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Protein

Zinc finger MYND domain-containing protein 11

Gene

Zmynd11

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Chromatin reader that specifically recognizes and binds histone H3.3 trimethylated at 'Lys-36' (H3.3K36me3) and regulates RNA polymerase II elongation. Does not bind other histone H3 subtypes (H3.1 or H3.2). Colocalizes with highly expressed genes and functions as a transcription corepressor by modulating RNA polymerase II at the elongation stage. Acts as a tumor-suppressor by repressing a transcriptional program essential for tumor cell growth.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi258 – 2581Zinc
Metal bindingi261 – 2611Zinc
Metal bindingi277 – 2771Zinc
Metal bindingi281 – 2811Zinc; via tele nitrogen

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri100 – 14849PHD-typePROSITE-ProRule annotationAdd
BLAST
Zinc fingeri563 – 59836MYND-typePROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

  • chromatin binding Source: GO_Central
  • histone binding Source: UniProtKB
  • methylated histone binding Source: UniProtKB
  • RNA polymerase II regulatory region sequence-specific DNA binding Source: GO_Central
  • transcription corepressor activity Source: UniProtKB
  • zinc ion binding Source: UniProtKB

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Chromatin regulator, Repressor

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding, Metal-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
Zinc finger MYND domain-containing protein 11
Gene namesi
Name:Zmynd11
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 13

Organism-specific databases

MGIiMGI:1913755. Zmynd11.

Subcellular locationi

  • Nucleus By similarity
  • Chromosome By similarity

  • Note: Associates with chromatin and mitotic chromosomes.By similarity

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Chromosome, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi168 – 1681R → A: Impaired H3.3K36me3 binding. 1 Publication
Mutagenesisi234 – 2363DSE → ASA: No effect on protein folding and histone binding. 1 Publication
Mutagenesisi251 – 2511E → A: Impaired H3.3K36me3 binding. 1 Publication
Mutagenesisi266 – 2661N → A: Impaired H3.3K36me3 binding. 1 Publication
Mutagenesisi291 – 2911F → A: Abolished H3.3K36me3 binding. 1 Publication
Mutagenesisi294 – 2941W → A: Abolished H3.3K36me3 binding. 1 Publication
Mutagenesisi307 – 3071D → A: Impaired H3.3K36me3 binding. 1 Publication
Mutagenesisi310 – 3101F → A: Abolished H3.3K36me3 binding. 1 Publication

Keywords - Diseasei

Tumor suppressor

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 602602Zinc finger MYND domain-containing protein 11PRO_0000211219Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Cross-linki407 – 407Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)By similarity
Modified residuei421 – 4211PhosphoserineBy similarity

Post-translational modificationi

Ubiquitinated, leading to proteasomal degradation.By similarity
Sumoylated following its interaction with PIAS1 and UBE2I.By similarity

Keywords - PTMi

Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiQ8R5C8.
MaxQBiQ8R5C8.
PaxDbiQ8R5C8.
PeptideAtlasiQ8R5C8.
PRIDEiQ8R5C8.

PTM databases

iPTMnetiQ8R5C8.
PhosphoSiteiQ8R5C8.

Expressioni

Gene expression databases

CleanExiMM_ZMYND11.
ExpressionAtlasiQ8R5C8. baseline and differential.
GenevisibleiQ8R5C8. MM.

Interactioni

Subunit structurei

Homooligomer; forms homooligomers via its C-terminus. Interacts with histone H3.3 trimethylated at 'Lys-36' (H3.3K36me3). Interacts (via MYND-type zinc finger) with NCOR1. Interacts (via MYND-type zinc finger) with MGA protein (via PXLXP motif). Interacts (via MYND-type zinc finger) with EZH2. Interacts with EMSY and E2F6. Interacts with PIAS1 and UBE2I (By similarity).By similarity

GO - Molecular functioni

  • histone binding Source: UniProtKB
  • methylated histone binding Source: UniProtKB

Protein-protein interaction databases

BioGridi211523. 1 interaction.
DIPiDIP-49596N.
IntActiQ8R5C8. 2 interactions.
MINTiMINT-4140623.
STRINGi10090.ENSMUSP00000106264.

