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- PDB-2na1: ULD complex -

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Basic information

Entry
Database: PDB / ID: 2na1
TitleULD complex
ComponentsPolycomb complex protein BMI-1, Polyhomeotic-like 2
KeywordsTRANSCRIPTION / bmi1 / phc2
Function / homology
Function and homology information


regulation of adaxial/abaxial pattern formation / SUMOylation of RNA binding proteins / Regulation of PTEN gene transcription / SUMOylation of DNA damage response and repair proteins / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / SUMOylation of transcription cofactors / SUMOylation of chromatin organization proteins / RING-like zinc finger domain binding / PRC1 complex / segment specification ...regulation of adaxial/abaxial pattern formation / SUMOylation of RNA binding proteins / Regulation of PTEN gene transcription / SUMOylation of DNA damage response and repair proteins / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / SUMOylation of transcription cofactors / SUMOylation of chromatin organization proteins / RING-like zinc finger domain binding / PRC1 complex / segment specification / rostrocaudal neural tube patterning / ubiquitin-protein transferase activator activity / somatic stem cell division / embryonic skeletal system morphogenesis / multicellular organism development / PcG protein complex / positive regulation of immature T cell proliferation in thymus / SUMOylation of DNA methylation proteins / SUMOylation of RNA binding proteins / positive regulation of ubiquitin-protein transferase activity / negative regulation of gene expression, epigenetic / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / Transcriptional Regulation by E2F6 / negative regulation of apoptotic signaling pathway / humoral immune response / hemopoiesis / heterochromatin / SUMOylation of DNA damage response and repair proteins / ubiquitin ligase complex / positive regulation of B cell proliferation / SUMOylation of chromatin organization proteins / SUMOylation of transcription cofactors / Regulation of PTEN gene transcription / promoter-specific chromatin binding / apoptotic signaling pathway / brain development / positive regulation of fibroblast proliferation / histone binding / spermatogenesis / regulation of gene expression / Oxidative Stress Induced Senescence / in utero embryonic development / nuclear body / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / chromatin binding / negative regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
FCS-type zinc finger superfamily / RAWUL domain / RAWUL domain RING finger- and WD40-associated ubiquitin-like / Zinc finger, FCS-type / Zinc finger FCS-type profile. / Zinc finger, C3HC4 type (RING finger) / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain ...FCS-type zinc finger superfamily / RAWUL domain / RAWUL domain RING finger- and WD40-associated ubiquitin-like / Zinc finger, FCS-type / Zinc finger FCS-type profile. / Zinc finger, C3HC4 type (RING finger) / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Sterile alpha motif/pointed domain superfamily / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Polyhomeotic-like 2 (Drosophila) / Polycomb complex protein BMI-1 / Polyhomeotic-like protein 2
Similarity search - Component
Biological speciesmouse (mice)
Homo sapiens (human)
MethodSOLUTION NMR / conformational sampling
Model detailslowest energy, model7
AuthorsCierpicki, T. / Gray, F. / Cho, H.
CitationJournal: Nat Commun / Year: 2016
Title: BMI1 regulates PRC1 architecture and activity through homo- and hetero-oligomerization.
Authors: Gray, F. / Cho, H.J. / Shukla, S. / He, S. / Harris, A. / Boytsov, B. / Jaremko, M. / Jaremko, M. / Demeler, B. / Lawlor, E.R. / Grembecka, J. / Cierpicki, T.
History
DepositionDec 17, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2016Group: Database references
Revision 1.2Jan 31, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polycomb complex protein BMI-1, Polyhomeotic-like 2


Theoretical massNumber of molelcules
Total (without water)18,2291
Polymers18,2291
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Polycomb complex protein BMI-1, Polyhomeotic-like 2 / Polycomb group RING finger protein 4 / RING finger protein 51


Mass: 18229.277 Da / Num. of mol.: 1
Fragment: UNP B1ASA2 residues 30-64, UNP P35226 residues 121-235
Source method: isolated from a genetically manipulated source
Details: Chimeric protein / Source: (gene. exp.) mouse, Homo sapiens / Gene: Phc2, BMI1, PCGF4, phc2, RNF51 / Production host: Escherichia coli (E. coli)
References: UniProt: B1ASA2, UniProt: P35226, UniProt: Q9QWH1*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D HN(CA)CB
1513D HNCA
1613D HN(CO)CA
1713D HNCO
1813D (H)CCH-TOCSY
1913D 1H-15N NOESY
11013D 1H-13C NOESY

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Sample preparation

DetailsContents: 0.2 mM [U-100% 13C; U-100% 15N] protein, 10 % [U-2H] D2O, 50 mM sodium chloride, 1 mM TCEP, 100 mM TRIS, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.2 mMentity-1[U-100% 13C; U-100% 15N]1
10 %D2O-2[U-2H]1
50 mMsodium chloride-31
1 mMTCEP-41
100 mMTRIS-51
Sample conditionsIonic strength: 50 / pH: 6.5 / Pressure: ambient / Temperature: 303.2 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospincollection
SparkyGoddarddata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
PSVSBhattacharya and Montelionedata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
Rosetta(Rosetta-Relax)- Tyka, Keedy, Andre, Dimaio, Song, Richardson, Richardson and Bakerrefinement
TALOSCornilescu, Delaglio and Baxgeometry optimization
RefinementMethod: conformational sampling / Software ordinal: 1 / Details: Rosetta relax program was used for refinement
NMR constraintsNOE constraints total: 144 / NOE intraresidue total count: 43 / NOE long range total count: 45 / NOE medium range total count: 11 / NOE sequential total count: 45 / Protein chi angle constraints total count: 0 / Protein phi angle constraints total count: 13 / Protein psi angle constraints total count: 13
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

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