotation. Source: Compara cartilage development involved in endochondral bone morphogenesis Inferred from electronic annotation. Source: Compara cellular response to amino acid stimulus Inferred from electronic annotation. Source: Compara cellular response to mechanical stimulus Inferred from electronic annotation. Source: Compara cellular response to retinoic acid Inferred from expression pattern PubMed 1921334. Source: RGD cellular response to transforming growth factor beta stimulus Inferred from expression pattern PubMed 19362560. Source: UniProtKB collagen biosynthetic process Inferred from electronic annotation. Source: Compara collagen fibril organization Inferred from electronic annotation. Source: Compara embryonic skeletal system development Inferred from electronic annotation. Source: Compara endochondral ossification Inferred from electronic annotation. Source: Compara face morphogenesis Inferred from electronic annotation. Source: Compara intramembranous ossification Inferred from electronic annotation. Source: Compara negative regulation of cell-substrate adhesion Inferred from electronic annotation. Source: Compara ossification Inferred from expression pattern PubMed 14595530. Source: RGD osteoblast differentiation Inferred from electronic annotation. Source: Compara positive regulation of canonical Wnt receptor signaling pathway Inferred from electronic annotation. Source: Compara positive regulation of cell migration Inferred from electronic annotation. Source: Compara positive regulation of epithelial to mesenchymal transition Inferred from electronic annotation. Source: Compara positive regulation of transcription, DNA-dependent Inferred from electronic annotation. Source: Compara protein heterotrimerization Inferred from electronic annotation. Source: Compara protein localization to nucleus Inferred from electronic annotation. Source: Compara protein transport Inferred from electronic annotation. Source: Compara response to cAMP Inferred from expression pattern PubMed 10679825. Source: RGD response to corticosteroid stimulus Inferred from expression pattern PubMed 14993121. Source: RGD response to hydrogen peroxide Inferred from expression pattern PubMed 10051504. Source: RGD response to mechanical stimulus Inferred from expression pattern PubMed 11748224 PubMed 18988763. Source: RGD response to nutrient Inferred from expression pattern PubMed 15042712. Source: RGD response to peptide hormone stimulus Inferred from expression pattern PubMed 10679825. Source: RGD sensory perception of sound Inferred from electronic annotation. Source: Compara skin morphogenesis Inferred from electronic annotation. Source: Compara tooth mineralization Inferred from electronic annotation. Source: Compara visual perception Inferred from electronic annotation. Source: Compara wound healing Inferred from mutant phenotype PubMed 20647009. Source: RGD
Cellular_component	collagen type I Inferred from electronic annotation. Source: Compara cytoplasm Inferred from electronic annotation. Source: Compara extracellular space Inferred from direct assay PubMed 2659889. Source: RGD
Molecular_function	extracellular matrix structural constituent Inferred from electronic annotation. Source: Compara metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Signal peptide

1 – 22

Potential

Propeptide

23 – 151

129

N-terminal propeptide

PRO_0000043358

Chain

152 – 1207

1056

Collagen alpha-1(I) chain

PRO_0000043359

Propeptide

1208 – 1453

246

C-terminal propeptide By similarity

PRO_0000043360

Regions

Domain

29 – 87

VWFC

Domain

1218 – 1453

236

Fibrillar collagen NC1

Region

152 – 167

Nonhelical region (N-terminal)

Region

168 – 1181

1014

Triple-helical region

Region

1176 – 1186

Major antigenic determinant (of neutral salt-extracted rat skin collagen)

Region

1182 – 1207

Nonhelical region (C-terminal)

Motif

734 – 736

Cell attachment site Potential

Motif

1082 – 1084

Cell attachment site Potential

Sites

Metal binding

1266

Calcium By similarity

Metal binding

1268

Calcium By similarity

Metal binding

1269

Calcium; via carbonyl oxygen By similarity

Metal binding

1271

Calcium; via carbonyl oxygen By similarity

Metal binding

1274

Calcium By similarity

Amino acid modifications

Modified residue

152

Pyrrolidone carboxylic acid Probable

Modified residue

160

Allysine

Modified residue

179

4-hydroxyproline Probable

Modified residue

182

4-hydroxyproline Probable

Modified residue

185

4-hydroxyproline Probable

Modified residue

194

4-hydroxyproline Probable

Modified residue

197

4-hydroxyproline Probable

Modified residue

200

4-hydroxyproline Probable

Modified residue

254

5-hydroxylysine

Modified residue

575

5-hydroxylysine Probable

Modified residue

698

5-hydroxylysine Probable

Modified residue

1153

3-hydroxyproline By similarity

Glycosylation

N-linked (GlcNAc...) Potential

Glycosylation

254

O-linked (Gal...)

