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- PDB-2ro1: NMR Solution Structures of Human KAP1 PHD finger-bromodomain -

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Basic information

Entry
Database: PDB / ID: 2ro1
TitleNMR Solution Structures of Human KAP1 PHD finger-bromodomain
ComponentsTranscription intermediary factor 1-beta
KeywordsTRANSCRIPTION / KAP / TIF / PHD finger / Bromodomain / SUMO / Acetylation / Alternative splicing / Metal-binding / Nucleus / Phosphoprotein / Repressor / Transcription regulation / Zinc / Zinc-finger
Function / homology
Function and homology information


convergent extension involved in axis elongation / Krueppel-associated box domain binding / embryonic placenta morphogenesis / : / suppression of viral release by host / genomic imprinting / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / chromo shadow domain binding / Generic Transcription Pathway / SUMO transferase activity ...convergent extension involved in axis elongation / Krueppel-associated box domain binding / embryonic placenta morphogenesis / : / suppression of viral release by host / genomic imprinting / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / chromo shadow domain binding / Generic Transcription Pathway / SUMO transferase activity / protein sumoylation / epithelial to mesenchymal transition / heterochromatin / embryo implantation / positive regulation of DNA repair / SUMOylation of transcription cofactors / Regulation of endogenous retroelements by KRAB-ZFP proteins / promoter-specific chromatin binding / RING-type E3 ubiquitin transferase / euchromatin / positive regulation of protein import into nucleus / HCMV Early Events / RNA polymerase II transcription regulator complex / ubiquitin-protein transferase activity / transcription corepressor activity / ubiquitin protein ligase activity / chromatin organization / proteasome-mediated ubiquitin-dependent protein catabolic process / transcription coactivator activity / protein kinase activity / innate immune response / DNA repair / negative regulation of DNA-templated transcription / chromatin binding / ubiquitin protein ligase binding / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Transcription intermediary factor 1-beta / TIF1-beta, RING finger, HC subclass / : / : / zinc-RING finger domain / B-box, C-terminal / B-Box C-terminal domain / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger ...Transcription intermediary factor 1-beta / TIF1-beta, RING finger, HC subclass / : / : / zinc-RING finger domain / B-box, C-terminal / B-Box C-terminal domain / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / Zinc finger, PHD-type, conserved site / PHD-finger / Ring finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, FYVE/PHD-type / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Transcription intermediary factor 1-beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
AuthorsZeng, L. / Yap, K.L. / Ivanov, A.V. / Wang, X. / Mujtaba, S. / Plotnikova, O. / Rauscher, F.J.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2008
Title: Structural insights into human KAP1 PHD finger-bromodomain and its role in gene silencing
Authors: Zeng, L. / Yap, K.L. / Ivanov, A.V. / Wang, X. / Mujtaba, S. / Plotnikova, O. / Rauscher, F.J. / Zhou, M.M.
History
DepositionMar 4, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0May 20, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcription intermediary factor 1-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1743
Polymers21,0431
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Transcription intermediary factor 1-beta / TIF1-beta / Tripartite motif-containing protein 28 / Nuclear corepressor KAP-1 / KRAB-associated ...TIF1-beta / Tripartite motif-containing protein 28 / Nuclear corepressor KAP-1 / KRAB-associated protein 1 / KAP-1 / KRAB-interacting protein 1 / KRIP-1 / RING finger protein 96


Mass: 21042.957 Da / Num. of mol.: 1 / Fragment: UNP residues 624-812
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRIM28, KAP1, RNF96, TIF1B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q13263
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N TOCSY
1213D 1H-13C NOESY

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Sample preparation

DetailsContents: 0.5mM [U-100% 13C; U-100% 15N] protein, 100% D2O / Solvent system: 100% D2O
SampleConc.: 0.5 mM / Component: protein / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 0.2 / pH: 6.5 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX6002
Bruker AvanceBrukerAVANCE8003

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1Brunger, Adams, Clore, Gros, Nilges, Readstructure solution
ARIA2.1Linge, O'Donoghue, Nilgesdata analysis
CNS1.1Brunger, Adams, Clore, Gros, Nilges, Readrefinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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