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Protein

Protocadherin beta-4

Gene

PCDHB4

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 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

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

Keywords - Biological processi

Cell adhesion

Keywords - Ligandi

Calcium

Names & Taxonomyi

Protein namesi
Recommended name:
Protocadherin beta-4
Short name:
PCDH-beta-4
Gene namesi
Name:PCDHB4
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 5

Organism-specific databases

HGNCiHGNC:8689. PCDHB4.

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini28 – 689662ExtracellularSequence analysisAdd
BLAST
Transmembranei690 – 71021HelicalSequence analysisAdd
BLAST
Topological domaini711 – 79585CytoplasmicSequence analysisAdd
BLAST

GO - Cellular componenti

  • cytoplasm Source: HPA
  • integral component of membrane Source: UniProtKB
  • integral component of plasma membrane Source: ProtInc
  • intermediate filament cytoskeleton Source: HPA
  • plasma membrane Source: HPA
Complete GO annotation...

Keywords - Cellular componenti

Cell membrane, Membrane

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA33038.

Polymorphism and mutation databases

BioMutaiPCDHB4.
DMDMi13431376.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 2727Sequence analysisAdd
BLAST
Chaini28 – 795768Protocadherin beta-4PRO_0000003920Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Glycosylationi183 – 1831N-linked (GlcNAc...)Sequence analysis
Glycosylationi417 – 4171N-linked (GlcNAc...)Sequence analysis
Glycosylationi435 – 4351N-linked (GlcNAc...)Sequence analysis
Glycosylationi566 – 5661N-linked (GlcNAc...)Sequence analysis

Keywords - PTMi

Glycoprotein

Proteomic databases

EPDiQ9Y5E5.
PaxDbiQ9Y5E5.
PeptideAtlasiQ9Y5E5.
PRIDEiQ9Y5E5.
TopDownProteomicsiQ9Y5E5.

PTM databases

iPTMnetiQ9Y5E5.
PhosphoSiteiQ9Y5E5.

Expressioni

Gene expression databases

BgeeiQ9Y5E5.
CleanExiHS_PCDHB4.
GenevisibleiQ9Y5E5. HS.

Organism-specific databases

HPAiHPA014466.

Structurei

3D structure databases

ProteinModelPortaliQ9Y5E5.
SMRiQ9Y5E5. Positions 30-676.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini34 – 13299Cadherin 1PROSITE-ProRule annotationAdd
BLAST
Domaini137 – 241105Cadherin 2PROSITE-ProRule annotationAdd
BLAST
Domaini246 – 346101Cadherin 3PROSITE-ProRule annotationAdd
BLAST
Domaini351 – 450100Cadherin 4PROSITE-ProRule annotationAdd
BLAST
Domaini455 – 560106Cadherin 5PROSITE-ProRule annotationAdd
BLAST
Domaini567 – 670104Cadherin 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.
InParanoidiQ9Y5E5.
KOiK16494.
OMAiVMVRILI.
OrthoDBiEOG7KSX80.
PhylomeDBiQ9Y5E5.
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.
IPR030729. PCDHB4.
[Graphical view]
PANTHERiPTHR24028:SF55. PTHR24028:SF55. 1 hit.
PfamiPF00028. Cadherin. 5 hits.
PF08266. Cadherin_2. 1 hit.
PF16492. Cadherin_C_2. 1 hit.
[Graphical view]
PRINTSiPR00205. CADHERIN.
SMARTiSM00112. CA. 5 hits.
[Graphical view]
SUPFAMiSSF49313. SSF49313. 6 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.

Q9Y5E5-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKKLGRIHPN RQVLAFILMV FLSQVRLEPI RYSVLEETES GSFVAHLAKD
60 70 80 90 100
LGLGIGELAS RSARVLSDDD KQRLQLDRQT GDLLLREKLD REELCGPIEP
110 120 130 140 150
CVLHFQVFLE MPVQFFQGEL LIQDINDHSP IFPEREVLLK ILENSQPGTL
160 170 180 190 200
FPLLIAEDLD VGSNGLQKYT ISPNSHFHIL TRNHSEGKKY PDLVQDKPLD
210 220 230 240 250
REEQPEFSLT LVALDGGSPP RSGTVMVRIL IMDINDNAPE FVHTPYGVQV
260 270 280 290 300
LENSPLDSPI VRVLARDIDA GNFGSVSYGL FQASDEIKQT FSINEVTGEI
310 320 330 340 350
LLKKKLDFEK IKSYHVEIEA TDGGGLSGKG TVVIEVVDVN DNPPELIISS
360 370 380 390 400
LTSSIPENAP ETVVSIFRIR DRDSGENGKM ICSIPDNLPF ILKPTLKNFY
410 420 430 440 450
TLVTERPLDR ETSAEYNITI AVTDLGTPRL KTQQNITVQV SDVNDNAPAF
460 470 480 490 500
TQTSYTLFVR ENNSPALHIG SVSATDRDSG TNAQVTYSLL PPQDPHLPLA
510 520 530 540 550
SLVSINADNG HLFALRSLDY EALQAFEFRV GASDRGSPAL SSEALVRVLV
560 570 580 590 600
LDTNDNSPFV LYPLQNGSAP CTELVPRAAE PGYLVTKVVA VDGDSGQNAW
610 620 630 640 650
LSYQLLKATE PGLFGVWAHN GEVRTARLLS ERDAAKHRLV VLVKDNGEPP
660 670 680 690 700
RSATATLHVL LVDGFSQPYL PLPEAAPAQA QADSLTVYLV VALASVSSLF
710 720 730 740 750
LFSVLLFVAV RLCRRSRAAS VGRCSVPEGP FPGHLVDVSG TGTLSQSYQY
760 770 780 790
EVCLTGDSGT GEFKFLKPIF PNLLVQDTGR EVKENPKFRN SLVFS
Length:795
Mass (Da):87,270
Last modified:November 1, 1999 - v1
Checksum:i32A521247DD6A56F
GO

