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Protein

Synaptonemal complex protein 3

Gene

SYCP3

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Component of the synaptonemal complexes (SCS), formed between homologous chromosomes during meiotic prophase. Required for centromere pairing during meiosis in male germ cells (By similarity). Required for normal meiosis during spermatogenesis and male fertility (PubMed:14643120). Plays a lesser role in female fertility. Required for efficient phosphorylation of HORMAD1 and HORMAD2 (By similarity).By similarity1 Publication

GO - Molecular functioni

GO - Biological processi

  • cell division Source: UniProtKB-KW
  • male meiosis I Source: UniProtKB
  • meiotic cell cycle Source: GO_Central
  • spermatid development Source: GO_Central
  • spermatogenesis Source: GO_Central
  • spermatogenesis, exchange of chromosomal proteins Source: UniProtKB

Keywordsi

Molecular functionDNA-binding
Biological processCell cycle, Cell division, Meiosis

Enzyme and pathway databases

ReactomeiR-HSA-1221632 Meiotic synapsis

Names & Taxonomyi

Protein namesi
Recommended name:
Synaptonemal complex protein 3
Short name:
SCP-3
Gene namesi
Name:SYCP3
Synonyms:SCP3
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 12

Organism-specific databases

EuPathDBiHostDB:ENSG00000139351.14
HGNCiHGNC:18130 SYCP3
MIMi604759 gene
neXtProtiNX_Q8IZU3

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

Keywords - Cellular componenti

Centromere, Chromosome, Nucleus

Pathology & Biotechi

Involvement in diseasei

Spermatogenic failure 4 (SPGF4)1 Publication
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionAn infertility disorder characterized by azoospermia, a condition of having no sperm present in the ejaculate. Testicular histology shows arrest of spermatogenesis at the pachytene stage of primary spermatocytes.
See also OMIM:270960
Pregnancy loss, recurrent, 4 (RPRGL4)1 Publication
Disease susceptibility is associated with variations affecting the gene represented in this entry.
Disease descriptionA common complication of pregnancy, resulting in spontaneous abortion before the fetus has reached viability. The term includes all miscarriages from the time of conception until 24 weeks of gestation. Recurrent pregnancy loss is defined as 3 or more consecutive spontaneous abortions.
See also OMIM:270960

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi52 – 57KRRKKR → AAAAAA: Impairs DNA binding. Abolishes DNA binding; when associated with 88-A--A-91. 1 Publication6
Mutagenesisi69 – 74EVQNML → AAAAAA: Abolishes fiber formation. 1 Publication6
Mutagenesisi88 – 91KRKR → AAAA: Impairs DNA binding. Abolishes DNA binding; when associated with 52-A--A-57. 1 Publication4
Mutagenesisi231 – 236Missing : Abolishes fiber formation. 1 Publication6

Organism-specific databases

DisGeNETi50511
MalaCardsiSYCP3
MIMi270960 phenotype
OpenTargetsiENSG00000139351
Orphaneti399805 Male infertility with azoospermia or oligozoospermia due to single gene mutation
PharmGKBiPA38298

Polymorphism and mutation databases

BioMutaiSYCP3
DMDMi74728444

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002290241 – 236Synaptonemal complex protein 3Add BLAST236

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei36PhosphoserineBy similarity1
Modified residuei38PhosphoserineBy similarity1
Modified residuei59PhosphoserineBy similarity1

Post-translational modificationi

Phosphorylated.By similarity

Keywords - PTMi

Phosphoprotein

Proteomic databases

PaxDbiQ8IZU3
PeptideAtlasiQ8IZU3
PRIDEiQ8IZU3
ProteomicsDBi71431

PTM databases

iPTMnetiQ8IZU3
PhosphoSitePlusiQ8IZU3

Expressioni

Tissue specificityi

Testis-specific.2 Publications

Gene expression databases

BgeeiENSG00000139351 Expressed in 124 organ(s), highest expression level in female gonad
CleanExiHS_SYCP3
ExpressionAtlasiQ8IZU3 baseline and differential
GenevisibleiQ8IZU3 HS

Organism-specific databases

HPAiCAB032978
HPA039635
HPA043938

Interactioni

Subunit structurei

Component of the lateral elements of synaptonemal complexes (By similarity). Homotetramer; the tetrameric helix bundles assemble end to end into long homopolimeric fibers that exhibit a transversal striation with a periodicity of about 20 nm (in vitro) (PubMed:24950965). Interacts with SYCP2 (By similarity).By similarity1 Publication

Protein-protein interaction databases

BioGridi119081, 6 interactors
DIPiDIP-59536N
IntActiQ8IZU3, 5 interactors
MINTiQ8IZU3
STRINGi9606.ENSP00000266743

Structurei

Secondary structure

1236
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliQ8IZU3
SMRiQ8IZU3
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni52 – 57Interaction with DNA1 Publication6
Regioni69 – 74Important for oligomerization and fiber formation1 Publication6
Regioni88 – 91Interaction with DNA1 Publication4
Regioni231 – 236Important for oligomerization and fiber formation1 Publication6

Coiled coil

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Coiled coili66 – 223Sequence analysis1 PublicationAdd BLAST158

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi88 – 91Nuclear localization signalSequence analysis4

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi105 – 232Gln-richAdd BLAST128

Domaini

Composed of a long central coiled coil domain. The N-terminal and C-terminal regions interact with DNA.1 Publication

Sequence similaritiesi

Belongs to the XLR/SYCP3 family.Curated

Keywords - Domaini

Coiled coil

Phylogenomic databases

eggNOGiENOG410IJ2Y Eukaryota
ENOG4111MZD LUCA
GeneTreeiENSGT00390000000062
HOGENOMiHOG000236293
HOVERGENiHBG100390
InParanoidiQ8IZU3
KOiK19528
OMAiVIEKHGK
OrthoDBiEOG091G0L3F
PhylomeDBiQ8IZU3
TreeFamiTF328876

Family and domain databases

InterProiView protein in InterPro
IPR006888 XLR/SYCP3/FAM9_dom
PfamiView protein in Pfam
PF04803 Cor1, 1 hit

Sequencei

Sequence statusi: Complete.

