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Protein

Pigment epithelium-derived factor

Gene

SERPINF1

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

Functioni

Neurotrophic protein; induces extensive neuronal differentiation in retinoblastoma cells. Potent inhibitor of angiogenesis. As it does not undergo the S (stressed) to R (relaxed) conformational transition characteristic of active serpins, it exhibits no serine protease inhibitory activity.2 Publications

GO - Molecular functioni

  • serine-type endopeptidase inhibitor activity Source: ProtInc

GO - Biological processi

Complete GO annotation...

Enzyme and pathway databases

BioCyciZFISH:ENSG00000132386-MONOMER.

Protein family/group databases

MEROPSiI04.979.

Names & Taxonomyi

Protein namesi
Recommended name:
Pigment epithelium-derived factor
Short name:
PEDF
Alternative name(s):
Cell proliferation-inducing gene 35 protein
EPC-1
Serpin F1
Gene namesi
Name:SERPINF1
Synonyms:PEDF
ORF Names:PIG35
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 17

Organism-specific databases

HGNCiHGNC:8824. SERPINF1.

Subcellular locationi

GO - Cellular componenti

  • axon hillock Source: Ensembl
  • basement membrane Source: Ensembl
  • extracellular exosome Source: UniProtKB
  • extracellular region Source: UniProtKB
  • extracellular space Source: BHF-UCL
  • melanosome Source: UniProtKB-SubCell
  • perinuclear region of cytoplasm Source: Ensembl
Complete GO annotation...

Keywords - Cellular componenti

Secreted

Pathology & Biotechi

Involvement in diseasei

Osteogenesis imperfecta 6 (OI6)1 Publication
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA form of osteogenesis imperfecta, a connective tissue disorder characterized by low bone mass, bone fragility and susceptibility to fractures after minimal trauma. Disease severity ranges from very mild forms without fractures to intrauterine fractures and perinatal lethality. Extraskeletal manifestations, which affect a variable number of patients, are dentinogenesis imperfecta, hearing loss, and blue sclerae. OI6 is a severe, autosomal recessive form compatible with OI type III in the Sillence classification.
See also OMIM:613982

Keywords - Diseasei

Dwarfism, Osteogenesis imperfecta

Organism-specific databases

DisGeNETi5176.
MalaCardsiSERPINF1.
MIMi613982. phenotype.
OpenTargetsiENSG00000132386.
Orphaneti216812. Osteogenesis imperfecta type 3.
PharmGKBiPA35508.

Polymorphism and mutation databases

BioMutaiSERPINF1.
DMDMi313104314.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 19Add BLAST19
ChainiPRO_000003250820 – 418Pigment epithelium-derived factorAdd BLAST399

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei20Pyrrolidone carboxylic acid1 Publication1
Modified residuei24Phosphoserine; by CK21 Publication1
Modified residuei114Phosphoserine; by CK21 Publication1
Modified residuei227Phosphoserine; by PKA1 Publication1
Glycosylationi285N-linked (GlcNAc...) (complex)4 Publications1

Post-translational modificationi

The N-terminus is blocked. Extracellular phosphorylation enhances antiangiogenic activity.1 Publication
N- and O-glycosylated. O-glycosylated with a core 1 or possibly core 8 glycan.5 Publications

Keywords - PTMi

Glycoprotein, Phosphoprotein, Pyrrolidone carboxylic acid

Proteomic databases

EPDiP36955.
MaxQBiP36955.
PaxDbiP36955.
PeptideAtlasiP36955.
PRIDEiP36955.

2D gel databases

REPRODUCTION-2DPAGEIPI00006114.

PTM databases

iPTMnetiP36955.
PhosphoSitePlusiP36955.

Expressioni

Tissue specificityi

Retinal pigment epithelial cells and blood plasma.1 Publication

Developmental stagei

Expressed in quiescent cells.

Gene expression databases

BgeeiENSG00000132386.
CleanExiHS_SERPINF1.
ExpressionAtlasiP36955. baseline and differential.
GenevisibleiP36955. HS.

Organism-specific databases

HPAiCAB004785.
HPA005825.

Interactioni

Binary interactionsi

WithEntry#Exp.IntActNotes
EPM2AIP1Q7L7755EBI-2932733,EBI-6255981

Protein-protein interaction databases

BioGridi111202. 12 interactors.
IntActiP36955. 7 interactors.
MINTiMINT-7711036.
STRINGi9606.ENSP00000254722.

