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Protein

Protocadherin beta-1

Gene

PCDHB1

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at transcript leveli

Functioni

Potential calcium-dependent cell-adhesion protein. May be involved in the establishment and maintenance of specific neuronal connections in the brain.

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

Cell adhesion

Keywords - Ligandi

Calcium

Names & Taxonomyi

Protein namesi
Recommended name:
Protocadherin beta-1
Short name:
PCDH-beta-1
Gene namesi
Name:PCDHB1
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 5

Organism-specific databases

HGNCiHGNC:8680. PCDHB1.

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini29 – 691663ExtracellularSequence analysisAdd
BLAST
Transmembranei692 – 71221HelicalSequence analysisAdd
BLAST
Topological domaini713 – 818106CytoplasmicSequence analysisAdd
BLAST

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cell membrane, Membrane

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA33025.

Polymorphism and mutation databases

BioMutaiPCDHB1.
DMDMi205371811.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 2828Sequence analysisAdd
BLAST
Chaini29 – 818790Protocadherin beta-1PRO_0000003914Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Glycosylationi169 – 1691N-linked (GlcNAc...)Sequence analysis
Glycosylationi209 – 2091N-linked (GlcNAc...)Sequence analysis
Glycosylationi257 – 2571N-linked (GlcNAc...)Sequence analysis
Glycosylationi419 – 4191N-linked (GlcNAc...)Sequence analysis
Glycosylationi568 – 5681N-linked (GlcNAc...)Sequence analysis

Keywords - PTMi

Glycoprotein

Proteomic databases

PaxDbiQ9Y5F3.
PeptideAtlasiQ9Y5F3.
PRIDEiQ9Y5F3.

PTM databases

iPTMnetiQ9Y5F3.
PhosphoSiteiQ9Y5F3.

Expressioni

Gene expression databases

BgeeiENSG00000171815.
CleanExiHS_PCDHB1.
GenevisibleiQ9Y5F3. HS.

Organism-specific databases

HPAiHPA053921.

Interactioni

Protein-protein interaction databases

STRINGi9606.ENSP00000307234.

Structurei

3D structure databases

ProteinModelPortaliQ9Y5F3.
SMRiQ9Y5F3. Positions 30-665.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini35 – 13399Cadherin 1PROSITE-ProRule annotationAdd
BLAST
Domaini138 – 242105Cadherin 2PROSITE-ProRule annotationAdd
BLAST
Domaini243 – 347105Cadherin 3PROSITE-ProRule annotationAdd
BLAST
Domaini348 – 452105Cadherin 4PROSITE-ProRule annotationAdd
BLAST
Domaini457 – 562106Cadherin 5PROSITE-ProRule annotationAdd
BLAST
Domaini577 – 67296Cadherin 6PROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Contains 6 cadherin domains.PROSITE-ProRule annotation

Keywords - Domaini

Repeat, Signal, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiKOG3594. Eukaryota.
ENOG410XQHI. LUCA.
GeneTreeiENSGT00840000129690.
HOGENOMiHOG000220892.
HOVERGENiHBG054878.
InParanoidiQ9Y5F3.
KOiK16494.
OMAiQEDSYIL.
OrthoDBiEOG091G024L.
PhylomeDBiQ9Y5F3.
TreeFamiTF332299.

Family and domain databases

Gene3Di2.60.40.60. 6 hits.
InterProiIPR002126. Cadherin.
IPR015919. Cadherin-like.
IPR032455. Cadherin_C.
IPR020894. Cadherin_CS.
IPR013164. Cadherin_N.
IPR030723. PCDHB1.
[Graphical view]
PANTHERiPTHR24028:SF12. PTHR24028:SF12. 1 hit.
PfamiPF00028. Cadherin. 5 hits.
PF08266. Cadherin_2. 1 hit.
PF16492. Cadherin_C_2. 1 hit.
[Graphical view]
PRINTSiPR00205. CADHERIN.
SMARTiSM00112. CA. 6 hits.
[Graphical view]
SUPFAMiSSF49313. SSF49313. 6 hits.
PROSITEiPS00232. CADHERIN_1. 5 hits.
PS50268. CADHERIN_2. 6 hits.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

Q9Y5F3-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAGTRRKSLQ NRQVGSLLIF LCISVGDATT IRYSVAEEME SGSFVANVAK
60 70 80 90 100
DLGLEVGKLA ARGARLVSEG NKMHFRLHRK TGDLFVKEKL DRESLCGKAD
110 120 130 140 150
PCVLHFEVVL VEPLQSFRAE VRVFDINDNA PVFLNKEPLL KIPESTPLGS
160 170 180 190 200
RFPLQSAQDL DVGLNGLQNY TLSANGYFHL HTRFCSHGPK YAELVLNKPL
210 220 230 240 250
DREEQPEVNL TITAVDGGSP PKSGTAHIHV VVLDVNDHVP QFSRLVYRAQ
260 270 280 290 300
VSENSPNGSL VATVTAVDLD EGTNKAITYS LAQNPEAILK TFQIDPQNGE
310 320 330 340 350
VRLRGPLDFE AIETYDIDIQ ATDGGGLSAH SKVLVEVVDV NDNPPEVMVS
360 370 380 390 400
SVSSPLPEDS PPQTVVALFT IRDRDIRVGG KVTCFLREDL PFVIKPTFGN
410 420 430 440 450
SYSLVTDRSL DREEVSGYNI TIVAMDTGPP SLSAETMIEV LISDVNDNPP
460 470 480 490 500
IFREDSYILT VRENNSPAVF IGKVHAEDLD LGENAQITYS LLPPKNGDLS
510 520 530 540 550
VFAYISINSG NGKLYALRTM DYEAIQDFQF VVKATDGGFL SLSSQVTVRV
560 570 580 590 600
VVLDDNDNRP MILYPLQNGT LPCNDLVPRS AEAGYLVTKV VAVDGDSGQN
610 620 630 640 650
SWLSYHLLKA TDLGLFSVQR QNGEIHTLRQ ISERDPMMQK LIILVQDHGQ
660 670 680 690 700
PALSTTVSLN ILLVDGFSEP YLQFQDPTKH SRKVNPSTKY LVISLVILSF
710 720 730 740 750
LFLLSVIVIF IIHVYQKIKY REKFTIQEHF YDDCNFSNNL VQGQGNGSLS
760 770 780 790 800
RPCPYEMCSA TGTGNSEFRF LKRFMPNFPF PHATGEIKME AGSSLPPNSD
810
RNKSQRLEGH DQVSDDYM
Length:818
Mass (Da):90,491
Last modified:September 2, 2008 - v2
Checksum:i4697DC76EDB7D604
GO

