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Protein

Vigilin

Gene

HDLBP

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

Functioni

Appears to play a role in cell sterol metabolism. It may function to protect cells from over-accumulation of cholesterol.

GO - Molecular functioni

  • cadherin binding involved in cell-cell adhesion Source: BHF-UCL
  • lipid binding Source: ProtInc
  • poly(A) RNA binding Source: UniProtKB

GO - Biological processi

  • cholesterol metabolic process Source: ProtInc
  • lipid transport Source: UniProtKB-KW
Complete GO annotation...

Keywords - Biological processi

Cholesterol metabolism, Lipid metabolism, Lipid transport, Steroid metabolism, Sterol metabolism, Transport

Keywords - Ligandi

RNA-binding

Enzyme and pathway databases

BioCyciZFISH:ENSG00000115677-MONOMER.
ReactomeiR-HSA-194223. HDL-mediated lipid transport.

Names & Taxonomyi

Protein namesi
Recommended name:
Vigilin
Alternative name(s):
High density lipoprotein-binding protein
Short name:
HDL-binding protein
Gene namesi
Name:HDLBP
Synonyms:HBP, VGL
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 2

Organism-specific databases

HGNCiHGNC:4857. HDLBP.

Subcellular locationi

GO - Cellular componenti

  • cell-cell adherens junction Source: BHF-UCL
  • cytoplasm Source: HPA
  • high-density lipoprotein particle Source: UniProtKB-KW
  • nucleus Source: UniProtKB-SubCell
  • plasma membrane Source: ProtInc
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, HDL, Nucleus

Pathology & Biotechi

Organism-specific databases

DisGeNETi3069.
PharmGKBiPA29235.

Polymorphism and mutation databases

BioMutaiHDLBP.
DMDMi218511884.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedCombined sources1 Publication
ChainiPRO_00000501312 – 1268VigilinAdd BLAST1267

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylserineCombined sources1 Publication1
Modified residuei8PhosphothreonineCombined sources1
Modified residuei11PhosphoserineCombined sources1
Modified residuei31PhosphoserineCombined sources1
Modified residuei35PhosphoserineBy similarity1
Modified residuei295PhosphothreonineSequence analysis1
Modified residuei296PhosphothreonineSequence analysis1
Modified residuei317PhosphoserineCombined sources1
Modified residuei437PhosphotyrosineCombined sources1
Modified residuei645PhosphoserineBy similarity1
Modified residuei991N6-acetyllysineBy similarity1
Modified residuei1247PhosphoserineCombined sources1
Modified residuei1252PhosphoserineCombined sources1

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

EPDiQ00341.
MaxQBiQ00341.
PaxDbiQ00341.
PeptideAtlasiQ00341.
PRIDEiQ00341.

PTM databases

iPTMnetiQ00341.
PhosphoSitePlusiQ00341.
SwissPalmiQ00341.

Expressioni

Gene expression databases

BgeeiENSG00000115677.
CleanExiHS_HDLBP.
ExpressionAtlasiQ00341. baseline and differential.
GenevisibleiQ00341. HS.

Organism-specific databases

HPAiCAB026457.
HPA004189.

Interactioni

Binary interactionsi

WithEntry#Exp.IntActNotes
CTCFP497114EBI-1049478,EBI-932887

GO - Molecular functioni

  • cadherin binding involved in cell-cell adhesion Source: BHF-UCL

Protein-protein interaction databases

BioGridi109319. 87 interactors.
IntActiQ00341. 30 interactors.
MINTiMINT-1189333.
STRINGi9606.ENSP00000312042.

