P13612 (ITA4_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Integrin alpha-4

Alternative name(s):
CD49 antigen-like family member D
Integrin alpha-IV
VLA-4 subunit alpha
CD_antigen=CD49d

Gene names

Name:	ITGA4
Synonyms:	CD49D

Organism

Homo sapiens (Human) [Reference proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Primates › Haplorrhini › Simiiformes › Catarrhini › Hominoidea › Hominidae › Homininae › Homo

Protein attributes

Sequence length	1032 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	Integrins alpha-4/beta-1 (VLA-4) and alpha-4/beta-7 are receptors for fibronectin. They recognize one or more domains within the alternatively spliced CS-1 and CS-5 regions of fibronectin. They are also receptors for VCAM1. Integrin alpha-4/beta-1 recognizes the sequence Q-I-D-S in VCAM1. Integrin alpha-4/beta-7 is also a receptor for MADCAM1. It recognizes the sequence L-D-T in MADCAM1. On activated endothelial cells integrin VLA-4 triggers homotypic aggregation for most VLA-4-positive leukocyte cell lines. It may also participate in cytolytic T-cell interactions with target cells.
Subunit structure	Heterodimer of an alpha and a beta subunit. The alpha subunit can sometimes be cleaved into two non-covalently associated fragments. Alpha-4 associates with either beta-1 or beta-7. Alpha-4 interacts with PXN, LPXN, and TGFB1I1/HIC5. Interacts with CSPG4 through CSPG4 chondroitin sulfate glycosaminoglycan. Ref.9 Ref.10
Subcellular location	Membrane; Single-pass type I membrane protein.
Domain	The SG1 motif is involved in binding to chondroitin sulfate glycosaminoglycan and cell adhesion. Ref.9
Post-translational modification	Phosphorylation on Ser-1027 inhibits PXN binding.
Sequence similarities	Belongs to the integrin alpha chain family. Contains 7 FG-GAP repeats.
Sequence caution	The sequence AAB59613.1 differs from that shown. Reason: Frameshift at position 13. The sequence CAA34852.1 differs from that shown. Reason: Frameshift at position 13.

Ontologies

Keywords
Biological process	Cell adhesion
Cellular component	Membrane
Coding sequence diversity	Polymorphism
Domain	Repeat Signal Transmembrane Transmembrane helix
Ligand	Calcium Metal-binding
Molecular function	Integrin Receptor
PTM	Disulfide bond Glycoprotein Phosphoprotein
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	B cell differentiation Inferred by curator PubMed 1715889. Source: BHF-UCL blood coagulation Traceable author statement. Source: Reactome blood vessel remodeling Inferred from electronic annotation. Source: Compara chorio-allantoic fusion Inferred from electronic annotation. Source: Compara face development Inferred from electronic annotation. Source: Compara heart development Inferred from electronic annotation. Source: Compara heterophilic cell-cell adhesion Inferred from electronic annotation. Source: Compara integrin-mediated signaling pathway Inferred from electronic annotation. Source: UniProtKB-KW leukocyte cell-cell adhesion Inferred from direct assay PubMed 1715889. Source: BHF-UCL leukocyte migration Traceable author statement. Source: Reactome regulation of immune response Traceable author statement. Source: Reactome
Cellular_component	cell surface Inferred from direct assay PubMed 1715889. Source: BHF-UCL external side of plasma membrane Inferred from electronic annotation. Source: Compara integrin complex Inferred from electronic annotation. Source: InterPro plasma membrane Traceable author statement. Source: Reactome
Molecular_function	metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
ITGB1	P05556	3	EBI-703044,EBI-703066
PXN	P49023	3	EBI-703044,EBI-702209
TGFB1I1	O43294	2	EBI-703044,EBI-1051449