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti385 – 3851F → L.
Corresponds to variant rs2233591 [ dbSNP | Ensembl ].
VAR_048541
Natural varianti390 – 3901L → F.
Corresponds to variant rs2233592 [ dbSNP | Ensembl ].
VAR_048542
Natural varianti524 – 5241A → V.
Corresponds to variant rs17208383 [ dbSNP | Ensembl ].
VAR_048543
Natural varianti611 – 6111T → I.
Corresponds to variant rs10476822 [ dbSNP | Ensembl ].
VAR_048544
Natural varianti712 – 7121I → T.
Corresponds to variant rs31738 [ dbSNP | Ensembl ].
VAR_048545
Natural varianti719 – 7191K → I.
Corresponds to variant rs2233595 [ dbSNP | Ensembl ].
VAR_048546
Natural varianti778 – 7781F → L.1 Publication
Corresponds to variant rs246679 [ dbSNP | Ensembl ].
VAR_048547

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF152488 mRNA. Translation: AAD43749.1.
CH471062 Genomic DNA. Translation: EAW61985.1.
BC112096 mRNA. Translation: AAI12097.1.
BC112098 mRNA. Translation: AAI12099.1.
CCDSiCCDS4243.1.
RefSeqiNP_037472.2. NM_013340.3.
UniGeneiHs.278950.

Genome annotation databases

EnsembliENST00000306549; ENSP00000307234; ENSG00000171815.
GeneIDi29930.
KEGGihsa:29930.
UCSCiuc003lik.3. human.

Keywords - Coding sequence diversityi

Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF152488 mRNA. Translation: AAD43749.1.
CH471062 Genomic DNA. Translation: EAW61985.1.
BC112096 mRNA. Translation: AAI12097.1.
BC112098 mRNA. Translation: AAI12099.1.
CCDSiCCDS4243.1.
RefSeqiNP_037472.2. NM_013340.3.
UniGeneiHs.278950.

3D structure databases

ProteinModelPortaliQ9Y5F3.
SMRiQ9Y5F3. Positions 30-665.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi9606.ENSP00000307234.

PTM databases

iPTMnetiQ9Y5F3.
PhosphoSiteiQ9Y5F3.

Polymorphism and mutation databases

BioMutaiPCDHB1.
DMDMi205371811.

Proteomic databases

PaxDbiQ9Y5F3.
PeptideAtlasiQ9Y5F3.
PRIDEiQ9Y5F3.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000306549; ENSP00000307234; ENSG00000171815.
GeneIDi29930.
KEGGihsa:29930.
UCSCiuc003lik.3. human.

Organism-specific databases

CTDi29930.
GeneCardsiPCDHB1.
HGNCiHGNC:8680. PCDHB1.
HPAiHPA053921.
MIMi604967. gene.
606327. gene.
neXtProtiNX_Q9Y5F3.
PharmGKBiPA33025.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG3594. Eukaryota.
ENOG410XQHI. LUCA.
GeneTreeiENSGT00840000129690.
HOGENOMiHOG000220892.
HOVERGENiHBG054878.
InParanoidiQ9Y5F3.
KOiK16494.
OMAiQEDSYIL.
OrthoDBiEOG091G024L.
PhylomeDBiQ9Y5F3.
TreeFamiTF332299.

Miscellaneous databases

GenomeRNAii29930.
PROiQ9Y5F3.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000171815.
CleanExiHS_PCDHB1.
GenevisibleiQ9Y5F3. HS.

Family and domain databases

Gene3Di2.60.40.60. 6 hits.
InterProiIPR002126. Cadherin.
IPR015919. Cadherin-like.
IPR032455. Cadherin_C.
IPR020894. Cadherin_CS.
IPR013164. Cadherin_N.
IPR030723. PCDHB1.
[Graphical view]
PANTHERiPTHR24028:SF12. PTHR24028:SF12. 1 hit.
PfamiPF00028. Cadherin. 5 hits.
PF08266. Cadherin_2. 1 hit.
PF16492. Cadherin_C_2. 1 hit.
[Graphical view]
PRINTSiPR00205. CADHERIN.
SMARTiSM00112. CA. 6 hits.
[Graphical view]
SUPFAMiSSF49313. SSF49313. 6 hits.
PROSITEiPS00232. CADHERIN_1. 5 hits.
PS50268. CADHERIN_2. 6 hits.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiPCDB1_HUMAN
AccessioniPrimary (citable) accession number: Q9Y5F3
Secondary accession number(s): Q2M257
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 27, 2001
Last sequence update: September 2, 2008
Last modified: September 7, 2016
This is version 130 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny 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.

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Human chromosome 5
    Human chromosome 5: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.