Structurei

Secondary structure

11268
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi151 – 156Combined sources6
Turni159 – 161Combined sources3
Helixi162 – 166Combined sources5
Beta strandi168 – 170Combined sources3
Helixi172 – 179Combined sources8
Beta strandi195 – 200Combined sources6
Helixi202 – 220Combined sources19
Beta strandi365 – 370Combined sources6
Helixi376 – 380Combined sources5
Turni381 – 384Combined sources4
Helixi386 – 393Combined sources8
Beta strandi395 – 401Combined sources7
Beta strandi403 – 405Combined sources3
Beta strandi407 – 412Combined sources6
Helixi414 – 434Combined sources21
Beta strandi436 – 442Combined sources7
Helixi446 – 450Combined sources5
Turni452 – 454Combined sources3
Helixi457 – 464Combined sources8
Beta strandi468 – 470Combined sources3
Beta strandi476 – 487Combined sources12
Helixi488 – 499Combined sources12
Beta strandi656 – 659Combined sources4
Helixi662 – 669Combined sources8
Beta strandi671 – 673Combined sources3
Helixi674 – 683Combined sources10
Beta strandi687 – 689Combined sources3
Turni693 – 696Combined sources4
Beta strandi699 – 704Combined sources6
Helixi706 – 723Combined sources18
Beta strandi973 – 978Combined sources6
Helixi981 – 988Combined sources8
Beta strandi990 – 992Combined sources3
Helixi993 – 1001Combined sources9
Beta strandi1005 – 1007Combined sources3
Turni1011 – 1013Combined sources3
Beta strandi1017 – 1022Combined sources6
Helixi1024 – 1050Combined sources27
Beta strandi1054 – 1058Combined sources5
Turni1061 – 1063Combined sources3
Helixi1064 – 1067Combined sources4
Beta strandi1070 – 1072Combined sources3
Helixi1074 – 1082Combined sources9
Beta strandi1085 – 1087Combined sources3
Turni1091 – 1093Combined sources3
Beta strandi1098 – 1105Combined sources8
Helixi1107 – 1126Combined sources20
Beta strandi1130 – 1133Combined sources4
Turni1136 – 1138Combined sources3
Helixi1139 – 1143Combined sources5
Beta strandi1145 – 1147Combined sources3
Helixi1149 – 1157Combined sources9
Beta strandi1160 – 1162Combined sources3
Beta strandi1173 – 1178Combined sources6
Helixi1180 – 1198Combined sources19

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1VIGNMR-A432-502[»]
1VIHNMR-A432-502[»]
2CTENMR-A142-222[»]
2CTFNMR-A346-434[»]
2CTJNMR-A645-726[»]
2CTKNMR-A964-1054[»]
2CTLNMR-A1044-1127[»]
2CTMNMR-A1119-1200[»]
ProteinModelPortaliQ00341.
SMRiQ00341.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ00341.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini158 – 229KH 1PROSITE-ProRule annotationAdd BLAST72
Domaini230 – 302KH 2PROSITE-ProRule annotationAdd BLAST73
Domaini303 – 371KH 3PROSITE-ProRule annotationAdd BLAST69
Domaini372 – 442KH 4PROSITE-ProRule annotationAdd BLAST71
Domaini443 – 514KH 5PROSITE-ProRule annotationAdd BLAST72
Domaini515 – 588KH 6PROSITE-ProRule annotationAdd BLAST74
Domaini589 – 660KH 7PROSITE-ProRule annotationAdd BLAST72
Domaini661 – 734KH 8PROSITE-ProRule annotationAdd BLAST74
Domaini735 – 807KH 9PROSITE-ProRule annotationAdd BLAST73
Domaini808 – 880KH 10PROSITE-ProRule annotationAdd BLAST73
Domaini881 – 979KH 11PROSITE-ProRule annotationAdd BLAST99
Domaini980 – 1059KH 12PROSITE-ProRule annotationAdd BLAST80
Domaini1060 – 1134KH 13PROSITE-ProRule annotationAdd BLAST75
Domaini1135 – 1209KH 14PROSITE-ProRule annotationAdd BLAST75

Sequence similaritiesi

Contains 14 KH domains.PROSITE-ProRule annotation

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiKOG2208. Eukaryota.
ENOG410XQFV. LUCA.
HOGENOMiHOG000007687.
HOVERGENiHBG054107.
InParanoidiQ00341.
PhylomeDBiQ00341.
TreeFamiTF323767.

Family and domain databases

Gene3Di3.30.1370.10. 15 hits.
InterProiIPR004087. KH_dom.
IPR004088. KH_dom_type_1.
[Graphical view]
PfamiPF00013. KH_1. 14 hits.
[Graphical view]
SMARTiSM00322. KH. 14 hits.
[Graphical view]
SUPFAMiSSF54791. SSF54791. 13 hits.
PROSITEiPS50084. KH_TYPE_1. 14 hits.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

