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Protein

Protocadherin gamma-B3

Gene

PCDHGB3

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein 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 gamma-B3
Short name:
PCDH-gamma-B3
Gene namesi
Name:PCDHGB3
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 5

Organism-specific databases

HGNCiHGNC:8710. PCDHGB3.

Subcellular locationi

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Topological domaini31 – 691ExtracellularSequence analysisAdd BLAST661
Transmembranei692 – 712HelicalSequence analysisAdd BLAST21
Topological domaini713 – 929CytoplasmicSequence analysisAdd BLAST217

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cell membrane, Membrane

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA33058.

Polymorphism and mutation databases

BioMutaiPCDHGB3.
DMDMi442570291.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 30Sequence analysisAdd BLAST30
ChainiPRO_000000397631 – 929Protocadherin gamma-B3Add BLAST899

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Glycosylationi136N-linked (GlcNAc...)Sequence analysis1
Glycosylationi419N-linked (GlcNAc...)Sequence analysis1
Glycosylationi545N-linked (GlcNAc...)Sequence analysis1

Keywords - PTMi

Glycoprotein

Proteomic databases

EPDiQ9Y5G1.
PaxDbiQ9Y5G1.
PeptideAtlasiQ9Y5G1.
PRIDEiQ9Y5G1.

PTM databases

iPTMnetiQ9Y5G1.
PhosphoSitePlusiQ9Y5G1.

Expressioni

Gene expression databases

BgeeiENSG00000262209.
ExpressionAtlasiQ9Y5G1. baseline and differential.
GenevisibleiQ9Y5G1. HS.

Organism-specific databases

HPAiHPA008755.
HPA035823.

Interactioni

Protein-protein interaction databases

BioGridi121042. 3 interactors.
STRINGi9606.ENSP00000461862.

Structurei

Secondary structure

1929
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi33 – 40Combined sources8
Beta strandi46 – 49Combined sources4
Helixi50 – 53Combined sources4
Helixi58 – 60Combined sources3
Helixi61 – 64Combined sources4
Beta strandi67 – 69Combined sources3
Beta strandi75 – 77Combined sources3
Turni79 – 81Combined sources3
Beta strandi83 – 86Combined sources4
Helixi92 – 95Combined sources4
Turni96 – 98Combined sources3
Beta strandi103 – 110Combined sources8
Turni111 – 114Combined sources4
Beta strandi115 – 124Combined sources10
Beta strandi136 – 143Combined sources8
Beta strandi151 – 153Combined sources3
Helixi163 – 165Combined sources3
Beta strandi168 – 172Combined sources5
Beta strandi176 – 184Combined sources9
Beta strandi190 – 196Combined sources7
Turni202 – 204Combined sources3
Beta strandi206 – 220Combined sources15
Beta strandi223 – 233Combined sources11
Beta strandi241 – 243Combined sources3
Beta strandi245 – 252Combined sources8
Beta strandi260 – 263Combined sources4
Helixi272 – 274Combined sources3
Beta strandi278 – 283Combined sources6
Helixi286 – 289Combined sources4
Beta strandi292 – 294Combined sources3
Turni296 – 298Combined sources3
Beta strandi300 – 303Combined sources4
Turni309 – 311Combined sources3
Beta strandi313 – 322Combined sources10
Beta strandi328 – 338Combined sources11
Beta strandi346 – 352Combined sources7
Beta strandi355 – 357Combined sources3
Beta strandi365 – 372Combined sources8
Helixi377 – 379Combined sources3
Beta strandi382 – 388Combined sources7
Beta strandi391 – 396Combined sources6
Beta strandi398 – 406Combined sources9
Turni412 – 414Combined sources3
Beta strandi417 – 426Combined sources10
Beta strandi428 – 430Combined sources3
Beta strandi433 – 443Combined sources11

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
5K8RX-ray2.50A31-444[»]
ProteinModelPortaliQ9Y5G1.
SMRiQ9Y5G1.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini31 – 133Cadherin 1PROSITE-ProRule annotationAdd BLAST103
Domaini134 – 242Cadherin 2PROSITE-ProRule annotationAdd BLAST109
Domaini243 – 347Cadherin 3PROSITE-ProRule annotationAdd BLAST105
Domaini348 – 452Cadherin 4PROSITE-ProRule annotationAdd BLAST105
Domaini453 – 562Cadherin 5PROSITE-ProRule annotationAdd BLAST110
Domaini570 – 675Cadherin 6PROSITE-ProRule annotationAdd BLAST106

Sequence similaritiesi

Contains 6 cadherin domains.PROSITE-ProRule annotation

Keywords - Domaini

Repeat, Signal, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiKOG3594. Eukaryota.
ENOG410XQHI. LUCA.
HOVERGENiHBG054878.
InParanoidiQ9Y5G1.
KOiK16496.
OrthoDBiEOG091G0229.
TreeFamiTF332299.

