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Protein

Zinc finger BED domain-containing protein 1

Gene

ZBED1

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

Functioni

Binds to 5'-TGTCG[CT]GA[CT]A-3' DNA elements found in the promoter regions of a number of genes related to cell proliferation. Binds to the histone H1 promoter and stimulates transcription. Was first identified as gene weakly similar to Ac transposable elements, but does not code for any transposase activity.1 Publication

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri20 – 7859BED-typePROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

  • DNA binding Source: UniProtKB-KW
  • metal ion binding Source: UniProtKB-KW
  • transposase activity Source: ProtInc

GO - Biological processi

  • metabolic process Source: GOC
Complete GO annotation...

Keywords - Ligandi

DNA-binding, Metal-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
Zinc finger BED domain-containing protein 1
Alternative name(s):
Putative Ac-like transposable element
dREF homolog
Gene namesi
Name:ZBED1
Synonyms:ALTE, DREF, KIAA0785, TRAMP
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640 Componenti: Chromosome X

Organism-specific databases

HGNCiHGNC:447. ZBED1.

Subcellular locationi

  • Nucleus 1 Publication

  • Note: In granular structures.

GO - Cellular componenti

  • nuclear chromosome Source: ProtInc
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA24753.

Polymorphism and mutation databases

BioMutaiZBED1.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 694694Zinc finger BED domain-containing protein 1PRO_0000066560Add
BLAST

Proteomic databases

MaxQBiO96006.
PaxDbiO96006.
PRIDEiO96006.

PTM databases

PhosphoSiteiO96006.

Expressioni

Tissue specificityi

Ubiquitously expressed at low levels. Expression is highest in skeletal muscle, heart, spleen and placenta.

Inductioni

Expression is linked to the cell cycle: low in serum-starved fibroblasts, increasing during the G1/S phase, highest during the S/G2 phase and then decreasing again.1 Publication

Gene expression databases

BgeeiO96006.
ExpressionAtlasiO96006. baseline and differential.
GenevisibleiO96006. HS.

Interactioni

Subunit structurei

Homodimer.Curated

Binary interactionsi

WithEntry#Exp.IntActNotes
A8K5H93EBI-740037,EBI-10174421
AMOTL2Q9Y2J4-43EBI-740037,EBI-10187270
C1orf109Q9NX044EBI-740037,EBI-8643161
LRRC20Q8TCA03EBI-740037,EBI-10274039
PIAS2O759283EBI-740037,EBI-348555
PRKAA1Q131313EBI-740037,EBI-1181405
SSX2BQ163853EBI-740037,EBI-2210673
UBE2IQ7KZS03EBI-740037,EBI-10180829
UCHL5Q9Y5K53EBI-740037,EBI-1051183

Protein-protein interaction databases

BioGridi114626. 35 interactions.
IntActiO96006. 26 interactions.
MINTiMINT-1436617.
STRINGi9606.ENSP00000370616.

Structurei

Secondary structure

1
694
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi27 – 293Combined sources
Beta strandi35 – 373Combined sources
Helixi39 – 413Combined sources
Turni48 – 514Combined sources
Helixi61 – 699Combined sources
Helixi72 – 787Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2CT5NMR-A23-82[»]
ProteinModelPortaliO96006.
SMRiO96006. Positions 24-83, 164-647.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO96006.

Family & Domainsi

Sequence similaritiesi

Contains 1 BED-type zinc finger.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri20 – 7859BED-typePROSITE-ProRule annotationAdd
BLAST

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiNOG317219.
GeneTreeiENSGT00530000063354.
HOGENOMiHOG000155760.
HOVERGENiHBG079365.
InParanoidiO96006.
OMAiLAEATWC.
OrthoDBiEOG7KM5S5.
PhylomeDBiO96006.
TreeFamiTF322818.