Glycosylation

1354

N-linked (GlcNAc...) Potential

Disulfide bond

1248 ↔ 1280

By similarity

Disulfide bond

1254

Interchain (with C-1271) By similarity

Disulfide bond

1271

Interchain (with C-1254) By similarity

Disulfide bond

1288 ↔ 1451

By similarity

Disulfide bond

1359 ↔ 1404

By similarity

Experimental info

Sequence conflict

143

P → L in CAB01633. Ref.1

Sequence conflict

202

A → G in CAB01633. Ref.1

Sequence conflict

209

R → P in CAB01633. Ref.1

Sequence conflict

232

E → Q AA sequence Ref.7

Sequence conflict

268

D → N AA sequence Ref.8

Sequence conflict

286

A → T in CAB01633. Ref.1

Sequence conflict

307

S → T in CAB01633. Ref.1

Sequence conflict

313

N → D AA sequence Ref.9

Sequence conflict

421

N → T in CAB01633. Ref.1

Sequence conflict

497

A → S in CAB01633. Ref.1

Sequence conflict

773

T → A in CAB01633. Ref.1

Sequence conflict

794

P → A in CAB01633. Ref.1

Sequence conflict

958

E → K in CAB01633. Ref.1

Sequence conflict

1111

S → P AA sequence Ref.13

Sequence conflict

1163

S → A AA sequence Ref.13

Sequence conflict

1166

A → S AA sequence Ref.13

Sequence conflict

1187

F → L AA sequence Ref.14

Sequence conflict

1190

L → F AA sequence Ref.14

Sequences

Sequence

Length

Mass (Da)

Tools

P02454 [UniParc].

Last modified September 22, 2009. Version 5.
Checksum: BCDDC40C3167AE59
Show »

FASTA

1,453

137,953

        10         20         30         40         50         60 
MFSFVDLRLL LLLGATALLT HGQEDIPEVS CIHNGLRVPN GETWKPDVCL ICICHNGTAV 

        70         80         90        100        110        120 
CDGVLCKEDL DCPNPQKREG ECCPFCPEEY VSPDAEVIGV EGPKGDPGPQ GPRGPVGPPG 

       130        140        150        160        170        180 
QDGIPGQPGL PGPPGPPGPP GPPGLGGNFA SQMSYGYDEK SAGVSVPGPM GPSGPRGLPG 

       190        200        210        220        230        240 
PPGAPGPQGF QGPPGEPGEP GASGPMGPRG PPGPPGKNGD DGEAGKPGRP GERGPPGPQG 

       250        260        270        280        290        300 
ARGLPGTAGL PGMKGHRGFS GLDGAKGDTG PAGPKGEPGS PGENGAPGQM GPRGLPGERG 

       310        320        330        340        350        360 
RPGPPGSAGA RGNDGAVGAA GPPGPTGPTG PPGFPGAAGA KGEAGPQGAR GSEGPQGVRG 

       370        380        390        400        410        420 
EPGPPGPAGA AGPAGNPGAD GQPGAKGANG APGIAGAPGF PGARGPSGPQ GPSGAPGPKG 

       430        440        450        460        470        480 
NSGEPGAPGN KGDTGAKGEP GPAGVQGPPG PAGEEGKRGA RGEPGPSGLP GPPGERGGPG 

       490        500        510        520        530        540 
SRGFPGADGV AGPKGPAGER GSPGPAGPKG SPGEAGRPGE AGLPGAKGLT GSPGSPGPDG 

       550        560        570        580        590        600 
KTGPPGPAGQ DGRPGPAGPP GARGQAGVMG FPGPKGTAGE PGKAGERGVP GPPGAVGPAG 

       610        620        630        640        650        660 
KDGEAGAQGA PGPAGPAGER GEQGPAGSPG FQGLPGPAGP PGEAGKPGEQ GVPGDLGAPG 

       670        680        690        700        710        720 
PSGARGERGF PGERGVQGPP GPAGPRGNNG APGNDGAKGD TGAPGAPGSQ GAPGLQGMPG 

       730        740        750        760        770        780 
ERGAAGLPGP KGDRGDAGPK GADGSPGKDG VRGLTGPIGP PGPAGAPGDK GETGPSGPAG 

