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Protein

Protocadherin alpha-4

Gene

Pcdha4

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Calcium-dependent cell-adhesion protein involved in cells self-recognition and non-self discrimination (Probable). Thereby, it is involved in the establishment and maintenance of specific neuronal connections in the brain (PubMed:27161523).1 Publication

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

Cell adhesion

Keywords - Ligandi

Calcium, Metal-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Protocadherin alpha-4Curated
Short name:
PCDH-alpha-4Curated
Gene namesi
Name:Pcdha4Imported
Synonyms:Cnr1
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 18

Organism-specific databases

MGIiMGI:1298406. Pcdha4.

Subcellular locationi

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Topological domaini30 – 697Extracellular1 PublicationAdd BLAST668
Transmembranei698 – 718HelicalSequence analysisAdd BLAST21
Topological domaini719 – 947Cytoplasmic1 PublicationAdd BLAST229

GO - Cellular componenti

  • endoplasmic reticulum Source: MGI
  • integral component of membrane Source: UniProtKB-KW
  • membrane Source: MGI
  • plasma membrane Source: UniProtKB-SubCell
  • synapse Source: MGI
Complete GO annotation...

Keywords - Cellular componenti

Cell membrane, Membrane

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 29Sequence analysisAdd BLAST29
ChainiPRO_000024066330 – 947Protocadherin alpha-4Add BLAST918

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Disulfide bondi96 ↔ 1022 PublicationsImported
Glycosylationi257N-linked (GlcNAc...)PROSITE-ProRule annotation1
Glycosylationi265N-linked (GlcNAc...)1 PublicationImported1
Glycosylationi438O-linked (Man)1 PublicationImported1
Glycosylationi440O-linked (Man)1 PublicationImported1
Glycosylationi442O-linked (Man)1 PublicationImported1
Glycosylationi548N-linked (GlcNAc...)PROSITE-ProRule annotation1

Keywords - PTMi

Disulfide bond, Glycoprotein

Proteomic databases

MaxQBiO88689.
PeptideAtlasiO88689.
PRIDEiO88689.

PTM databases

PhosphoSitePlusiO88689.

Expressioni

Tissue specificityi

Detected in brain throughout embryonic development. Detected in adult brain, in particular in cerebellum and forebrain.1 Publication

Gene expression databases

BgeeiENSMUSG00000007440.
CleanExiMM_CNR1.
MM_PCDHA4.
GenevisibleiO88689. MM.

Interactioni

Subunit structurei

Forms homodimers in trans (molecules expressed by two different cells) (PubMed:27161523). Forms promiscuous heterodimers in cis (at the plasma membrane of the same cell) with other protocadherins (PubMed:27161523). Interacts with FYN (PubMed:9655502).2 Publications

Protein-protein interaction databases

DIPiDIP-41020N.
MINTiMINT-113982.

Structurei

Secondary structure

1947
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi31 – 38Combined sources8
Beta strandi44 – 46Combined sources3
Helixi48 – 51Combined sources4
Helixi56 – 59Combined sources4
Turni60 – 63Combined sources4
Beta strandi65 – 71Combined sources7
Beta strandi73 – 78Combined sources6
Turni79 – 82Combined sources4
Beta strandi83 – 86Combined sources4
Helixi92 – 95Combined sources4
Beta strandi97 – 101Combined sources5
Beta strandi103 – 110Combined sources8
Turni111 – 114Combined sources4
Beta strandi115 – 124Combined sources10
Beta strandi136 – 140Combined sources5
Helixi164 – 166Combined sources3
Beta strandi168 – 172Combined sources5
Beta strandi176 – 181Combined sources6
Beta strandi193 – 196Combined sources4
Turni202 – 204Combined sources3
Beta strandi206 – 220Combined sources15
Beta strandi223 – 231Combined sources9
Beta strandi241 – 243Combined sources3
Beta strandi245 – 251Combined sources7
Beta strandi260 – 263Combined sources4
Helixi272 – 274Combined sources3
Beta strandi277 – 281Combined sources5
Helixi287 – 292Combined sources6
Beta strandi293 – 295Combined sources3
Turni297 – 299Combined sources3
Beta strandi301 – 304Combined sources4
Turni310 – 312Combined sources3
Beta strandi314 – 324Combined sources11
Beta strandi326 – 328Combined sources3
Beta strandi331 – 340Combined sources10
Beta strandi349 – 355Combined sources7
Beta strandi358 – 360Combined sources3
Beta strandi368 – 375Combined sources8
Helixi380 – 383Combined sources4
Beta strandi385 – 389Combined sources5
Beta strandi391 – 394Combined sources4
Beta strandi396 – 401Combined sources6
Beta strandi404 – 408Combined sources5
Turni415 – 417Combined sources3
Beta strandi420 – 429Combined sources10
Beta strandi436 – 446Combined sources11

