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Protein

Protocadherin beta-6

Gene

PCDHB6

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at transcript leveli

Functioni

Calcium-dependent cell-adhesion protein involved in cells self-recognition and non-self discrimination. Thereby, it is involved in the establishment and maintenance of specific neuronal connections in the brain.By similarity

GO - Molecular functioni

GO - Biological processi

  • calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules Source: UniProtKB
  • cell adhesion Source: ProtInc
  • chemical synaptic transmission Source: UniProtKB
  • homophilic cell adhesion via plasma membrane adhesion molecules Source: InterPro
  • nervous system development Source: ProtInc
  • synapse assembly Source: UniProtKB
Complete GO annotation...

Keywords - Biological processi

Cell adhesion

Keywords - Ligandi

Calcium, Metal-binding

Enzyme and pathway databases

BioCyciZFISH:ENSG00000113211-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Protocadherin beta-6Curated
Short name:
PCDH-beta-6Curated
Gene namesi
Name:PCDHB6Imported
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 5

Organism-specific databases

HGNCiHGNC:8691. PCDHB6.

Subcellular locationi

  • Cell membrane By similarity; Single-pass type I membrane protein By similarity

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Topological domaini28 – 688ExtracellularBy similarityAdd BLAST661
Transmembranei689 – 709HelicalSequence analysisAdd BLAST21
Topological domaini710 – 794CytoplasmicBy similarityAdd BLAST85

GO - Cellular componenti

  • integral component of membrane Source: UniProtKB
  • integral component of plasma membrane Source: ProtInc
Complete GO annotation...

Keywords - Cellular componenti

Cell membrane, Membrane

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA33040.

Polymorphism and mutation databases

BioMutaiPCDHB6.
DMDMi13431374.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 27By similarityAdd BLAST27
ChainiPRO_000000392428 – 794Protocadherin beta-6Add BLAST767

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Glycosylationi46N-linked (GlcNAc...)Sequence analysis1
Disulfide bondi95 ↔ 101By similarity
Glycosylationi183N-linked (GlcNAc...)Sequence analysis1
Glycosylationi416N-linked (GlcNAc...)Sequence analysis1
Glycosylationi565N-linked (GlcNAc...)Sequence analysis1

Keywords - PTMi

Disulfide bond, Glycoprotein

Proteomic databases

EPDiQ9Y5E3.
PaxDbiQ9Y5E3.
PeptideAtlasiQ9Y5E3.
PRIDEiQ9Y5E3.

PTM databases

iPTMnetiQ9Y5E3.
PhosphoSitePlusiQ9Y5E3.

Expressioni

Gene expression databases

BgeeiENSG00000113211.
CleanExiHS_PCDHB6.
ExpressionAtlasiQ9Y5E3. baseline and differential.
GenevisibleiQ9Y5E3. HS.

Organism-specific databases

HPAiHPA029566.

Interactioni

Subunit structurei

Forms homodimers in trans (molecules expressed by two different cells). Forms promiscuous heterodimers in cis (at the plasma membrane of the same cell) with other protocadherins.By similarity

Protein-protein interaction databases

BioGridi121070. 1 interactor.

Structurei

3D structure databases

ProteinModelPortaliQ9Y5E3.
SMRiQ9Y5E3.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini34 – 132Cadherin 1PROSITE-ProRule annotationAdd BLAST99
Domaini137 – 241Cadherin 2PROSITE-ProRule annotationAdd BLAST105
Domaini246 – 345Cadherin 3PROSITE-ProRule annotationAdd BLAST100
Domaini350 – 449Cadherin 4PROSITE-ProRule annotationAdd BLAST100
Domaini454 – 559Cadherin 5PROSITE-ProRule annotationAdd BLAST106
Domaini566 – 669Cadherin 6PROSITE-ProRule annotationAdd BLAST104

Domaini

Cadherin 1 to cadherin 4 domains mediate homophilic trans-interaction, the interaction with an identical protocadherin expressed by a neighboring cell. This is a head-to-tail interaction, the cadherin 1 domain interacting with the cadherin 4 domain and the cadherin 2 domain interacting the cadherin 3 domain of the other protocadherin. The cadherin 6 domain mediates promiscuous interactions with protocadherins on the same cell membrane. Each cadherin domain binds three calcium ions.By similarity

Sequence similaritiesi

Contains 6 cadherin domains.PROSITE-ProRule annotation

Keywords - Domaini

Repeat, Signal, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiKOG3594. Eukaryota.
ENOG410XQHI. LUCA.
HOGENOMiHOG000220892.
HOVERGENiHBG054878.
InParanoidiQ9Y5E3.
KOiK16494.
OrthoDBiEOG091G024L.
PhylomeDBiQ9Y5E3.
TreeFamiTF332299.

Family and domain databases

Gene3Di2.60.40.60. 5 hits.
InterProiIPR002126. Cadherin.
IPR015919. Cadherin-like.
IPR032455. Cadherin_C.
IPR020894. Cadherin_CS.
IPR013164. Cadherin_N.
[Graphical view]
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. 5 hits.
PROSITEiPS00232. CADHERIN_1. 5 hits.
PS50268. CADHERIN_2. 5 hits.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