Family and domain databases

InterProiIPR008906. HATC_dom_C.
IPR012337. RNaseH-like_dom.
IPR003656. Znf_BED.
[Graphical view]
PfamiPF05699. Dimer_Tnp_hAT. 1 hit.
PF02892. zf-BED. 1 hit.
[Graphical view]
SMARTiSM00614. ZnF_BED. 1 hit.
[Graphical view]
SUPFAMiSSF53098. SSF53098. 1 hit.
PROSITEiPS50808. ZF_BED. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

O96006-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MENKSLESSQ TDLKLVAHPR AKSKVWKYFG FDTNAEGCIL QWKKIYCRIC
60 70 80 90 100
MAQIAYSGNT SNLSYHLEKN HPEEFCEFVK SNTEQMREAF ATAFSKLKPE
110 120 130 140 150
SSQQPGQDAL AVKAGHGYDS KKQQELTAAV LGLICEGLYP ASIVDEPTFK
160 170 180 190 200
VLLKTADPRY ELPSRKYIST KAIPEKYGAV REVILKELAE ATWCGISTDM
210 220 230 240 250
WRSENQNRAY VTLAAHFLGL GAPNCLSMGS RCLKTFEVPE ENTAETITRV
260 270 280 290 300
LYEVFIEWGI SAKVFGATTN YGKDIVKACS LLDVAVHMPC LGHTFNAGIQ
310 320 330 340 350
QAFQLPKLGA LLSRCRKLVE YFQQSAVAMY MLYEKQKQQN VAHCMLVSNR
360 370 380 390 400
VSWWGSTLAM LQRLKEQQFV IAGVLVEDSN NHHLMLEASE WATIEGLVEL
410 420 430 440 450
LQPFKQVAEM LSASRYPTIS MVKPLLHMLL NTTLNIKETD SKELSMAKEV
460 470 480 490 500
IAKELSKTYQ ETPEIDMFLN VATFLDPRYK RLPFLSAFER QQVENRVVEE
510 520 530 540 550
AKGLLDKVKD GGYRPAEDKI FPVPEEPPVK KLMRTSTPPP ASVINNMLAE
560 570 580 590 600
IFCQTGGVED QEEWHAQVVE ELSNFKSQKV LGLNEDPLKW WSDRLALFPL
610 620 630 640 650
LPKVLQKYWC VTATRVAPER LFGSAANVVS AKRNRLAPAH VDEQVFLYEN
660 670 680 690
ARSGAEAEPE DQDEGEWGLD QEQVFSLGDG VSGGFFGIRD SSFL
Length:694
Mass (Da):78,156
Last modified:May 1, 1999 - v1
Checksum:i40404497B17283AF
GO

Sequence cautioni

The sequence BAA34505.2 differs from that shown. Reason: Erroneous initiation. Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti295 – 2951F → L in AAH15030 (PubMed:15489334).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Y16947 mRNA. Translation: CAA76545.1.
Y17156 Genomic DNA. Translation: CAA76660.1.
AB018328 mRNA. Translation: BAA34505.2. Different initiation.
AC079176 Genomic DNA. No translation available.
BC015030 mRNA. Translation: AAH15030.1.
CCDSiCCDS14118.1.
RefSeqiNP_001164606.1. NM_001171135.1.
NP_001164607.1. NM_001171136.1.
NP_004720.1. NM_004729.3.
UniGeneiHs.131452.

Genome annotation databases

EnsembliENST00000381218; ENSP00000370616; ENSG00000214717.
ENST00000381222; ENSP00000370620; ENSG00000214717.
ENST00000381223; ENSP00000370621; ENSG00000214717.
GeneIDi9189.
KEGGihsa:9189.
UCSCiuc004cqg.2. human.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Y16947 mRNA. Translation: CAA76545.1.
Y17156 Genomic DNA. Translation: CAA76660.1.
AB018328 mRNA. Translation: BAA34505.2. Different initiation.
AC079176 Genomic DNA. No translation available.
BC015030 mRNA. Translation: AAH15030.1.
CCDSiCCDS14118.1.
RefSeqiNP_001164606.1. NM_001171135.1.
NP_001164607.1. NM_001171136.1.
NP_004720.1. NM_004729.3.
UniGeneiHs.131452.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2CT5NMR-A23-82[»]
ProteinModelPortaliO96006.
SMRiO96006. Positions 24-83, 164-647.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi114626. 35 interactions.
IntActiO96006. 26 interactions.
MINTiMINT-1436617.
STRINGi9606.ENSP00000370616.

PTM databases

PhosphoSiteiO96006.

Polymorphism and mutation databases

BioMutaiZBED1.

Proteomic databases

MaxQBiO96006.
PaxDbiO96006.
PRIDEiO96006.