Structurei

Secondary structure

1
602
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi155 – 17117Combined sources
Helixi173 – 1753Combined sources
Helixi188 – 1914Combined sources
Helixi198 – 2069Combined sources
Helixi213 – 23119Combined sources
Helixi236 – 25722Combined sources
Helixi259 – 2679Combined sources
Helixi272 – 2743Combined sources
Beta strandi283 – 2875Combined sources
Turni289 – 2913Combined sources
Beta strandi293 – 30210Combined sources
Beta strandi305 – 3128Combined sources
Helixi313 – 3153Combined sources
Beta strandi317 – 3215Combined sources
Helixi322 – 3243Combined sources
Beta strandi325 – 3273Combined sources
Turni332 – 3343Combined sources
Helixi341 – 35919Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4N4GX-ray1.95A154-371[»]
4N4HX-ray2.30A154-371[»]
4N4IX-ray2.00A154-371[»]
ProteinModelPortaliQ8R5C8.
SMRiQ8R5C8. Positions 99-366.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini168 – 23871BromoPROSITE-ProRule annotationAdd
BLAST
Domaini280 – 33152PWWPPROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni291 – 31020Aromatic cage required for H3.3K36me3-specific bindingAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi394 – 4007Nuclear localization signalSequence analysis

Domaini

The PWWP domain specifically recognizes and binds histone H3.3 trimethylated at 'Lys-36' (H3.3K36me3) and adopts a five-bladed beta-barrel fold with an extended C-terminal alpha-helix, with a conserved H3.3K36me3-binding aromatic cage formed by Phe-291 and Trp-294 of the beta1-beta2 loop and Phe-310 of the beta3-beta4 loop. Specific recognition of H3.3 histone is mediated by the encapsulation of the H3.3-specific 'Ser 31' residue in a composite pocket formed by the tandem bromo-PWWP domains (PubMed:24590075).1 Publication

Sequence similaritiesi

Contains 1 bromo domain.PROSITE-ProRule annotation
Contains 1 MYND-type zinc finger.PROSITE-ProRule annotation
Contains 1 PHD-type zinc finger.PROSITE-ProRule annotation
Contains 1 PWWP domain.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri100 – 14849PHD-typePROSITE-ProRule annotationAdd
BLAST
Zinc fingeri563 – 59836MYND-typePROSITE-ProRule annotationAdd
BLAST

Keywords - Domaini

Bromodomain, Zinc-finger

Phylogenomic databases

eggNOGiKOG3612. Eukaryota.
ENOG410XTCC. LUCA.
GeneTreeiENSGT00530000063428.
HOGENOMiHOG000038026.
HOVERGENiHBG054949.
InParanoidiQ8R5C8.
OrthoDBiEOG700875.