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Signal peptide

1 – 33

33

Ref.7

Chain

34 – 1032

999

Integrin alpha-4

PRO_0000016244

Regions

Topological domain

35 – 977

943

Extracellular Potential

Transmembrane

978 – 1001

24

Helical; Potential

Topological domain

1002 – 1032

31

Cytoplasmic Potential

Repeat

35 – 100

66

FG-GAP 1

Repeat

110 – 177

68

FG-GAP 2

Repeat

185 – 237

53

FG-GAP 3

Repeat

238 – 293

56

FG-GAP 4

Repeat

294 – 351

58

FG-GAP 5

Repeat

355 – 412

58

FG-GAP 6

Repeat

416 – 478

63

FG-GAP 7

Calcium binding

314 – 322

9

Potential

Calcium binding

377 – 385

9

Potential

Calcium binding

439 – 447

9

Potential

Motif

606 – 616

11

SG1

Motif

1003 – 1007

5

GFFKR motif

Sites

Site

591 – 592

2

Cleavage

Amino acid modifications

Modified residue

1021

1

Phosphoserine Ref.11 Ref.13

Glycosylation

79

1

N-linked (GlcNAc...) Potential

Glycosylation

138

1

N-linked (GlcNAc...) Potential

Glycosylation

229

1

N-linked (GlcNAc...) Potential

Glycosylation

480

1

N-linked (GlcNAc...) Ref.12

Glycosylation

518

1

N-linked (GlcNAc...) Ref.12

Glycosylation

538

1

N-linked (GlcNAc...) Ref.12

Glycosylation

626

1

N-linked (GlcNAc...) Potential

Glycosylation

645

1

N-linked (GlcNAc...) Ref.12

Glycosylation

660

1

N-linked (GlcNAc...) Potential

Glycosylation

806

1

N-linked (GlcNAc...) Potential

Glycosylation

821

1

N-linked (GlcNAc...) Potential

Disulfide bond

91 ↔ 101

By similarity

Disulfide bond

144 ↔ 165

By similarity

Disulfide bond

183 ↔ 198

By similarity

Disulfide bond

486 ↔ 495

By similarity

Disulfide bond

501 ↔ 557

By similarity

Disulfide bond

622 ↔ 627

By similarity

Disulfide bond

698 ↔ 711

By similarity

Disulfide bond

852 ↔ 890

By similarity

Disulfide bond

897 ↔ 902

By similarity

Natural variations

Natural variant

634

1

S → T.
Corresponds to variant rs35322532 [ dbSNP | Ensembl ].

VAR_047423

Natural variant

824

1

V → A.
Corresponds to variant rs1143675 [ dbSNP | Ensembl ].

VAR_047424

Natural variant

878

1

R → Q. Ref.3 Ref.5
Corresponds to variant rs1143676 [ dbSNP | Ensembl ].

VAR_003978

Experimental info

Mutagenesis

590

1

K → Q: Abolishes almost completely cleavage. Ref.8

Mutagenesis

591

1

R → L: Abolishes completely cleavage. Ref.8

Mutagenesis

1021

1

S → A: Abolishes phosphorylation. Ref.11

Mutagenesis

1021

1

S → D: Reduces PXN binding. Ref.11

Mutagenesis

1024

1

Y → A: Disrupts PXN binding. Ref.10

Secondary structure

1

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1032

Helix Strand Turn

Details...