       790        800        810        820        830        840 
PTGARGAPGD RGEPGPPGPA GFAGPPGADG QPGAKGEPGD TGVKGDAGPP GPAGPAGPPG 

       850        860        870        880        890        900 
PIGNVGAPGP KGSRGAAGPP GATGFPGAAG RVGPPGPSGN AGPPGPPGPV GKEGGKGPRG 

       910        920        930        940        950        960 
ETGPAGRPGE VGPPGPPGPA GEKGSPGADG PAGSPGTPGP QGIAGQRGVV GLPGQRGERG 

       970        980        990       1000       1010       1020 
FPGLPGPSGE PGKQGPSGAS GERGPPGPMG PPGLAGPPGE SGREGSPGAE GSPGRDGAPG 

      1030       1040       1050       1060       1070       1080 
AKGDRGETGP AGPPGAPGAP GAPGPVGPAG KNGDRGETGP AGPAGPIGPA GARGPAGPQG 

      1090       1100       1110       1120       1130       1140 
PRGDKGETGE QGDRGIKGHR GFSGLQGPPG SPGSPGEQGP SGASGPAGPR GPPGSAGSPG 

      1150       1160       1170       1180       1190       1200 
KDGLNGLPGP IGPPGPRGRT GDSGPAGPPG PPGPPGPPGP PSGGYDFSFL PQPPQEKSQD 

      1210       1220       1230       1240       1250       1260 
GGRYYRADDA NVVRDRDLEV DTTLKSLSQQ IENIRSPEGS RKNPARTCRD LKMCHSDWKS 

      1270       1280       1290       1300       1310       1320 
GEYWIDPNQG CNLDAIKVYC NMETGQTCVF PTQPSVPQKN WYISPNPKEK KHVWFGESMT 

      1330       1340       1350       1360       1370       1380 
DGFQFEYGSE GSDPADVAIQ LTFLRLMSTE ASQNITYHCK NSVAYMDQQT GNLKKSLLLQ 

      1390       1400       1410       1420       1430       1440 
GSNEIELRGE GNSRFTYSTL VDGCTSHTGT WGKTVIEYKT TKTSRLPIID VAPLDIGAPD 

      1450 
QEFGMDIGPA CFV

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Expression of collagen alpha1(I) mRNA variants during tooth and bone formation in the rat." Brandsten C., Lundmark C., Christersson C., Hammarstroem L., Wurtz T. J. Dent. Res. 78:11-19(1999) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA]. Strain: Sprague-Dawley. Tissue: Bone and Tooth.
[2]	Mural R.J., Adams M.D., Myers E.W., Smith H.O., Venter J.C. Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: Brown Norway.
[3]	"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)." The MGC Project Team Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Strain: Brown Norway. Tissue: Lung.
[4]	"Comparative sequence studies of rat skin and tendon collagen. II. The absence of a short sequence at the amino terminus of the skin alpha-1 chain." Bornstein P. Biochemistry 8:63-71(1969) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 152-170.
[5]	"The amino acid sequence of peptides from the cross-linking region of rat skin collagen." Kang A.H., Bornstein P., Piez K.A. Biochemistry 6:788-795(1967) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 156-170.
[6]	"The incomplete hydroxylation of individual prolyl residues in collagen." Bornstein P. J. Biol. Chem. 242:2572-2574(1967) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 171-206.
[7]	"Chemical studies on the cyanogen bromide peptides of rat skin collagen. Amino acid sequence of alpha 1-CB4." Butler W.T., Ponds S.L. Biochemistry 10:2076-2081(1971) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 207-253.
[8]	"Chemical studies on the cyanogen bromide peptides of rat skin collagen. The covalent structure of alpha 1-CB5, the major hexose-containing cyanogen bromide peptide of alpha 1." Butler W.T. Biochemistry 9:44-50(1970) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 254-290.
[9]	"Structure of rat skin collagen alpha 1-CB8. Amino acid sequence of the hydroxylamine-produced fragment HA1." Balian G., Click E.M., Bornstein P. Biochemistry 10:4470-4478(1971) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 291-389.
[10]	"Structure of rat skin collagen alpha 1-CBB. Amino acid sequence of the hydroxyl amine-produced fragment HA2." Balian G., Click E.M., Hermodson M.A., Bornstein P. Biochemistry 11:3798-3806(1972) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 390-569.
[11]	"Chemical studies on the cyanogen bromide peptides of rat skin collagen. Amino acid sequence of alpha 1-CB3." Butler W.T., Underwood S.P., Finch J.E. Jr. Biochemistry 13:2946-2953(1974) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 570-718.
[12]	"Construction of DNA sequences complementary to rat alpha 1 and alpha 2 collagen mRNA and their use in studying the regulation of type I collagen synthesis by 1,25-dihydroxyvitamin D." Genovese C., Rowe D., Kream B. Biochemistry 23:6210-6216(1984) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 680-718.
[13]	"Structural and immunogenic properties of a major antigenic determinant in neutral salt-extracted rat-skin collagen." Stoltz M., Timpl R., Furthmayr H., Kuehn K. Eur. J. Biochem. 37:287-294(1973) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 1103-1186.
[14]	"Non-helical regions in rat collagen alpha 1-chain." Stoltz M., Timpl R., Kuehn K. FEBS Lett. 26:61-65(1972) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 1186-1206.
[15]	"Endo180 binds to the C-terminal region of type I collagen." Thomas E.K., Nakamura M., Wienke D., Isacke C.M., Pozzi A., Liang P. J. Biol. Chem. 280:22596-22605(2005) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH MRC2. Strain: Sprague-Dawley.
[16]	"A new procedure for rapid, high yield purification of Type I collagen for tissue engineering." Xiong X., Ghosh R., Hiller E., Drepper F., Knapp B., Brunner H., Rupp S. Process Biochem. 44:1200-1212(2009) Cited for: IDENTIFICATION BY MASS SPECTROMETRY, PHOSPHORYLATION.
[17]	"Microfibrillar structure of type I collagen in situ." Orgel J.P.R.O., Irving T.C., Miller A., Wess T.J. Proc. Natl. Acad. Sci. U.S.A. 103:9001-9005(2006) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (5.16 ANGSTROMS) OF 152-1207.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