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti168 – 1681K → R.
Corresponds to variant rs34350292 [ dbSNP | Ensembl ].
VAR_048548
Natural varianti255 – 2551P → L.
Corresponds to variant rs3733697 [ dbSNP | Ensembl ].
VAR_048549
Natural varianti255 – 2551P → S.
Corresponds to variant rs3733698 [ dbSNP | Ensembl ].
VAR_048550
Natural varianti421 – 4211A → T.
Corresponds to variant rs3776099 [ dbSNP | Ensembl ].
VAR_021878
Natural varianti553 – 5531T → A.
Corresponds to variant rs246669 [ dbSNP | Ensembl ].
VAR_048551

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF152497 mRNA. Translation: AAD43758.1.
AF217754 mRNA. Translation: AAK51621.1.
BC098139 mRNA. Translation: AAH98139.1.
BC098346 mRNA. Translation: AAH98346.1.
CCDSiCCDS4246.1.
RefSeqiNP_061761.1. NM_018938.3.
UniGeneiHs.591250.

Genome annotation databases

EnsembliENST00000194152; ENSP00000194152; ENSG00000081818.
GeneIDi56131.
KEGGihsa:56131.
UCSCiuc003lip.3. human.

Keywords - Coding sequence diversityi

Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF152497 mRNA. Translation: AAD43758.1.
AF217754 mRNA. Translation: AAK51621.1.
BC098139 mRNA. Translation: AAH98139.1.
BC098346 mRNA. Translation: AAH98346.1.
CCDSiCCDS4246.1.
RefSeqiNP_061761.1. NM_018938.3.
UniGeneiHs.591250.

3D structure databases

ProteinModelPortaliQ9Y5E5.
SMRiQ9Y5E5. Positions 30-676.
ModBaseiSearch...
MobiDBiSearch...

PTM databases

iPTMnetiQ9Y5E5.
PhosphoSiteiQ9Y5E5.

Polymorphism and mutation databases

BioMutaiPCDHB4.
DMDMi13431376.

Proteomic databases

EPDiQ9Y5E5.
PaxDbiQ9Y5E5.
PeptideAtlasiQ9Y5E5.
PRIDEiQ9Y5E5.
TopDownProteomicsiQ9Y5E5.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000194152; ENSP00000194152; ENSG00000081818.
GeneIDi56131.
KEGGihsa:56131.
UCSCiuc003lip.3. human.

Organism-specific databases

CTDi56131.
GeneCardsiPCDHB4.
HGNCiHGNC:8689. PCDHB4.
HPAiHPA014466.
MIMi604967. gene.
606330. gene.
neXtProtiNX_Q9Y5E5.
PharmGKBiPA33038.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG3594. Eukaryota.
ENOG410XQHI. LUCA.
GeneTreeiENSGT00840000129690.
HOGENOMiHOG000220892.
HOVERGENiHBG054878.
InParanoidiQ9Y5E5.
KOiK16494.
OMAiVMVRILI.
OrthoDBiEOG7KSX80.
PhylomeDBiQ9Y5E5.
TreeFamiTF332299.

Miscellaneous databases

ChiTaRSiPCDHB4. human.
GeneWikiiPCDHB4.
GenomeRNAii56131.
PROiQ9Y5E5.
SOURCEiSearch...

Gene expression databases

BgeeiQ9Y5E5.
CleanExiHS_PCDHB4.
GenevisibleiQ9Y5E5. 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.
IPR030729. PCDHB4.
[Graphical view]
PANTHERiPTHR24028:SF55. PTHR24028:SF55. 1 hit.
PfamiPF00028. Cadherin. 5 hits.
PF08266. Cadherin_2. 1 hit.
PF16492. Cadherin_C_2. 1 hit.
[Graphical view]
PRINTSiPR00205. CADHERIN.
SMARTiSM00112. CA. 5 hits.
[Graphical view]
SUPFAMiSSF49313. SSF49313. 6 hits.
PROSITEiPS00232. CADHERIN_1. 5 hits.
PS50268. CADHERIN_2. 5 hits.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "A striking organization of a large family of human neural cadherin-like cell adhesion genes."
    Wu Q., Maniatis T.
    Cell 97:779-790(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
  2. "The human and murine protocadherin-beta one-exon gene families show high evolutionary conservation, despite the difference in gene number."
    Vanhalst K., Kools P., Vanden Eynde E., van Roy F.
    FEBS Lett. 495:120-125(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
  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].

Entry informationi

Entry nameiPCDB4_HUMAN
AccessioniPrimary (citable) accession number: Q9Y5E5
Secondary accession number(s): Q4V761
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 27, 2001
Last sequence update: November 1, 1999
Last modified: July 6, 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.