Beta strand

42 – 45

4

Beta strand

54 – 61

8

Beta strand

64 – 71

8

Beta strand

87 – 95

9

Beta strand

102 – 104

3

Beta strand

127 – 133

7

Beta strand

141 – 145

5

Turn

152 – 156

5

Beta strand

165 – 168

4

Helix

174 – 176

3

Beta strand

178 – 180

3

Turn

193 – 197

5

Beta strand

202 – 206

5

Beta strand

208 – 215

8

Helix

218 – 221

4

Beta strand

223 – 229

7

Turn

230 – 233

4

Beta strand

234 – 237

4

Beta strand

253 – 258

6

Beta strand

267 – 272

6

Helix

275 – 277

3

Beta strand

280 – 286

7

Beta strand

288 – 298

11

Beta strand

308 – 313

6

Beta strand

318 – 320

3

Beta strand

322 – 327

6

Beta strand

332 – 334

3

Beta strand

338 – 344

7

Beta strand

346 – 349

4

Beta strand

351 – 353

3

Beta strand

381 – 383

3

Beta strand

386 – 390

5

Helix

393 – 396

4

Beta strand

398 – 403

6

Beta strand

415 – 419

5

Helix

420 – 422

3

Beta strand

429 – 438

10

Beta strand

440 – 445

6

Beta strand

447 – 452

6

Helix

453 – 455

3

Beta strand

457 – 461

5

Beta strand

466 – 474

9

Beta strand

495 – 505

11

Beta strand

511 – 522

12

Beta strand

532 – 534

3

Beta strand

536 – 538

3

Beta strand

542 – 554

13

Beta strand

556 – 564

9

Beta strand

575 – 583

9

Beta strand

610 – 617

8

Sequences

	Sequence		Length	Mass (Da)
	P13612 [UniParc]. Last modified November 2, 2010. Version 3. Checksum: 73EC1204DE78CD35	FASTA	1,032	114,900
	10 20 30 40 50 60 MAWEARREPG PRRAAVRETV MLLLCLGVPT GRPYNVDTES ALLYQGPHNT LFGYSVVLHS 70 80 90 100 110 120 HGANRWLLVG APTANWLANA SVINPGAIYR CRIGKNPGQT CEQLQLGSPN GEPCGKTCLE 130 140 150 160 170 180 ERDNQWLGVT LSRQPGENGS IVTCGHRWKN IFYIKNENKL PTGGCYGVPP DLRTELSKRI 190 200 210 220 230 240 APCYQDYVKK FGENFASCQA GISSFYTKDL IVMGAPGSSY WTGSLFVYNI TTNKYKAFLD 250 260 270 280 290 300 KQNQVKFGSY LGYSVGAGHF RSQHTTEVVG GAPQHEQIGK AYIFSIDEKE LNILHEMKGK 310 320 330 340 350 360 KLGSYFGASV CAVDLNADGF SDLLVGAPMQ STIREEGRVF VYINSGSGAV MNAMETNLVG 370 380 390 400 410 420 SDKYAARFGE SIVNLGDIDN DGFEDVAIGA PQEDDLQGAI YIYNGRADGI SSTFSQRIEG 430 440 450 460 470 480 LQISKSLSMF GQSISGQIDA DNNGYVDVAV GAFRSDSAVL LRTRPVVIVD ASLSHPESVN 490 500 510 520 530 540 RTKFDCVENG WPSVCIDLTL CFSYKGKEVP GYIVLFYNMS LDVNRKAESP PRFYFSSNGT 550 560 570 580 590 600 SDVITGSIQV SSREANCRTH QAFMRKDVRD ILTPIQIEAA YHLGPHVISK RSTEEFPPLQ 610 620 630 640 650 660 PILQQKKEKD IMKKTINFAR FCAHENCSAD LQVSAKIGFL KPHENKTYLA VGSMKTLMLN 670 680 690 700 710 720 VSLFNAGDDA YETTLHVKLP VGLYFIKILE LEEKQINCEV TDNSGVVQLD CSIGYIYVDH 730 740 750 760 770 780 LSRIDISFLL DVSSLSRAEE DLSITVHATC ENEEEMDNLK HSRVTVAIPL KYEVKLTVHG 790 800 810 820 830 840 FVNPTSFVYG SNDENEPETC MVEKMNLTFH VINTGNSMAP NVSVEIMVPN SFSPQTDKLF 850 860 870 880 890 900 NILDVQTTTG ECHFENYQRV CALEQQKSAM QTLKGIVRFL SKTDKRLLYC IKADPHCLNF 910 920 930 940 950 960 LCNFGKMESG KEASVHIQLE GRPSILEMDE TSALKFEIRA TGFPEPNPRV IELNKDENVA 970 980 990 1000 1010 1020 HVLLEGLHHQ RPKRYFTIVI ISSSLLLGLI VLLLISYVMW KAGFFKRQYK SILQEENRRD 1030 SWSYINSKSN DD