Structurei

Secondary structure

1418
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi45 – 48Combined sources4
Helixi50 – 72Combined sources23
Beta strandi78 – 80Combined sources3
Helixi82 – 92Combined sources11
Helixi93 – 95Combined sources3
Helixi98 – 107Combined sources10
Helixi110 – 112Combined sources3
Helixi118 – 129Combined sources12
Beta strandi136 – 144Combined sources9
Helixi152 – 162Combined sources11
Helixi173 – 187Combined sources15
Turni188 – 190Combined sources3
Beta strandi204 – 214Combined sources11
Beta strandi217 – 219Combined sources3
Helixi223 – 225Combined sources3
Beta strandi227 – 236Combined sources10
Beta strandi238 – 256Combined sources19
Turni257 – 260Combined sources4
Beta strandi261 – 268Combined sources8
Turni269 – 271Combined sources3
Beta strandi272 – 281Combined sources10
Helixi287 – 290Combined sources4
Helixi295 – 304Combined sources10
Beta strandi306 – 315Combined sources10
Beta strandi317 – 324Combined sources8
Helixi326 – 330Combined sources5
Turni331 – 335Combined sources5
Helixi336 – 339Combined sources4
Turni344 – 346Combined sources3
Beta strandi353 – 364Combined sources12
Beta strandi368 – 370Combined sources3
Beta strandi387 – 389Combined sources3
Beta strandi394 – 400Combined sources7
Turni401 – 403Combined sources3
Beta strandi406 – 413Combined sources8

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1IMVX-ray2.85A21-418[»]
ProteinModelPortaliP36955.
SMRiP36955.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP36955.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni371 – 383O-glycosylated at one siteAdd BLAST13

Domaini

The N-terminal (AA 44-121) exhibits neurite outgrowth-inducing activity. The C-terminal exposed loop (AA 382-418) is essential for serpin activity.

Sequence similaritiesi

Belongs to the serpin family.Curated

Keywords - Domaini

Signal

Phylogenomic databases

eggNOGiKOG2392. Eukaryota.
COG4826. LUCA.
GeneTreeiENSGT00850000132312.
HOGENOMiHOG000115489.
HOVERGENiHBG106911.
InParanoidiP36955.
KOiK19614.
OMAiLQDFHLD.
OrthoDBiEOG091G09UU.
PhylomeDBiP36955.
TreeFamiTF317350.

Family and domain databases

CDDicd02052. PEDF. 1 hit.
InterProiIPR033832. PEDF.
IPR023795. Serpin_CS.
IPR023796. Serpin_dom.
IPR000215. Serpin_fam.
[Graphical view]
PANTHERiPTHR11461. PTHR11461. 1 hit.
PfamiPF00079. Serpin. 1 hit.
[Graphical view]
SMARTiSM00093. SERPIN. 1 hit.
[Graphical view]
SUPFAMiSSF56574. SSF56574. 1 hit.
PROSITEiPS00284. SERPIN. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

P36955-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MQALVLLLCI GALLGHSSCQ NPASPPEEGS PDPDSTGALV EEEDPFFKVP
60 70 80 90 100
VNKLAAAVSN FGYDLYRVRS STSPTTNVLL SPLSVATALS ALSLGAEQRT
110 120 130 140 150
ESIIHRALYY DLISSPDIHG TYKELLDTVT APQKNLKSAS RIVFEKKLRI
160 170 180 190 200
KSSFVAPLEK SYGTRPRVLT GNPRLDLQEI NNWVQAQMKG KLARSTKEIP
210 220 230 240 250
DEISILLLGV AHFKGQWVTK FDSRKTSLED FYLDEERTVR VPMMSDPKAV
260 270 280 290 300
LRYGLDSDLS CKIAQLPLTG SMSIIFFLPL KVTQNLTLIE ESLTSEFIHD
310 320 330 340 350
IDRELKTVQA VLTVPKLKLS YEGEVTKSLQ EMKLQSLFDS PDFSKITGKP
360 370 380 390 400
IKLTQVEHRA GFEWNEDGAG TTPSPGLQPA HLTFPLDYHL NQPFIFVLRD
410
TDTGALLFIG KILDPRGP
Length:418
Mass (Da):46,312
Last modified:November 30, 2010 - v4
Checksum:i7630DD2B4026A0D3
GO

Sequence cautioni

The sequence AAA84914 differs from that shown. Reason: Frameshift at position 356.Curated
The sequence AAA93524 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti97 – 98EQ → DE in AAA60058 (PubMed:8434014).Curated2
Sequence conflicti97 – 98EQ → DE in AAB38685 (Ref. 10) Curated2

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_00912672T → M Polymorphism; confirmed at protein level. 10 PublicationsCorresponds to variant rs1136287dbSNPEnsembl.1
Natural variantiVAR_025500132P → R.1 PublicationCorresponds to variant rs1804145dbSNPEnsembl.1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M76979 mRNA. Translation: AAA60058.1.
U29953 Genomic DNA. Translation: AAA84914.1. Frameshift.
AF400442 mRNA. Translation: AAK92491.1.
BT007222 mRNA. Translation: AAP35886.1.
AY513280 mRNA. Translation: AAT08033.1.
AB593011 mRNA. Translation: BAJ83966.1.
AB593012 mRNA. Translation: BAJ83967.1.
AB593013 mRNA. Translation: BAJ83968.1.
AC130343 Genomic DNA. No translation available.
AC130689 Genomic DNA. No translation available.
CH471108 Genomic DNA. Translation: EAW90577.1.
BC000522 mRNA. Translation: AAH00522.1.
BC013984 mRNA. Translation: AAH13984.1.
AH004879 Genomic DNA. Translation: AAB38685.1.
M90439 mRNA. Translation: AAA93524.1. Different initiation.
CCDSiCCDS11012.1.
PIRiA46046.
A47281.
RefSeqiNP_001316832.1. NM_001329903.1.
NP_002606.3. NM_002615.6.
UniGeneiHs.532768.