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1WUZNMR-A27-129[»]
5DZWX-ray2.43A30-450[»]
ProteinModelPortaliO88689.
SMRiO88689.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO88689.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini30 – 133Cadherin 1PROSITE-ProRule annotationAdd BLAST104
Domaini134 – 242Cadherin 2PROSITE-ProRule annotationAdd BLAST109
Domaini243 – 350Cadherin 3PROSITE-ProRule annotationAdd BLAST108
Domaini351 – 455Cadherin 4PROSITE-ProRule annotationAdd BLAST105
Domaini456 – 565Cadherin 5PROSITE-ProRule annotationAdd BLAST110
Domaini573 – 681Cadherin 6PROSITE-ProRule annotationAdd BLAST109
Repeati734 – 737PXXP 14
Repeati774 – 777PXXP 24
Repeati796 – 799PXXP 34
Repeati829 – 832PXXP 44
Repeati870 – 873PXXP 54
Repeati888 – 891PXXP 64

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni734 – 8916 X 4 AA repeats of P-X-X-PAdd BLAST158
Regioni738 – 947Required for interaction with FYN1 PublicationAdd BLAST210

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi920 – 927Poly-LysSequence analysis8

Domaini

Cadherin 1 to cadherin 4 domains mediate homophilic trans-interaction, the interaction with an identical protocadherin expressed by a neighboring cell (PubMed:27161523). This is an 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 (PubMed:27161523). The cadherin 6 domain mediates promiscuous interactions with protocadherins on the same cell membrane (PubMed:27161523). Each cadherin domain binds three calcium ions (PubMed:27161523).1 PublicationImported

Sequence similaritiesi

Contains 6 cadherin domains.PROSITE-ProRule annotation

Keywords - Domaini

Repeat, Signal, Transmembrane, Transmembrane helix

Phylogenomic databases

GeneTreeiENSGT00850000132246.
HOGENOMiHOG000220892.
HOVERGENiHBG054878.
InParanoidiO88689.
KOiK16493.
OMAiDNVPDLE.
OrthoDBiEOG091G00KR.

Family and domain databases

Gene3Di2.60.40.60. 6 hits.
InterProiIPR002126. Cadherin.
IPR015919. Cadherin-like.
IPR031904. Cadherin_CBD.
IPR020894. Cadherin_CS.
IPR013164. Cadherin_N.
[Graphical view]
PfamiPF00028. Cadherin. 5 hits.
PF08266. Cadherin_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 (3)i

Sequence statusi: Complete.