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The primary structure of the alpha 4 subunit of VLA-4: homology to other integrins and a possible cell-cell adhesion function." Takada Y., Elices M.J., Crouse C., Hemler M.E. EMBO J. 8:1361-1368(1989) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA].
[2]	"A single mRNA encodes the alpha 150 and alpha 80/70 forms of the alpha subunit of VLA4." Rubio M., Nueda A., Vara A., Corbi-Lopez A.L. Eur. J. Immunol. 22:1099-1102(1992) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA].
[3]	"Identification of two variants of the human integrin alpha 4 subunit." Szabo M.C., McIntyre B.W. Mol. Immunol. 32:1453-1454(1995) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA], VARIANT GLN-878.
[4]	"Generation and annotation of the DNA sequences of human chromosomes 2 and 4." Hillier L.W., Graves T.A., Fulton R.S., Fulton L.A., Pepin K.H., Minx P., Wagner-McPherson C., Layman D., Wylie K., Sekhon M., Becker M.C., Fewell G.A., Delehaunty K.D., Miner T.L., Nash W.E., Kremitzki C., Oddy L., Du H. , Sun H., Bradshaw-Cordum H., Ali J., Carter J., Cordes M., Harris A., Isak A., van Brunt A., Nguyen C., Du F., Courtney L., Kalicki J., Ozersky P., Abbott S., Armstrong J., Belter E.A., Caruso L., Cedroni M., Cotton M., Davidson T., Desai A., Elliott G., Erb T., Fronick C., Gaige T., Haakenson W., Haglund K., Holmes A., Harkins R., Kim K., Kruchowski S.S., Strong C.M., Grewal N., Goyea E., Hou S., Levy A., Martinka S., Mead K., McLellan M.D., Meyer R., Randall-Maher J., Tomlinson C., Dauphin-Kohlberg S., Kozlowicz-Reilly A., Shah N., Swearengen-Shahid S., Snider J., Strong J.T., Thompson J., Yoakum M., Leonard S., Pearman C., Trani L., Radionenko M., Waligorski J.E., Wang C., Rock S.M., Tin-Wollam A.-M., Maupin R., Latreille P., Wendl M.C., Yang S.-P., Pohl C., Wallis J.W., Spieth J., Bieri T.A., Berkowicz N., Nelson J.O., Osborne J., Ding L., Meyer R., Sabo A., Shotland Y., Sinha P., Wohldmann P.E., Cook L.L., Hickenbotham M.T., Eldred J., Williams D., Jones T.A., She X., Ciccarelli F.D., Izaurralde E., Taylor J., Schmutz J., Myers R.M., Cox D.R., Huang X., McPherson J.D., Mardis E.R., Clifton S.W., Warren W.C., Chinwalla A.T., Eddy S.R., Marra M.A., Ovcharenko I., Furey T.S., Miller W., Eichler E.E., Bork P., Suyama M., Torrents D., Waterston R.H., Wilson R.K. Nature 434:724-731(2005) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[5]	Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C. Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA], VARIANT GLN-878.
[6]	"Characterization of the alpha 4 integrin gene promoter." Rosen G.D., Birkenmeier T.M., Dean D.C. Proc. Natl. Acad. Sci. U.S.A. 88:4094-4098(1991) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 1-87.
[7]	"The very late antigen family of heterodimers is part of a superfamily of molecules involved in adhesion and embryogenesis." Takada Y., Strominger J.L., Hemler M.E. Proc. Natl. Acad. Sci. U.S.A. 84:3239-3243(1987) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 34-47.
[8]	"Functional and structural analysis of VLA-4 integrin alpha 4 subunit cleavage." Teixido J., Parker C.M., Kassner P.D., Hemler M.E. J. Biol. Chem. 267:1786-1791(1992) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 592-601, PROTEOLYTIC PROCESSING, MUTAGENESIS OF LYS-590 AND ARG-591.
[9]	"A role of chondroitin sulfate glycosaminoglycan binding site in alpha4beta1 integrin-mediated melanoma cell adhesion." Iida J., Meijne A.M.L., Oegema T.R. Jr., Yednock T.A., Kovach N.L., Furcht L.T., McCarthy J.B. J. Biol. Chem. 273:5955-5962(1998) [PubMed] [Europe PMC] [Abstract] Cited for: DOMAIN, INTERACTION WITH CSPG4.
[10]	"Binding of paxillin to alpha4 integrins modifies integrin-dependent biological responses." Liu S., Thomas S.M., Woodside D.G., Rose D.M., Kiosses W.B., Pfaff M., Ginsberg M.H. Nature 402:676-681(1999) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH PXN; LPXN AND TGFB1I1, MUTAGENESIS OF TYR-1024.
[11]	"Phosphorylation of the integrin alpha 4 cytoplasmic domain regulates paxillin binding." Han J., Liu S., Rose D.M., Schlaepfer D.D., McDonald H., Ginsberg M.H. J. Biol. Chem. 276:40903-40909(2001) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION AT SER-1021, MUTAGENESIS OF SER-1021.
[12]	"Mass-spectrometric identification and relative quantification of N-linked cell surface glycoproteins." Wollscheid B., Bausch-Fluck D., Henderson C., O'Brien R., Bibel M., Schiess R., Aebersold R., Watts J.D. Nat. Biotechnol. 27:378-386(2009) [PubMed] [Europe PMC] [Abstract] Cited for: GLYCOSYLATION [LARGE SCALE ANALYSIS] AT ASN-480; ASN-518; ASN-538 AND ASN-645, MASS SPECTROMETRY. Tissue: Leukemic T-cell.
[13]	"Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions." Mayya V., Lundgren D.H., Hwang S.-I., Rezaul K., Wu L., Eng J.K., Rodionov V., Han D.K. Sci. Signal. 2:RA46-RA46(2009) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-1021, MASS SPECTROMETRY. Tissue: Leukemic T-cell.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