Genome annotation databases

EnsembliENST00000254722; ENSP00000254722; ENSG00000132386.
GeneIDi5176.
KEGGihsa:5176.
UCSCiuc002ftl.4. human.

Keywords - Coding sequence diversityi

Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M76979 mRNA. Translation: AAA60058.1.
U29953 Genomic DNA. Translation: AAA84914.1. Frameshift.
AF400442 mRNA. Translation: AAK92491.1.
BT007222 mRNA. Translation: AAP35886.1.
AY513280 mRNA. Translation: AAT08033.1.
AB593011 mRNA. Translation: BAJ83966.1.
AB593012 mRNA. Translation: BAJ83967.1.
AB593013 mRNA. Translation: BAJ83968.1.
AC130343 Genomic DNA. No translation available.
AC130689 Genomic DNA. No translation available.
CH471108 Genomic DNA. Translation: EAW90577.1.
BC000522 mRNA. Translation: AAH00522.1.
BC013984 mRNA. Translation: AAH13984.1.
AH004879 Genomic DNA. Translation: AAB38685.1.
M90439 mRNA. Translation: AAA93524.1. Different initiation.
CCDSiCCDS11012.1.
PIRiA46046.
A47281.
RefSeqiNP_001316832.1. NM_001329903.1.
NP_002606.3. NM_002615.6.
UniGeneiHs.532768.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1IMVX-ray2.85A21-418[»]
ProteinModelPortaliP36955.
SMRiP36955.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi111202. 12 interactors.
IntActiP36955. 7 interactors.
MINTiMINT-7711036.
STRINGi9606.ENSP00000254722.

Protein family/group databases

MEROPSiI04.979.

PTM databases

iPTMnetiP36955.
PhosphoSitePlusiP36955.

Polymorphism and mutation databases

BioMutaiSERPINF1.
DMDMi313104314.

2D gel databases

REPRODUCTION-2DPAGEIPI00006114.

Proteomic databases

EPDiP36955.
MaxQBiP36955.
PaxDbiP36955.
PeptideAtlasiP36955.
PRIDEiP36955.

Protocols and materials databases

DNASUi5176.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000254722; ENSP00000254722; ENSG00000132386.
GeneIDi5176.
KEGGihsa:5176.
UCSCiuc002ftl.4. human.

Organism-specific databases

CTDi5176.
DisGeNETi5176.
GeneCardsiSERPINF1.
H-InvDBHIX0013408.
HGNCiHGNC:8824. SERPINF1.
HPAiCAB004785.
HPA005825.
MalaCardsiSERPINF1.
MIMi172860. gene.
613982. phenotype.
neXtProtiNX_P36955.
OpenTargetsiENSG00000132386.
Orphaneti216812. Osteogenesis imperfecta type 3.
PharmGKBiPA35508.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG2392. Eukaryota.
COG4826. LUCA.
GeneTreeiENSGT00850000132312.
HOGENOMiHOG000115489.
HOVERGENiHBG106911.
InParanoidiP36955.
KOiK19614.
OMAiLQDFHLD.
OrthoDBiEOG091G09UU.
PhylomeDBiP36955.
TreeFamiTF317350.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000132386-MONOMER.

Miscellaneous databases

ChiTaRSiSERPINF1. human.
EvolutionaryTraceiP36955.
GeneWikiiPEDF.
GenomeRNAii5176.
PROiP36955.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000132386.
CleanExiHS_SERPINF1.
ExpressionAtlasiP36955. baseline and differential.
GenevisibleiP36955. HS.

Family and domain databases

CDDicd02052. PEDF. 1 hit.
InterProiIPR033832. PEDF.
IPR023795. Serpin_CS.
IPR023796. Serpin_dom.
IPR000215. Serpin_fam.
[Graphical view]
PANTHERiPTHR11461. PTHR11461. 1 hit.
PfamiPF00079. Serpin. 1 hit.
[Graphical view]
SMARTiSM00093. SERPIN. 1 hit.
[Graphical view]
SUPFAMiSSF56574. SSF56574. 1 hit.
PROSITEiPS00284. SERPIN. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiPEDF_HUMAN
AccessioniPrimary (citable) accession number: P36955
Secondary accession number(s): F1T092
, Q13236, Q2TU83, Q96CT1, Q96R01, Q9BWA4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 1, 1994
Last sequence update: November 30, 2010
Last modified: November 30, 2016
This is version 175 of the entry and version 4 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

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Human chromosome 17
    Human chromosome 17: 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. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. 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.