Protocols and materials databases

DNASUi9189.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000381218; ENSP00000370616; ENSG00000214717.
ENST00000381222; ENSP00000370620; ENSG00000214717.
ENST00000381223; ENSP00000370621; ENSG00000214717.
GeneIDi9189.
KEGGihsa:9189.
UCSCiuc004cqg.2. human.

Organism-specific databases

CTDi9189.
GeneCardsiGC0XM002320.
HGNCiHGNC:447. ZBED1.
MIMi300178. gene.
neXtProtiNX_O96006.
PharmGKBiPA24753.
HUGEiSearch...
GenAtlasiSearch...

Phylogenomic databases

eggNOGiNOG317219.
GeneTreeiENSGT00530000063354.
HOGENOMiHOG000155760.
HOVERGENiHBG079365.
InParanoidiO96006.
OMAiLAEATWC.
OrthoDBiEOG7KM5S5.
PhylomeDBiO96006.
TreeFamiTF322818.

Miscellaneous databases

EvolutionaryTraceiO96006.
GeneWikiiZBED1.
GenomeRNAii9189.
NextBioi34457.
PROiO96006.
SOURCEiSearch...

Gene expression databases

BgeeiO96006.
ExpressionAtlasiO96006. baseline and differential.
GenevisibleiO96006. HS.