X16983 mRNA. Translation: CAA34852.1. Frameshift.
L12002 mRNA. Translation: AAB59613.1. Frameshift.
AC020595 Genomic DNA. No translation available.
CH471058 Genomic DNA. Translation: EAX10985.1.
CH471058 Genomic DNA. Translation: EAX10987.1.

IPI

IPI00009803.

PIR

S06046.

RefSeq

NP_000876.3. NM_000885.4.

UniGene

Hs.440955.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
3V4P	X-ray	3.15	A/C	34-620	[»]
3V4V	X-ray	3.10	A/C	34-620	[»]

ProteinModelPortal

P13612.

SMR

P13612. Positions 34-985.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-34971N.

IntAct

P13612. 10 interactions.

STRING

9606.ENSP00000380227.

PTM databases

PhosphoSite

P13612.

Polymorphism databases

DMDM

311033436.

Proteomic databases

PaxDb

P13612.

PRIDE

P13612.

Protocols and materials databases

DNASU

3676.

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENST00000397033; ENSP00000380227; ENSG00000115232.

GeneID

3676.

KEGG

hsa:3676.

UCSC

uc002unu.3. human.

Organism-specific databases

CTD

3676.

GeneCards

GC02P182285.

HGNC

HGNC:6140. ITGA4.

MIM

192975. gene.

neXtProt

NX_P13612.

PharmGKB

PA29940.

GenAtlas

Search...

Phylogenomic databases

eggNOG

NOG324320.

HOGENOM

HOG000088626.

HOVERGEN

HBG004538.

InParanoid

P13612.

KO

K06483.

OMA

APCYQDY.

OrthoDB

EOG4PK271.

Enzyme and pathway databases

Pathway_Interaction_DB

a4b1_a4b7_pathway. a4b1 and a4b7 Integrin signaling.
arf6_traffickingpathway. Arf6 trafficking events.
a4b1_paxdep_pathway. Paxillin-dependent events mediated by a4b1.
a4b1_paxindep_pathway. Paxillin-independent events mediated by a4b1 and a4b7.
lymphangiogenesis_pathway. VEGFR3 signaling in lymphatic endothelium.

Reactome

REACT_111102. Signal Transduction.
REACT_604. Hemostasis.
REACT_6900. Immune System.

Gene expression databases

ArrayExpress

P13612.

Bgee

P13612.

CleanEx

HS_ITGA4.

Genevestigator

P13612.

GermOnline

ENSG00000115232. Homo sapiens.

Family and domain databases

InterPro

IPR013517. FG-GAP.
IPR013519. Int_alpha_beta-p.
IPR000413. Integrin_alpha.
IPR013649. Integrin_alpha-2.
IPR018184. Integrin_alpha_C_CS.
[Graphical view]

Pfam

PF01839. FG-GAP. 2 hits.
PF08441. Integrin_alpha2. 1 hit.
[Graphical view]

PRINTS

PR01185. INTEGRINA.

SMART

SM00191. Int_alpha. 5 hits.
[Graphical view]

PROSITE

PS51470. FG_GAP. 7 hits.
PS00242. INTEGRIN_ALPHA. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

BindingDB

P13612.

ChEMBL

CHEMBL278.

ChiTaRS

ITGA4. human.

DrugBank

DB00108. Natalizumab.

GenomeRNAi

3676.

NextBio

14391.

SOURCE

Search...

Entry information

Entry name

ITA4_HUMAN

Accession

Primary (citable) accession number: P13612
Secondary accession number(s): D3DPG4

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 1, 1990
Last sequence update:	November 2, 2010
Last modified:	May 1, 2013
This is version 142 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Disclaimer

Any medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.