Family and domain databases

Gene3Di1.20.920.10. 1 hit.
3.30.40.10. 1 hit.
InterProiIPR001487. Bromodomain.
IPR000313. PWWP_dom.
IPR019786. Zinc_finger_PHD-type_CS.
IPR011011. Znf_FYVE_PHD.
IPR002893. Znf_MYND.
IPR001965. Znf_PHD.
IPR019787. Znf_PHD-finger.
IPR013083. Znf_RING/FYVE/PHD.
[Graphical view]
PfamiPF00439. Bromodomain. 1 hit.
PF00855. PWWP. 1 hit.
[Graphical view]
SMARTiSM00297. BROMO. 1 hit.
SM00249. PHD. 1 hit.
SM00293. PWWP. 1 hit.
[Graphical view]
SUPFAMiSSF47370. SSF47370. 1 hit.
SSF57903. SSF57903. 1 hit.
PROSITEiPS50014. BROMODOMAIN_2. 1 hit.
PS50812. PWWP. 1 hit.
PS01360. ZF_MYND_1. 1 hit.
PS50865. ZF_MYND_2. 1 hit.
PS01359. ZF_PHD_1. 1 hit.
PS50016. ZF_PHD_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q8R5C8-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MARLTKRRQA DTKAIQHLWA AIEIIRNQKQ IANIDRITKY MSRVHGMHPK
60 70 80 90 100
ETTRQLSLAV KDGLIVETLT VGCKGSKAGI EQEGYWLPGD EIDWETETHD
110 120 130 140 150
WYCFECHLPG EVLICDLCFR VYHSKCLSDE FRLRDSSSHW QCPVCRSIKK
160 170 180 190 200
KHSNKQEMGT YLRFIVSRMK ERAIDLNKKG KDSKHPMYRR LVHSAVDVPT
210 220 230 240 250
IQEKVNEGKY RSYEEFKADA QLLLHNTVIF YGADSEQADI ARMLYKDTCH
260 270 280 290 300
ELDELQLCKN CFYLSNARPD NWFCYPCIPN HELVWAKMKG FGFWPAKVMQ
310 320 330 340 350
KEDNQVDVRF FGHHHQRAWI PSENIQDITV NVHRLHVKRS MGWKKACDEL
360 370 380 390 400
ELHQRFLREG RFWKSKNEDR GEEEAESSIS STSNEQLKVT QEPRAKKGRR
410 420 430 440 450
NQSVEPKKEE PEPETEAVSS SQEIPTMPQP IERVSVSTQT KKLSASSPRM
460 470 480 490 500
LHRSTQTTSD GVCQSMCHDK YTKIFNDFKD RMKSDHKRET ERVVREALEK
510 520 530 540 550
LRSEMEEEKR QAVNKAVASL QGDMDRKGKQ LKEKCKEEFV EEIKKLAAQH
560 570 580 590 600
KQLISQTKKK QWCYNCEEEA MYHCCWNTSY CSIKCQQEHW HAEHKRTCRR

KR
Length:602
Mass (Da):70,838
Last modified:November 28, 2012 - v2
Checksum:i963A9EF2ABBCD3C2
GO

Sequence cautioni

The sequence AAH22945.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti371 – 3711G → S in BAC26199 (PubMed:16141072).Curated
Sequence conflicti519 – 5191S → N in AAH22945 (PubMed:15489334).Curated
Sequence conflicti523 – 5231D → E in AAH22945 (PubMed:15489334).Curated
Sequence conflicti528 – 5281G → C in AAH22945 (PubMed:15489334).Curated
Sequence conflicti531 – 5311L → V in AAH22945 (PubMed:15489334).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AC146596 Genomic DNA. No translation available.
AC153144 Genomic DNA. No translation available.
CH466588 Genomic DNA. Translation: EDL32291.1.
CH466588 Genomic DNA. Translation: EDL32294.1.
BC022945 mRNA. Translation: AAH22945.1. Different initiation.
AK028931 mRNA. Translation: BAC26199.1.
CCDSiCCDS56870.1.
RefSeqiNP_001186070.1. NM_001199141.1.
XP_006516569.1. XM_006516506.2.
UniGeneiMm.397307.

Genome annotation databases

EnsembliENSMUST00000110634; ENSMUSP00000106264; ENSMUSG00000021156.
ENSMUST00000110636; ENSMUSP00000106266; ENSMUSG00000021156.
GeneIDi66505.
KEGGimmu:66505.
UCSCiuc007pkx.1. mouse.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AC146596 Genomic DNA. No translation available.
AC153144 Genomic DNA. No translation available.
CH466588 Genomic DNA. Translation: EDL32291.1.
CH466588 Genomic DNA. Translation: EDL32294.1.
BC022945 mRNA. Translation: AAH22945.1. Different initiation.
AK028931 mRNA. Translation: BAC26199.1.
CCDSiCCDS56870.1.
RefSeqiNP_001186070.1. NM_001199141.1.
XP_006516569.1. XM_006516506.2.
UniGeneiMm.397307.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4N4GX-ray1.95A154-371[»]
4N4HX-ray2.30A154-371[»]
4N4IX-ray2.00A154-371[»]
ProteinModelPortaliQ8R5C8.
SMRiQ8R5C8. Positions 99-366.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi211523. 1 interaction.
DIPiDIP-49596N.
IntActiQ8R5C8. 2 interactions.
MINTiMINT-4140623.
STRINGi10090.ENSMUSP00000106264.