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

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: O88689-1) [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
MEFSWGSGQE SQRLLLSFLL LAIWEAGNSQ IHYSIPEEAK HGTFVGRIAQ
60 70 80 90 100
DLGLELTELV PRLFRVASKD RGDLLEVNLQ NGILFVNSRI DREELCGRSA
110 120 130 140 150
ECSIHLEVIV DRPLQVFHVE VEVRDINDNP PRFPTTQKNL FIAESRPLDT
160 170 180 190 200
WFPLEGASDA DIGINAVLTY RLSPNDYFSL EKPSNDERVK GLGLVLRKSL
210 220 230 240 250
DREETPEIIL VLTVTDGGKP ELTGSVQLLI TVLDANDNAP VFDRSLYTVK
260 270 280 290 300
LPENVPNGTL VVKVNASDLD EGVNGDIMYS FSTDISPNVK YKFHIDPVSG
310 320 330 340 350
EIIVKGYIDF EECKSYEILI EGIDKGQLPL SGHCKVIVQV EDINDNVPEL
360 370 380 390 400
EFKSLSLPIR ENSPVGTVIA LISVSDRDTG VNGQVTCSLT SHVPFKLVST
410 420 430 440 450
FKNYYSLVLD SALDRETTAD YKVVVTARDG GSPSLWATAS VSVEVADVND
460 470 480 490 500
NAPVFAQPEY TVFVKENNPP GAHIFTVSAM DADAQENALV SYSLVERRVG
510 520 530 540 550
ERLLSSYVSV HAESGKVFAL QPLDHEELEL LRFQVSARDA GVPALGSNVT
560 570 580 590 600
LQVFVLDEND NAPTLLEPEA GVSGGIVSRL VSRSVGAGHV VAKVRAVDAD
610 620 630 640 650
SGYNAWLSYE LQSSEGNSRS LFRVGLYTGE ISTTRILDEA DSPRQRLLVL
660 670 680 690 700
VKDHGDPAMI VTATVLVSLV ENGPVPKAPS RVSTSVTHSE ASLVDVNVYL
710 720 730 740 750
IIAICAVSSL LVLTLLLYTA LRCSTVPSES VCGPPKPVMV CSSAVGSWSY
760 770 780 790 800
SQQRRQRVCS GEYPPKTDLM AFSPSLSDSR DREDQLQSAE DSSGKPRQPN
810 820 830 840 850
PDWRYSASLR AGMHSSVHLE EAGILRAGPG GPDQQWPTVS SATPEPEAGE
860 870 880 890 900
VSPPVGAGVN SNSWTFKYGP GNPKQSGPGE LPDKFIIPGS PAIISIRQEP
910 920 930 940
ANNQIDKSDF ITFGKKEETK KKKKKKKGNK TQEKKEKGNS TTDNSDQ
Length:947
Mass (Da):103,143
Last modified:November 1, 1998 - v1
Checksum:i082497DBBAEFB503
GO
Isoform 2 (identifier: O88689-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     535-795: Missing.
     879-947: GELPDKFIIP...GNSTTDNSDQ → EPKKQTQVSFLPRRKGEASQPRQ

Show »
Length:640
Mass (Da):70,430
Checksum:i7B8393620F457915
GO
Isoform 3 (identifier: O88689-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     796-947: PRQPNPDWRY...GNSTTDNSDQ → QAPPNTDWRF...KKKSGKKEKK

Show »
Length:919
Mass (Da):99,666
Checksum:i21D65CCE53617EB5
GO

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_019413535 – 795Missing in isoform 2. 1 PublicationAdd BLAST261
Alternative sequenceiVSP_019414796 – 947PRQPN…DNSDQ → QAPPNTDWRFSQAQRPGTSG SQNGDETGTWPNNQFDTEML QAMILASASEAADGSSTLGG GAGTMGLSARYGPQFTLQHV PDYRQNVYIPGSNATLTNAA GKRDGKAPAGGNGNKKKSGK KEKK in isoform 3. 1 PublicationAdd BLAST152
Alternative sequenceiVSP_019415879 – 947GELPD…DNSDQ → EPKKQTQVSFLPRRKGEASQ PRQ in isoform 2. 1 PublicationAdd BLAST69

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D86916 mRNA. Translation: BAA29045.1.
AY013762 mRNA. Translation: AAK26051.1.
AF464178 Genomic DNA. Translation: AAM93577.1.
AF464180 mRNA. Translation: AAM93579.1.
BC060211 mRNA. Translation: AAH60211.1.
AK149282 mRNA. Translation: BAE28788.1.
CCDSiCCDS37776.1. [O88689-1]
RefSeqiNP_001167625.1. NM_001174154.2. [O88689-3]
NP_031792.1. NM_007766.2. [O88689-1]
UniGeneiMm.247203.
Mm.308500.