Z78279 mRNA. Translation: CAB01633.1.
CH473948 Genomic DNA. Translation: EDM05727.1.
BC133728 mRNA. Translation: AAI33729.1.
M11432 mRNA. Translation: AAA40832.1. Sequence problems.

IPI

IPI00188909.

PIR

CGRT1S. A90559.

RefSeq

NP_445756.1. NM_053304.1.

UniGene

Rn.2953.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
3HQV	fiber diffraction	5.16	A/C	152-1207	[»]
3HR2	fiber diffraction	5.16	A/C	152-1207	[»]

ProteinModelPortal

P02454.

ModBase

Search...

Protein-protein interaction databases

IntAct

P02454. 2 interactions.

Proteomic databases

PaxDb

P02454.

PRIDE

P02454.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENSRNOT00000005311; ENSRNOP00000005311; ENSRNOG00000003897.

GeneID

29393.

KEGG

rno:29393.

UCSC

RGD:61817. rat.

Organism-specific databases

CTD

1277.

RGD

61817. Col1a1.

Phylogenomic databases

eggNOG

NOG12793.

GeneTree

ENSGT00660000095287.

HOGENOM

HOG000085654.

HOVERGEN

HBG004933.

InParanoid

A3KNA1.

K06236.

OMA

VAYMDQQ.

Enzyme and pathway databases

Reactome

REACT_150387. Gelatin degradation by MMP19.

Gene expression databases

ArrayExpress

P02454.

Genevestigator

P02454.

GermOnline

ENSRNOG00000003897. Rattus norvegicus.

Family and domain databases

InterPro

IPR008160. Collagen.
IPR000885. Fib_collagen_C.
IPR001007. VWF_C.
[Graphical view]

Pfam

PF01410. COLFI. 1 hit.
PF01391. Collagen. 12 hits.
PF00093. VWC. 1 hit.
[Graphical view]

ProDom

PD002078. Fib_collagen_C. 1 hit.
[Graphical view] [Entries sharing at least one domain]

SMART

SM00038. COLFI. 1 hit.
SM00214. VWC. 1 hit.
[Graphical view]

PROSITE

PS51461. NC1_FIB. 1 hit.
PS01208. VWFC_1. 1 hit.
PS50184. VWFC_2. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P02454.

NextBio

609017.

Entry information

Entry name

CO1A1_RAT

Accession

Primary (citable) accession number: P02454
Secondary accession number(s): A3KNA1, P02455, Q63079

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 21, 1986
Last sequence update:	September 22, 2009
Last modified:	April 3, 2013
This is version 118 of the entry and version 5 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Relevant documents

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Regions

Sites

Amino acid modifications

Experimental info

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Other

Entry information

Relevant documents