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- PDB-1fp0: SOLUTION STRUCTURE OF THE PHD DOMAIN FROM THE KAP-1 COREPRESSOR -

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Entry
Database: PDB / ID: 1fp0
TitleSOLUTION STRUCTURE OF THE PHD DOMAIN FROM THE KAP-1 COREPRESSOR
ComponentsKAP-1 COREPRESSOR
KeywordsTRANSCRIPTION / PHD domain / C3HC4 type zinc binding domain / NMR-structure
Function / homology
Function and homology information


convergent extension involved in axis elongation / : / Krueppel-associated box domain binding / embryonic placenta morphogenesis / positive regulation of DNA methylation-dependent heterochromatin formation / suppression of viral release by host / epigenetic programming of gene expression / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / genomic imprinting / chromo shadow domain binding ...convergent extension involved in axis elongation / : / Krueppel-associated box domain binding / embryonic placenta morphogenesis / positive regulation of DNA methylation-dependent heterochromatin formation / suppression of viral release by host / epigenetic programming of gene expression / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / genomic imprinting / 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 / promoter-specific chromatin binding / euchromatin / RING-type E3 ubiquitin transferase / HCMV Early Events / positive regulation of protein import into nucleus / RNA polymerase II transcription regulator complex / ubiquitin-protein transferase activity / transcription corepressor activity / ubiquitin protein ligase activity / chromatin organization / transcription coactivator activity / protein kinase activity / innate immune response / DNA repair / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / chromatin 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/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Transcription intermediary factor 1-beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry, simulated annealing
AuthorsCapili, A.D. / Schultz, D.C. / Rauscher III, F.J. / Borden, K.L.B.
CitationJournal: EMBO J. / Year: 2001
Title: Solution structure of the PHD domain from the KAP-1 corepressor: structural determinants for PHD, RING and LIM zinc-binding domains.
Authors: Capili, A.D. / Schultz, D.C. / RauscherIII, F.J. / Borden, K.L.
History
DepositionAug 29, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Assembly

Deposited unit
A: KAP-1 COREPRESSOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,0703
Polymers9,9391
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
RepresentativeModel #1closest to the average

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Components

#1: Protein KAP-1 COREPRESSOR / TRANSCRIPTION INTERMEDIARY FACTOR 1-BETA / NUCLEAR COREPRESSOR / KAP-1 / KRAB-ASSOCIATED PROTEIN 1


Mass: 9939.204 Da / Num. of mol.: 1 / Fragment: PHD DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PQE50 / Production host: Escherichia coli (E. coli) / 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 detailsText: First 17 residues (MRGSHHHHHHGSDIIDE) and last 9 residues (VDLQACKLN) do not belong to the natural protein molecule, residues 618 to 679 corresponds to KAP-1, structured region corresponds to ...Text: First 17 residues (MRGSHHHHHHGSDIIDE) and last 9 residues (VDLQACKLN) do not belong to the natural protein molecule, residues 618 to 679 corresponds to KAP-1, structured region corresponds to residues 627-670 which contain the PHD domain

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5-3.0 mM 15N-labelled or unlabelled KAP-1 PHD, 20 mM NaH2PO4, 500 mM NaCl, 5 mM DTT, pH 7.590% H2O/10% D2O
21.5-3.0 mM unlabelled KAP-1 PHD, 20 mM NaH2PO4, 500 mM NaCl, 5 mM DTT, pH 7.5100% D2O
Sample conditionspH: 7.50 / Pressure: AMBIENT / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

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Processing

NMR softwareName: X-PLOR / Version: 3.851 / Developer: Brunger / Classification: refinement
RefinementMethod: distance geometry, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformers submitted total number: 1

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