Family and domain databases

Gene3Di2.60.40.60. 6 hits.
InterProiIPR002126. Cadherin.
IPR015919. Cadherin-like.
IPR032455. Cadherin_C.
IPR031904. Cadherin_CBD.
IPR020894. Cadherin_CS.
IPR013164. Cadherin_N.
[Graphical view]
PfamiPF00028. Cadherin. 5 hits.
PF08266. Cadherin_2. 1 hit.
PF16492. Cadherin_C_2. 1 hit.
PF15974. Cadherin_tail. 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]

Sequences (2)i

Sequence statusi: Complete.

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

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q9Y5G1-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MGNSSGWRGP AGQRRMLFLF LLSLLDQVLS EPIRYAIPEE LDRGSLVGNL
60 70 80 90 100
AKDLGFGVGD LPTRNLRVIA EKKFFTVSPE NGNLLVSDRI DREEICGKKS
110 120 130 140 150
TCVLEFEMVA EKPLNFFHVT VLIQDINDNP PTFSQNITEL EISELALTGA
160 170 180 190 200
TFALESAQDP DVGVNSLQQY YLSPDPHFSL IQKENLDGSR YPELVLKAPL
210 220 230 240 250
DREEQPHHHL VLTAVDGGEP SRSCTTQIRV IVADANDNPP VFTQDMYRVN
260 270 280 290 300
VAENLPAGSS VLKVMAIDMD EGINAEIIYA FINIGKEVRQ LFKLDSKTGE
310 320 330 340 350
LTTIGELDFE ERDSYTIGVE AKDGGHHTAY CKVQIDISDE NDNAPEITLA
360 370 380 390 400
SESQHIQEDA ELGTAVALIK THDLDSGFNG EILCQLKGNF PFKIVQDTKN
410 420 430 440 450
TYRLVTDGAL DREQIPEYNV TITATDKGNP PLSSSKTITL HILDVNDNVP
460 470 480 490 500
VFHQASYTVH VAENNPPGAS IAHVRASDPD LGPNGLVSYY IVASDLEPRE
510 520 530 540 550
LSSYVSVSAR SGVVFAQRAF DHEQLRAFEL TLQARDQGSP TLSANVSLRV
560 570 580 590 600
LVDDRNDNAP LVLYPALGPE GSALFDMVPR SAEPGYLVTK VVAVDADSGY
610 620 630 640 650
NAWLSYHIVQ ASEPGLFSLG LRTGEVRTAR TLGDREAARQ RLLVTVRDGG
660 670 680 690 700
QQPLSATVML HLIFADSLQE IQPDLSDRPT PSDPQAELQF HLVVALALIS
710 720 730 740 750
VLFLLAVILA ISLRLRCSSR PATEGYFQPG VCFKTVPGVL PTYSERTLPY
760 770 780 790 800
SYNPCAASHS SNTEFKFLNI KAENAAPQDL LCDEASWFES NDNPEMPSNS
810 820 830 840 850
GNLQKQAPPN TDWRFSQAQR PGTSGSQNGD DTGTWPNNQF DTEMLQAMIL
860 870 880 890 900
ASASEAADGS STLGGGAGTM GLSARYGPQF TLQHVPDYRQ NVYIPGSNAT
910 920
LTNAAGKRDG KAPAGGNGNK KKSGKKEKK
Length:929
Mass (Da):101,232
Last modified:January 9, 2013 - v3
Checksum:i47052AF74FF01809
GO
Isoform 2 (identifier: Q9Y5G1-2) [UniParc]FASTAAdd to basket
Also known as: Short

The sequence of this isoform differs from the canonical sequence as follows:
     806-814: QAPPNTDWR → VSFFKPFLP
     815-929: Missing.