Genome annotation databases

EnsembliENSMUST00000115661; ENSMUSP00000111325; ENSMUSG00000103458. [O88689-3]
ENSMUST00000192295; ENSMUSP00000142103; ENSMUSG00000104252. [O88689-2]
ENSMUST00000192512; ENSMUSP00000141408; ENSMUSG00000104252. [O88689-1]
GeneIDi100384868.
12936.
KEGGimmu:100384868.
mmu:12936.
UCSCiuc008eox.3. mouse. [O88689-1]
uc008eoy.2. mouse. [O88689-3]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D86916 mRNA. Translation: BAA29045.1.
AY013762 mRNA. Translation: AAK26051.1.
AF464178 Genomic DNA. Translation: AAM93577.1.
AF464180 mRNA. Translation: AAM93579.1.
BC060211 mRNA. Translation: AAH60211.1.
AK149282 mRNA. Translation: BAE28788.1.
CCDSiCCDS37776.1. [O88689-1]
RefSeqiNP_001167625.1. NM_001174154.2. [O88689-3]
NP_031792.1. NM_007766.2. [O88689-1]
UniGeneiMm.247203.
Mm.308500.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1WUZNMR-A27-129[»]
5DZWX-ray2.43A30-450[»]
ProteinModelPortaliO88689.
SMRiO88689.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-41020N.
MINTiMINT-113982.

PTM databases

PhosphoSitePlusiO88689.

Proteomic databases

MaxQBiO88689.
PeptideAtlasiO88689.
PRIDEiO88689.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000115661; ENSMUSP00000111325; ENSMUSG00000103458. [O88689-3]
ENSMUST00000192295; ENSMUSP00000142103; ENSMUSG00000104252. [O88689-2]
ENSMUST00000192512; ENSMUSP00000141408; ENSMUSG00000104252. [O88689-1]
GeneIDi100384868.
12936.
KEGGimmu:100384868.
mmu:12936.
UCSCiuc008eox.3. mouse. [O88689-1]
uc008eoy.2. mouse. [O88689-3]

Organism-specific databases

CTDi56144.
MGIiMGI:1298406. Pcdha4.

Phylogenomic databases

GeneTreeiENSGT00850000132246.
HOGENOMiHOG000220892.
HOVERGENiHBG054878.
InParanoidiO88689.
KOiK16493.
OMAiDNVPDLE.
OrthoDBiEOG091G00KR.

Miscellaneous databases

EvolutionaryTraceiO88689.
PROiO88689.
SOURCEiSearch...

Gene expression databases

BgeeiENSMUSG00000007440.
CleanExiMM_CNR1.
MM_PCDHA4.
GenevisibleiO88689. MM.

Family and domain databases

Gene3Di2.60.40.60. 6 hits.
InterProiIPR002126. Cadherin.
IPR015919. Cadherin-like.
IPR031904. Cadherin_CBD.
IPR020894. Cadherin_CS.
IPR013164. Cadherin_N.
[Graphical view]
PfamiPF00028. Cadherin. 5 hits.
PF08266. Cadherin_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 nameiPCDA4_MOUSE
AccessioniPrimary (citable) accession number: O88689
Secondary accession number(s): Q3UEX3
, Q6PAM9, Q8K487, Q8K489
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 27, 2006
Last sequence update: November 1, 1998
Last modified: November 30, 2016
This is version 121 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Miscellaneous

The protocadherins alpha are expressed from a single gene cluster similarly to immunoglobulin and T-cell receptors. The N-terminal region containing the 6 extracellular cadherin domains, unique to each protocadherin alpha, is encoded by one of the large exons found in tandem array within the gene cluster. The C-terminal region, identical to all protocadherins alpha, is encoded by 3 shared exons.1 Publication

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. 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.