Family and domain databases

InterProiIPR008906. HATC_dom_C.
IPR012337. RNaseH-like_dom.
IPR003656. Znf_BED.
[Graphical view]
PfamiPF05699. Dimer_Tnp_hAT. 1 hit.
PF02892. zf-BED. 1 hit.
[Graphical view]
SMARTiSM00614. ZnF_BED. 1 hit.
[Graphical view]
SUPFAMiSSF53098. SSF53098. 1 hit.
PROSITEiPS50808. ZF_BED. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "A novel pseudoautosomal human gene encodes a putative protein similar to Ac-like transposases."
    Esposito T., Gianfrancesco F., Ciccodicola A., Montanini L., Mumm S., D'Urso M., Forabosco A.
    Hum. Mol. Genet. 8:61-67(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA].
    Tissue: Teratocarcinoma.
  2. "Prediction of the coding sequences of unidentified human genes. XI. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro."
    Nagase T., Ishikawa K., Suyama M., Kikuno R., Miyajima N., Tanaka A., Kotani H., Nomura N., Ohara O.
    DNA Res. 5:277-286(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Brain.
  3. "The DNA sequence of the human X chromosome."
    Ross M.T., Grafham D.V., Coffey A.J., Scherer S., McLay K., Muzny D., Platzer M., Howell G.R., Burrows C., Bird C.P., Frankish A., Lovell F.L., Howe K.L., Ashurst J.L., Fulton R.S., Sudbrak R., Wen G., Jones M.C.
    , Hurles M.E., Andrews T.D., Scott C.E., Searle S., Ramser J., Whittaker A., Deadman R., Carter N.P., Hunt S.E., Chen R., Cree A., Gunaratne P., Havlak P., Hodgson A., Metzker M.L., Richards S., Scott G., Steffen D., Sodergren E., Wheeler D.A., Worley K.C., Ainscough R., Ambrose K.D., Ansari-Lari M.A., Aradhya S., Ashwell R.I., Babbage A.K., Bagguley C.L., Ballabio A., Banerjee R., Barker G.E., Barlow K.F., Barrett I.P., Bates K.N., Beare D.M., Beasley H., Beasley O., Beck A., Bethel G., Blechschmidt K., Brady N., Bray-Allen S., Bridgeman A.M., Brown A.J., Brown M.J., Bonnin D., Bruford E.A., Buhay C., Burch P., Burford D., Burgess J., Burrill W., Burton J., Bye J.M., Carder C., Carrel L., Chako J., Chapman J.C., Chavez D., Chen E., Chen G., Chen Y., Chen Z., Chinault C., Ciccodicola A., Clark S.Y., Clarke G., Clee C.M., Clegg S., Clerc-Blankenburg K., Clifford K., Cobley V., Cole C.G., Conquer J.S., Corby N., Connor R.E., David R., Davies J., Davis C., Davis J., Delgado O., Deshazo D., Dhami P., Ding Y., Dinh H., Dodsworth S., Draper H., Dugan-Rocha S., Dunham A., Dunn M., Durbin K.J., Dutta I., Eades T., Ellwood M., Emery-Cohen A., Errington H., Evans K.L., Faulkner L., Francis F., Frankland J., Fraser A.E., Galgoczy P., Gilbert J., Gill R., Gloeckner G., Gregory S.G., Gribble S., Griffiths C., Grocock R., Gu Y., Gwilliam R., Hamilton C., Hart E.A., Hawes A., Heath P.D., Heitmann K., Hennig S., Hernandez J., Hinzmann B., Ho S., Hoffs M., Howden P.J., Huckle E.J., Hume J., Hunt P.J., Hunt A.R., Isherwood J., Jacob L., Johnson D., Jones S., de Jong P.J., Joseph S.S., Keenan S., Kelly S., Kershaw J.K., Khan Z., Kioschis P., Klages S., Knights A.J., Kosiura A., Kovar-Smith C., Laird G.K., Langford C., Lawlor S., Leversha M., Lewis L., Liu W., Lloyd C., Lloyd D.M., Loulseged H., Loveland J.E., Lovell J.D., Lozado R., Lu J., Lyne R., Ma J., Maheshwari M., Matthews L.H., McDowall J., McLaren S., McMurray A., Meidl P., Meitinger T., Milne S., Miner G., Mistry S.L., Morgan M., Morris S., Mueller I., Mullikin J.C., Nguyen N., Nordsiek G., Nyakatura G., O'dell C.N., Okwuonu G., Palmer S., Pandian R., Parker D., Parrish J., Pasternak S., Patel D., Pearce A.V., Pearson D.M., Pelan S.E., Perez L., Porter K.M., Ramsey Y., Reichwald K., Rhodes S., Ridler K.A., Schlessinger D., Schueler M.G., Sehra H.K., Shaw-Smith C., Shen H., Sheridan E.M., Shownkeen R., Skuce C.D., Smith M.L., Sotheran E.C., Steingruber H.E., Steward C.A., Storey R., Swann R.M., Swarbreck D., Tabor P.E., Taudien S., Taylor T., Teague B., Thomas K., Thorpe A., Timms K., Tracey A., Trevanion S., Tromans A.C., d'Urso M., Verduzco D., Villasana D., Waldron L., Wall M., Wang Q., Warren J., Warry G.L., Wei X., West A., Whitehead S.L., Whiteley M.N., Wilkinson J.E., Willey D.L., Williams G., Williams L., Williamson A., Williamson H., Wilming L., Woodmansey R.L., Wray P.W., Yen J., Zhang J., Zhou J., Zoghbi H., Zorilla S., Buck D., Reinhardt R., Poustka A., Rosenthal A., Lehrach H., Meindl A., Minx P.J., Hillier L.W., Willard H.F., Wilson R.K., Waterston R.H., Rice C.M., Vaudin M., Coulson A., Nelson D.L., Weinstock G., Sulston J.E., Durbin R.M., Hubbard T., Gibbs R.A., Beck S., Rogers J., Bentley D.R.
    Nature 434:325-337(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  4. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Uterus.
  5. "Identification of a human homologue of the DREF transcription factor with a potential role in regulation of the histone H1 gene."
    Ohshima N., Takahashi M., Hirose F.
    J. Biol. Chem. 278:22928-22938(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INDUCTION, SUBCELLULAR LOCATION.
  6. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  7. "An enzyme assisted RP-RPLC approach for in-depth analysis of human liver phosphoproteome."
    Bian Y., Song C., Cheng K., Dong M., Wang F., Huang J., Sun D., Wang L., Ye M., Zou H.
    J. Proteomics 96:253-262(2014) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Liver.
  8. "Solution structure of the zinc finger BED domain of the zinc finger BED domain containing protein 1."
    RIKEN structural genomics initiative (RSGI)
    Submitted (NOV-2005) to the PDB data bank
    Cited for: STRUCTURE BY NMR OF 23-82.

Entry informationi

Entry nameiZBED1_HUMAN
AccessioniPrimary (citable) accession number: O96006
Secondary accession number(s): Q96BY4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 16, 2004
Last sequence update: May 1, 1999
Last modified: June 24, 2015
This is version 122 of the entry and version 1 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

Miscellaneous

The gene coding for this protein is located in the pseudoautosomal region 1 (PAR1) of X and Y chromosomes.

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome X
    Human chromosome X: entries, gene names and cross-references to MIM
  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. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.