PTM databases

iPTMnetiQ8R5C8.
PhosphoSiteiQ8R5C8.

Proteomic databases

EPDiQ8R5C8.
MaxQBiQ8R5C8.
PaxDbiQ8R5C8.
PeptideAtlasiQ8R5C8.
PRIDEiQ8R5C8.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000110634; ENSMUSP00000106264; ENSMUSG00000021156.
ENSMUST00000110636; ENSMUSP00000106266; ENSMUSG00000021156.
GeneIDi66505.
KEGGimmu:66505.
UCSCiuc007pkx.1. mouse.

Organism-specific databases

CTDi10771.
MGIiMGI:1913755. Zmynd11.

Phylogenomic databases

eggNOGiKOG3612. Eukaryota.
ENOG410XTCC. LUCA.
GeneTreeiENSGT00530000063428.
HOGENOMiHOG000038026.
HOVERGENiHBG054949.
InParanoidiQ8R5C8.
OrthoDBiEOG700875.

Miscellaneous databases

ChiTaRSiZmynd11. mouse.
PROiQ8R5C8.
SOURCEiSearch...

Gene expression databases

CleanExiMM_ZMYND11.
ExpressionAtlasiQ8R5C8. baseline and differential.
GenevisibleiQ8R5C8. MM.

Family and domain databases

Gene3Di1.20.920.10. 1 hit.
3.30.40.10. 1 hit.
InterProiIPR001487. Bromodomain.
IPR000313. PWWP_dom.
IPR019786. Zinc_finger_PHD-type_CS.
IPR011011. Znf_FYVE_PHD.
IPR002893. Znf_MYND.
IPR001965. Znf_PHD.
IPR019787. Znf_PHD-finger.
IPR013083. Znf_RING/FYVE/PHD.
[Graphical view]
PfamiPF00439. Bromodomain. 1 hit.
PF00855. PWWP. 1 hit.
[Graphical view]
SMARTiSM00297. BROMO. 1 hit.
SM00249. PHD. 1 hit.
SM00293. PWWP. 1 hit.
[Graphical view]
SUPFAMiSSF47370. SSF47370. 1 hit.
SSF57903. SSF57903. 1 hit.
PROSITEiPS50014. BROMODOMAIN_2. 1 hit.
PS50812. PWWP. 1 hit.
PS01360. ZF_MYND_1. 1 hit.
PS50865. ZF_MYND_2. 1 hit.
PS01359. ZF_PHD_1. 1 hit.
PS50016. ZF_PHD_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: C57BL/6J.
  2. Mural R.J., Adams M.D., Myers E.W., Smith H.O., Venter J.C.
    Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  3. "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].
  4. "The transcriptional landscape of the mammalian genome."
    Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.
    , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.
    Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 101-602.
    Strain: C57BL/6J.
    Tissue: Skin.
  5. "ZMYND11 links histone H3.3K36me3 to transcription elongation and tumour suppression."
    Wen H., Li Y., Xi Y., Jiang S., Stratton S., Peng D., Tanaka K., Ren Y., Xia Z., Wu J., Li B., Barton M.C., Li W., Li H., Shi X.
    Nature 508:263-268(2014) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS) OF 154-371 IN COMPLEXES WITH HISTONE 3.3 TAIL AND ZINC, FUNCTION, MUTAGENESIS OF ARG-168; 234-ASP--GLU-236; GLU-251; ASN-266; PHE-291; TRP-294; ASP-307 AND PHE-310.

Entry informationi

Entry nameiZMY11_MOUSE
AccessioniPrimary (citable) accession number: Q8R5C8
Secondary accession number(s): G5E8Q2, Q8C155
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 10, 2004
Last sequence update: November 28, 2012
Last modified: July 6, 2016
This is version 115 of the entry and version 2 of the sequence. [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
  3. 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.