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

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q00341-1) [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
MSSVAVLTQE SFAEHRSGLV PQQIKVATLN SEEESDPPTY KDAFPPLPEK
60 70 80 90 100
AACLESAQEP SGAWGNKIRP IKASVITQVF HVPLEERKYK DMNQFGEGEQ
110 120 130 140 150
AKICLEIMQR TGAHLELSLA KDQGLSIMVS GKLDAVMKAR KDIVARLQTQ
160 170 180 190 200
ASATVAIPKE HHRFVIGKNG EKLQDLELKT ATKIQIPRPD DPSNQIKITG
210 220 230 240 250
TKEGIEKARH EVLLISAEQD KRAVERLEVE KAFHPFIAGP YNRLVGEIMQ
260 270 280 290 300
ETGTRINIPP PSVNRTEIVF TGEKEQLAQA VARIKKIYEE KKKKTTTIAV
310 320 330 340 350
EVKKSQHKYV IGPKGNSLQE ILERTGVSVE IPPSDSISET VILRGEPEKL
360 370 380 390 400
GQALTEVYAK ANSFTVSSVA APSWLHRFII GKKGQNLAKI TQQMPKVHIE
410 420 430 440 450
FTEGEDKITL EGPTEDVNVA QEQIEGMVKD LINRMDYVEI NIDHKFHRHL
460 470 480 490 500
IGKSGANINR IKDQYKVSVR IPPDSEKSNL IRIEGDPQGV QQAKRELLEL
510 520 530 540 550
ASRMENERTK DLIIEQRFHR TIIGQKGERI REIRDKFPEV IINFPDPAQK
560 570 580 590 600
SDIVQLRGPK NEVEKCTKYM QKMVADLVEN SYSISVPIFK QFHKNIIGKG
610 620 630 640 650
GANIKKIREE SNTKIDLPAE NSNSETIIIT GKRANCEAAR SRILSIQKDL
660 670 680 690 700
ANIAEVEVSI PAKLHNSLIG TKGRLIRSIM EECGGVHIHF PVEGSGSDTV
710 720 730 740 750
VIRGPSSDVE KAKKQLLHLA EEKQTKSFTV DIRAKPEYHK FLIGKGGGKI
760 770 780 790 800
RKVRDSTGAR VIFPAAEDKD QDLITIIGKE DAVREAQKEL EALIQNLDNV
810 820 830 840 850
VEDSMLVDPK HHRHFVIRRG QVLREIAEEY GGVMVSFPRS GTQSDKVTLK
860 870 880 890 900
GAKDCVEAAK KRIQEIIEDL EAQVTLECAI PQKFHRSVMG PKGSRIQQIT
910 920 930 940 950
RDFSVQIKFP DREENAVHST EPVVQENGDE AGEGREAKDC DPGSPRRCDI
960 970 980 990 1000
IIISGRKEKC EAAKEALEAL VPVTIEVEVP FDLHRYVIGQ KGSGIRKMMD
1010 1020 1030 1040 1050
EFEVNIHVPA PELQSDIIAI TGLAANLDRA KAGLLERVKE LQAEQEDRAL
1060 1070 1080 1090 1100
RSFKLSVTVD PKYHPKIIGR KGAVITQIRL EHDVNIQFPD KDDGNQPQDQ
1110 1120 1130 1140 1150
ITITGYEKNT EAARDAILRI VGELEQMVSE DVPLDHRVHA RIIGARGKAI
1160 1170 1180 1190 1200
RKIMDEFKVD IRFPQSGAPD PNCVTVTGLP ENVEEAIDHI LNLEEEYLAD
1210 1220 1230 1240 1250
VVDSEALQVY MKPPAHEEAK APSRGFVVRD APWTASSSEK APDMSSSEEF
1260
PSFGAQVAPK TLPWGPKR
Length:1,268
Mass (Da):141,456
Last modified:December 16, 2008 - v2
Checksum:i530C61A3CA9239CD
GO
Isoform 2 (identifier: Q00341-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-1: M → MHLAERDRWLFVATVMMHFVSIKSGFPGLCVGVRSTM
     291-359: Missing.

Note: No experimental confirmation available.
Show »
Length:1,235
Mass (Da):137,987
Checksum:i9A49873E7937B9D4
GO

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_04797661S → A.Combined sources3 PublicationsCorresponds to variant rs11891776dbSNPEnsembl.1
Natural variantiVAR_055981229V → I.Corresponds to variant rs7572799dbSNPEnsembl.1
Natural variantiVAR_024511418N → S.Corresponds to variant rs7578199dbSNPEnsembl.1
Natural variantiVAR_036052568K → N in a breast cancer sample; somatic mutation. 1 Publication1
Natural variantiVAR_036053939D → V in a breast cancer sample; somatic mutation. 1 Publication1
Natural variantiVAR_0292791264W → L.Corresponds to variant rs12281dbSNPEnsembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0449241M → MHLAERDRWLFVATVMMHFV SIKSGFPGLCVGVRSTM in isoform 2. 1 Publication1
Alternative sequenceiVSP_044925291 – 359Missing in isoform 2. 1 PublicationAdd BLAST69

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M64098 mRNA. Translation: AAA35962.1.
AK300312 mRNA. Translation: BAG62064.1.
AC104841 Genomic DNA. Translation: AAY14717.1.
BC001179 mRNA. Translation: AAH01179.1.
CCDSiCCDS2547.1. [Q00341-1]
CCDS58760.1. [Q00341-2]
PIRiA44125.
RefSeqiNP_001230829.1. NM_001243900.2.
NP_001307894.1. NM_001320965.1.
NP_001307895.1. NM_001320966.1.
NP_005327.1. NM_005336.5.
NP_976221.1. NM_203346.4.
XP_005247059.2. XM_005247002.3.
XP_005247060.2. XM_005247003.4.
XP_006712538.1. XM_006712475.3.
XP_011509360.1. XM_011511058.2.
XP_011509362.1. XM_011511060.2.
XP_016859429.1. XM_017003940.1.
UniGeneiHs.471851.
Hs.732361.

