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Protein

Protocadherin alpha-4

Gene

Pcdha4

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: -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

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

GO - Molecular functioni

  • calcium ion binding Source: UniProtKB
  • identical protein binding Source: UniProtKB

GO - Biological processi

  • cell adhesion Source: GO_Central
  • homophilic cell adhesion via plasma membrane adhesion molecules Source: UniProtKB

Keywordsi

Biological processCell adhesion
LigandCalcium, 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 lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaMyomorphaMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 18

Organism-specific databases

MGIiMGI:1298406 Pcdha4

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Topology

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

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...) asparaginePROSITE-ProRule annotation1
Glycosylationi265N-linked (GlcNAc...) asparagine1 PublicationImported1
Glycosylationi438O-linked (Man) threonine1 PublicationImported1
Glycosylationi440O-linked (Man) serine1 PublicationImported1
Glycosylationi442O-linked (Man) serine1 PublicationImported1
Glycosylationi548N-linked (GlcNAc...) asparaginePROSITE-ProRule annotation1

Keywords - PTMi

Disulfide bond, Glycoprotein

Proteomic databases

MaxQBiO88689
PeptideAtlasiO88689
PRIDEiO88689

PTM databases

iPTMnetiO88689
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

BgeeiENSMUSG00000103458 Expressed in 2 organ(s), highest expression level in cerebellum
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

Binary interactionsi

WithEntry#Exp.IntActNotes
HgsQ99LI82EBI-15880299,EBI-2119135

GO - Molecular functioni

Protein-protein interaction databases

CORUMiO88689
DIPiDIP-41020N
IntActiO88689, 2 interactors

Structurei

Secondary structure

1947
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

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

Keywords - Domaini

Repeat, Signal, Transmembrane, Transmembrane helix

Phylogenomic databases

GeneTreeiENSGT00920000148958
HOGENOMiHOG000220892
HOVERGENiHBG054878
InParanoidiO88689
KOiK16493
OMAiIMVKGYI
OrthoDBiEOG091G00KR

Family and domain databases

InterProiView protein in InterPro
IPR002126 Cadherin-like_dom
IPR015919 Cadherin-like_sf
IPR031904 Cadherin_CBD
IPR020894 Cadherin_CS
IPR013164 Cadherin_N
PfamiView protein in Pfam
PF00028 Cadherin, 5 hits
PF08266 Cadherin_2, 1 hit
PF15974 Cadherin_tail, 1 hit
PRINTSiPR00205 CADHERIN
SMARTiView protein in SMART
SM00112 CA, 6 hits
SUPFAMiSSF49313 SSF49313, 6 hits
PROSITEiView protein in PROSITE
PS00232 CADHERIN_1, 5 hits
PS50268 CADHERIN_2, 6 hits

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

Similar proteinsi

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

CORUMiO88689
DIPiDIP-41020N
IntActiO88689, 2 interactors

PTM databases

iPTMnetiO88689
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

GeneTreeiENSGT00920000148958
HOGENOMiHOG000220892
HOVERGENiHBG054878
InParanoidiO88689
KOiK16493
OMAiIMVKGYI
OrthoDBiEOG091G00KR

Miscellaneous databases

EvolutionaryTraceiO88689
PROiPR:O88689
SOURCEiSearch...

Gene expression databases

BgeeiENSMUSG00000103458 Expressed in 2 organ(s), highest expression level in cerebellum
CleanExiMM_CNR1
MM_PCDHA4
GenevisibleiO88689 MM

Family and domain databases

InterProiView protein in InterPro
IPR002126 Cadherin-like_dom
IPR015919 Cadherin-like_sf
IPR031904 Cadherin_CBD
IPR020894 Cadherin_CS
IPR013164 Cadherin_N
PfamiView protein in Pfam
PF00028 Cadherin, 5 hits
PF08266 Cadherin_2, 1 hit
PF15974 Cadherin_tail, 1 hit
PRINTSiPR00205 CADHERIN
SMARTiView protein in SMART
SM00112 CA, 6 hits
SUPFAMiSSF49313 SSF49313, 6 hits
PROSITEiView protein in PROSITE
PS00232 CADHERIN_1, 5 hits
PS50268 CADHERIN_2, 6 hits
ProtoNetiSearch...

Entry informationi

Entry nameiPCDA4_MOUSE
AccessioniPrimary (citable) accession number: O88689
Secondary accession number(s): Q3UEX3
, Q6PAM9, Q8K487, Q8K489
Entry historyiIntegrated into UniProtKB/Swiss-Prot: June 27, 2006
Last sequence update: November 1, 1998
Last modified: November 7, 2018
This is version 133 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

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
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