Q9Y5E3-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MMQTKVQNKK RQVAFFILLM LWGEVGSESI QYSVLEETES GTFVANLTKD
60 70 80 90 100
LGLRVGELAS RGARVVFKGN RQHLQFDPQT HDLLLNEKLD REELCGSTEP
110 120 130 140 150
CVLPFQVLLE NPLQFFQASL RVRDINDHAP EFPAREMLLK ISEITMPGKI
160 170 180 190 200
FPLKMAHDLD TGSNGLQRYT ISSNPHFHVL TRNRSEGRKF PELVLDKPLD
210 220 230 240 250
REEQPQLRLT LIALDGGSPP RSGTSEIQIQ VLDINDNVPE FAQELYEAQV
260 270 280 290 300
PENNPLGSLV ITVSARDLDA GSFGKVSYAL FQVDDVNQPF EINAITGEIR
310 320 330 340 350
LRKALDFEEI QSYDVDVEAT DGGGLSGKCS LVVRVLDVND NAPELTMSFF
360 370 380 390 400
ISLIPENLPE ITVAVFSVSD ADSGHNQQVI CSIENNLPFL LRPSVENFYT
410 420 430 440 450
LVTEGALDRE SRAEYNITIT VTDLGTPRLK TQQSITVQVS DVNDNVPAFT
460 470 480 490 500
QTSYTLFVRE NNSPALHIGS VSATDRDSGI NAQVTYSLLP PQDPHLPLSS
510 520 530 540 550
LVSINADNGH LFALRSLDYE ALQSFEFRVG ATDRGSPALS SEALVRLLVL
560 570 580 590 600
DANDNSPFVL YPLQNGSAPC TELVPRAAEP GYLVTKVVAV DGDSGQNAWL
610 620 630 640 650
SYQLLKATEL GLFGVWAHNG EVRTARLLSE RDAAKHRLVV LVKDNGEPPR
660 670 680 690 700
SATATLHVLL VDGFSQPYLP LPEAAPAQAQ ADSLTVYLVV ALASVSSLFL
710 720 730 740 750
FSVLLFVAVR LCRRSRAASV GRYSVPEGPF PGHLVDVSGT GTLSQSYQYK
760 770 780 790
VCLTGGSETN EFKFLKPIMP NFPPQGTERE MEETPTSRNS FPFS
Length:794
Mass (Da):87,350
Last modified:November 1, 1999 - v1
Checksum:iA4E84E17896C168D
GO

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_021879231V → I.Corresponds to variant rs3776096dbSNPEnsembl.1
Natural variantiVAR_033705232L → F.Corresponds to variant rs10076554dbSNPEnsembl.1
Natural variantiVAR_070665446V → A.1 PublicationCorresponds to variant rs246707dbSNPEnsembl.1
Natural variantiVAR_033706636H → Q.1 PublicationCorresponds to variant rs246703dbSNPEnsembl.1
Natural variantiVAR_033707747Y → H.Corresponds to variant rs17685621dbSNPEnsembl.1
Natural variantiVAR_070666776G → D.1 PublicationCorresponds to variant rs17844444dbSNPEnsembl.1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF152499 mRNA. Translation: AAD43760.1.
AF217752 mRNA. Translation: AAK51619.1.
AK313482 mRNA. Translation: BAG36266.1.
CCDSiCCDS4248.1.
RefSeqiNP_001290074.1. NM_001303145.1.
NP_061762.2. NM_018939.3.
UniGeneiHs.283085.

Genome annotation databases

EnsembliENST00000231136; ENSP00000231136; ENSG00000113211.
GeneIDi56130.
KEGGihsa:56130.
UCSCiuc003lir.4. human.

Keywords - Coding sequence diversityi

Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF152499 mRNA. Translation: AAD43760.1.
AF217752 mRNA. Translation: AAK51619.1.
AK313482 mRNA. Translation: BAG36266.1.
CCDSiCCDS4248.1.
RefSeqiNP_001290074.1. NM_001303145.1.
NP_061762.2. NM_018939.3.
UniGeneiHs.283085.

3D structure databases

ProteinModelPortaliQ9Y5E3.
SMRiQ9Y5E3.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi121070. 1 interactor.

PTM databases

iPTMnetiQ9Y5E3.
PhosphoSitePlusiQ9Y5E3.

Polymorphism and mutation databases

BioMutaiPCDHB6.
DMDMi13431374.

Proteomic databases

EPDiQ9Y5E3.
PaxDbiQ9Y5E3.
PeptideAtlasiQ9Y5E3.
PRIDEiQ9Y5E3.

Protocols and materials databases

DNASUi56130.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000231136; ENSP00000231136; ENSG00000113211.
GeneIDi56130.
KEGGihsa:56130.
UCSCiuc003lir.4. human.

Organism-specific databases

CTDi56130.
GeneCardsiPCDHB6.
HGNCiHGNC:8691. PCDHB6.
HPAiHPA029566.
MIMi604967. gene.
606332. gene.
neXtProtiNX_Q9Y5E3.
PharmGKBiPA33040.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG3594. Eukaryota.
ENOG410XQHI. LUCA.
HOGENOMiHOG000220892.
HOVERGENiHBG054878.
InParanoidiQ9Y5E3.
KOiK16494.
OrthoDBiEOG091G024L.
PhylomeDBiQ9Y5E3.
TreeFamiTF332299.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000113211-MONOMER.

Miscellaneous databases

GenomeRNAii56130.
PROiQ9Y5E3.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000113211.
CleanExiHS_PCDHB6.
ExpressionAtlasiQ9Y5E3. baseline and differential.
GenevisibleiQ9Y5E3. HS.

Family and domain databases

Gene3Di2.60.40.60. 5 hits.
InterProiIPR002126. Cadherin.
IPR015919. Cadherin-like.
IPR032455. Cadherin_C.
IPR020894. Cadherin_CS.
IPR013164. Cadherin_N.
[Graphical view]
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. 5 hits.
PROSITEiPS00232. CADHERIN_1. 5 hits.
PS50268. CADHERIN_2. 5 hits.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiPCDB6_HUMAN
AccessioniPrimary (citable) accession number: Q9Y5E3
Secondary accession number(s): B2R8R9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 27, 2001
Last sequence update: November 1, 1999
Last modified: November 30, 2016
This is version 135 of the entry and version 1 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.