Genome annotation databases

EnsembliENST00000427183; ENSP00000399139; ENSG00000115677.
GeneIDi3069.
KEGGihsa:3069.
UCSCiuc021vzg.1. human. [Q00341-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M64098 mRNA. Translation: AAA35962.1.
AK300312 mRNA. Translation: BAG62064.1.
AC104841 Genomic DNA. Translation: AAY14717.1.
BC001179 mRNA. Translation: AAH01179.1.
CCDSiCCDS2547.1. [Q00341-1]
CCDS58760.1. [Q00341-2]
PIRiA44125.
RefSeqiNP_001230829.1. NM_001243900.2.
NP_001307894.1. NM_001320965.1.
NP_001307895.1. NM_001320966.1.
NP_005327.1. NM_005336.5.
NP_976221.1. NM_203346.4.
XP_005247059.2. XM_005247002.3.
XP_005247060.2. XM_005247003.4.
XP_006712538.1. XM_006712475.3.
XP_011509360.1. XM_011511058.2.
XP_011509362.1. XM_011511060.2.
XP_016859429.1. XM_017003940.1.
UniGeneiHs.471851.
Hs.732361.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1VIGNMR-A432-502[»]
1VIHNMR-A432-502[»]
2CTENMR-A142-222[»]
2CTFNMR-A346-434[»]
2CTJNMR-A645-726[»]
2CTKNMR-A964-1054[»]
2CTLNMR-A1044-1127[»]
2CTMNMR-A1119-1200[»]
ProteinModelPortaliQ00341.
SMRiQ00341.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi109319. 87 interactors.
IntActiQ00341. 30 interactors.
MINTiMINT-1189333.
STRINGi9606.ENSP00000312042.

PTM databases

iPTMnetiQ00341.
PhosphoSitePlusiQ00341.
SwissPalmiQ00341.

Polymorphism and mutation databases

BioMutaiHDLBP.
DMDMi218511884.

Proteomic databases

EPDiQ00341.
MaxQBiQ00341.
PaxDbiQ00341.
PeptideAtlasiQ00341.
PRIDEiQ00341.

Protocols and materials databases

DNASUi3069.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000427183; ENSP00000399139; ENSG00000115677.
GeneIDi3069.
KEGGihsa:3069.
UCSCiuc021vzg.1. human. [Q00341-1]

Organism-specific databases

CTDi3069.
DisGeNETi3069.
GeneCardsiHDLBP.
HGNCiHGNC:4857. HDLBP.
HPAiCAB026457.
HPA004189.
MIMi142695. gene.
neXtProtiNX_Q00341.
PharmGKBiPA29235.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG2208. Eukaryota.
ENOG410XQFV. LUCA.
HOGENOMiHOG000007687.
HOVERGENiHBG054107.
InParanoidiQ00341.
PhylomeDBiQ00341.
TreeFamiTF323767.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000115677-MONOMER.
ReactomeiR-HSA-194223. HDL-mediated lipid transport.

Miscellaneous databases

ChiTaRSiHDLBP. human.
EvolutionaryTraceiQ00341.
GeneWikiiHDLBP.
GenomeRNAii3069.
PROiQ00341.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000115677.
CleanExiHS_HDLBP.
ExpressionAtlasiQ00341. baseline and differential.
GenevisibleiQ00341. HS.

Family and domain databases

Gene3Di3.30.1370.10. 15 hits.
InterProiIPR004087. KH_dom.
IPR004088. KH_dom_type_1.
[Graphical view]
PfamiPF00013. KH_1. 14 hits.
[Graphical view]
SMARTiSM00322. KH. 14 hits.
[Graphical view]
SUPFAMiSSF54791. SSF54791. 13 hits.
PROSITEiPS50084. KH_TYPE_1. 14 hits.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiVIGLN_HUMAN
AccessioniPrimary (citable) accession number: Q00341
Secondary accession number(s): B4DTQ2
, E7EM71, Q53QU2, Q9UCY3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: December 16, 2008
Last modified: November 30, 2016
This is version 168 of the entry and version 2 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 2
    Human chromosome 2: 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.