Q8IZU3-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MVSSGKKYSR KSGKPSVEDQ FTRAYDFETE DKKDLSGSEE DVIEGKTAVI
60 70 80 90 100
EKRRKKRSSA GVVEDMGGEV QNMLEGVGVD INKALLAKRK RLEMYTKASL
110 120 130 140 150
KTSNQKIEHV WKTQQDQRQK LNQEYSQQFL TLFQQWDLDM QKAEEQEEKI
160 170 180 190 200
LNMFRQQQKI LQQSRIVQSQ RLKTIKQLYE QFIKSMEELE KNHDNLLTGA
210 220 230
QNEFKKEMAM LQKKIMMETQ QQEIASVRKS LQSMLF
Length:236
Mass (Da):27,729
Last modified:March 1, 2003 - v1
Checksum:iD871B6AEA279ABDD
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF492003 mRNA Translation: AAN06611.1
AF517774 mRNA Translation: AAP47204.1
BC062662 mRNA Translation: AAH62662.1
CCDSiCCDS9087.1
RefSeqiNP_001171419.1, NM_001177948.1
NP_001171420.1, NM_001177949.1
NP_710161.1, NM_153694.4
UniGeneiHs.506504

Genome annotation databases

EnsembliENST00000266743; ENSP00000266743; ENSG00000139351
ENST00000392924; ENSP00000376655; ENSG00000139351
ENST00000392927; ENSP00000376658; ENSG00000139351
GeneIDi50511
KEGGihsa:50511
UCSCiuc001tiq.4 human

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF492003 mRNA Translation: AAN06611.1
AF517774 mRNA Translation: AAP47204.1
BC062662 mRNA Translation: AAH62662.1
CCDSiCCDS9087.1
RefSeqiNP_001171419.1, NM_001177948.1
NP_001171420.1, NM_001177949.1
NP_710161.1, NM_153694.4
UniGeneiHs.506504

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4CPCX-ray2.24A/B/C/D/E/F/G/H66-230[»]
ProteinModelPortaliQ8IZU3
SMRiQ8IZU3
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi119081, 6 interactors
DIPiDIP-59536N
IntActiQ8IZU3, 5 interactors
MINTiQ8IZU3
STRINGi9606.ENSP00000266743

PTM databases

iPTMnetiQ8IZU3
PhosphoSitePlusiQ8IZU3

Polymorphism and mutation databases

BioMutaiSYCP3
DMDMi74728444

Proteomic databases

PaxDbiQ8IZU3
PeptideAtlasiQ8IZU3
PRIDEiQ8IZU3
ProteomicsDBi71431

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000266743; ENSP00000266743; ENSG00000139351
ENST00000392924; ENSP00000376655; ENSG00000139351
ENST00000392927; ENSP00000376658; ENSG00000139351
GeneIDi50511
KEGGihsa:50511
UCSCiuc001tiq.4 human

Organism-specific databases

CTDi50511
DisGeNETi50511
EuPathDBiHostDB:ENSG00000139351.14
GeneCardsiSYCP3
HGNCiHGNC:18130 SYCP3
HPAiCAB032978
HPA039635
HPA043938
MalaCardsiSYCP3
MIMi270960 phenotype
604759 gene
neXtProtiNX_Q8IZU3
OpenTargetsiENSG00000139351
Orphaneti399805 Male infertility with azoospermia or oligozoospermia due to single gene mutation
PharmGKBiPA38298
GenAtlasiSearch...

Phylogenomic databases

eggNOGiENOG410IJ2Y Eukaryota
ENOG4111MZD LUCA
GeneTreeiENSGT00390000000062
HOGENOMiHOG000236293
HOVERGENiHBG100390
InParanoidiQ8IZU3
KOiK19528
OMAiVIEKHGK
OrthoDBiEOG091G0L3F
PhylomeDBiQ8IZU3
TreeFamiTF328876

Enzyme and pathway databases

ReactomeiR-HSA-1221632 Meiotic synapsis

Miscellaneous databases

ChiTaRSiSYCP3 human
GeneWikiiSYCP3
GenomeRNAii50511
PROiPR:Q8IZU3
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000139351 Expressed in 124 organ(s), highest expression level in female gonad
CleanExiHS_SYCP3
ExpressionAtlasiQ8IZU3 baseline and differential
GenevisibleiQ8IZU3 HS

Family and domain databases

InterProiView protein in InterPro
IPR006888 XLR/SYCP3/FAM9_dom
PfamiView protein in Pfam
PF04803 Cor1, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiSYCP3_HUMAN
AccessioniPrimary (citable) accession number: Q8IZU3
Entry historyiIntegrated into UniProtKB/Swiss-Prot: March 21, 2006
Last sequence update: March 1, 2003
Last modified: November 7, 2018
This is version 131 of the entry and version 1 of the sequence. See 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. SIMILARITY comments
    Index of protein domains and families
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. Human chromosome 12
    Human chromosome 12: entries, gene names and cross-references to MIM
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Main funding by: National Institutes of Health

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