Show »
Length:814
Mass (Da):89,370
Checksum:iB3033646C8F71265
GO

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_04856920F → Y.Corresponds to variant rs6860590dbSNPEnsembl.1
Natural variantiVAR_06107328V → A.1 PublicationCorresponds to variant rs6860609dbSNPEnsembl.1
Natural variantiVAR_048570389N → K.Corresponds to variant rs2240697dbSNPEnsembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_008688806 – 814QAPPNTDWR → VSFFKPFLP in isoform 2. 1 Publication9
Alternative sequenceiVSP_008689815 – 929Missing in isoform 2. 1 PublicationAdd BLAST115

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF152332 mRNA. Translation: AAD43726.1.
AF152519 mRNA. Translation: AAD43779.1.
AC005366 Genomic DNA. No translation available.
AC005618 Genomic DNA. No translation available.
AC008781 Genomic DNA. No translation available.
CH471062 Genomic DNA. Translation: EAW61951.1.
BC150172 mRNA. Translation: AAI50173.1.
CCDSiCCDS58980.1. [Q9Y5G1-1]
CCDS75334.1. [Q9Y5G1-2]
RefSeqiNP_061747.2. NM_018924.4.
NP_115268.2. NM_032097.2.
UniGeneiHs.368160.

Genome annotation databases

EnsembliENST00000576222; ENSP00000461862; ENSG00000262209.
GeneIDi56102.
KEGGihsa:56102.
UCSCiuc003ljw.3. human. [Q9Y5G1-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF152332 mRNA. Translation: AAD43726.1.
AF152519 mRNA. Translation: AAD43779.1.
AC005366 Genomic DNA. No translation available.
AC005618 Genomic DNA. No translation available.
AC008781 Genomic DNA. No translation available.
CH471062 Genomic DNA. Translation: EAW61951.1.
BC150172 mRNA. Translation: AAI50173.1.
CCDSiCCDS58980.1. [Q9Y5G1-1]
CCDS75334.1. [Q9Y5G1-2]
RefSeqiNP_061747.2. NM_018924.4.
NP_115268.2. NM_032097.2.
UniGeneiHs.368160.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
5K8RX-ray2.50A31-444[»]
ProteinModelPortaliQ9Y5G1.
SMRiQ9Y5G1.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi121042. 3 interactors.
STRINGi9606.ENSP00000461862.

PTM databases

iPTMnetiQ9Y5G1.
PhosphoSitePlusiQ9Y5G1.

Polymorphism and mutation databases

BioMutaiPCDHGB3.
DMDMi442570291.

Proteomic databases

EPDiQ9Y5G1.
PaxDbiQ9Y5G1.
PeptideAtlasiQ9Y5G1.
PRIDEiQ9Y5G1.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000576222; ENSP00000461862; ENSG00000262209.
GeneIDi56102.
KEGGihsa:56102.
UCSCiuc003ljw.3. human. [Q9Y5G1-1]

Organism-specific databases

CTDi56102.
GeneCardsiPCDHGB3.
HGNCiHGNC:8710. PCDHGB3.
HPAiHPA008755.
HPA035823.
MIMi604968. gene.
606301. gene.
neXtProtiNX_Q9Y5G1.
PharmGKBiPA33058.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG3594. Eukaryota.
ENOG410XQHI. LUCA.
HOVERGENiHBG054878.
InParanoidiQ9Y5G1.
KOiK16496.
OrthoDBiEOG091G0229.
TreeFamiTF332299.

Miscellaneous databases

GenomeRNAii56102.
PROiQ9Y5G1.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000262209.
ExpressionAtlasiQ9Y5G1. baseline and differential.
GenevisibleiQ9Y5G1. HS.

Family and domain databases

Gene3Di2.60.40.60. 6 hits.
InterProiIPR002126. Cadherin.
IPR015919. Cadherin-like.
IPR032455. Cadherin_C.
IPR031904. Cadherin_CBD.
IPR020894. Cadherin_CS.
IPR013164. Cadherin_N.
[Graphical view]
PfamiPF00028. Cadherin. 5 hits.
PF08266. Cadherin_2. 1 hit.
PF16492. Cadherin_C_2. 1 hit.
PF15974. Cadherin_tail. 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 nameiPCDGF_HUMAN
AccessioniPrimary (citable) accession number: Q9Y5G1
Secondary accession number(s): A7E229, Q9Y5C7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 24, 2003
Last sequence update: January 9, 2013
Last modified: November 30, 2016
This is version 126 of the entry and version 3 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

3D-structure, 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. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. 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.