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- PDB-5c13: Crystal Structure of TAF3 PHD finger bound to histone H3C4me3 peptide -

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Basic information

Entry
Database: PDB / ID: 5c13
TitleCrystal Structure of TAF3 PHD finger bound to histone H3C4me3 peptide
Components
  • H3 peptide
  • Transcription initiation factor TFIID subunit 3
KeywordsHYDROLASE / zinc finger protein
Function / homology
Function and homology information


maintenance of protein location in nucleus / transcription regulator inhibitor activity / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation ...maintenance of protein location in nucleus / transcription regulator inhibitor activity / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / positive regulation of transcription initiation by RNA polymerase II / Chromatin modifying enzymes / epigenetic regulation of gene expression / RNA polymerase II preinitiation complex assembly / RNA Polymerase II Pre-transcription Events / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / PRC2 methylates histones and DNA / male germ cell nucleus / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / mRNA transcription by RNA polymerase II / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / negative regulation of DNA-binding transcription factor activity / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / p53 binding / gene expression / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / nuclear membrane / Estrogen-dependent gene expression / Regulation of TP53 Activity through Phosphorylation / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / metal ion binding / nucleus
Similarity search - Function
Bromodomain associated / Bromodomain transcription factors and PHD domain containing proteins / Bromodomain associated domain / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger ...Bromodomain associated / Bromodomain transcription factors and PHD domain containing proteins / Bromodomain associated domain / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Histone H3 signature 1. / Zinc finger, PHD-type / PHD zinc finger / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Zinc finger, FYVE/PHD-type / Histone-fold / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Histone H3.1 / Transcription initiation factor TFIID subunit 3
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.101 Å
AuthorsLi, H. / Huang, J.
Funding support China, 1items
OrganizationGrant numberCountry
ational Natural Science Foundation of China31270763 China
CitationJournal: Nat Commun / Year: 2015
Title: Crystal Structure of Jarid1a PHD finger bound to histone H3C4me3 peptide
Authors: Huang, J. / Li, H.
History
DepositionJun 12, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Data collection / Derived calculations / Experimental preparation
Category: diffrn_detector / exptl_crystal_grow / pdbx_struct_oper_list
Item: _diffrn_detector.detector / _exptl_crystal_grow.pdbx_details / _pdbx_struct_oper_list.symmetry_operation
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_conn_type
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcription initiation factor TFIID subunit 3
P: H3 peptide
C: Transcription initiation factor TFIID subunit 3
D: H3 peptide
E: Transcription initiation factor TFIID subunit 3
F: H3 peptide
G: Transcription initiation factor TFIID subunit 3
H: H3 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,67416
Polymers34,1518
Non-polymers5238
Water1,40578
1
A: Transcription initiation factor TFIID subunit 3
P: H3 peptide
E: Transcription initiation factor TFIID subunit 3
F: H3 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3378
Polymers17,0764
Non-polymers2624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Transcription initiation factor TFIID subunit 3
D: H3 peptide
G: Transcription initiation factor TFIID subunit 3
H: H3 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3378
Polymers17,0764
Non-polymers2624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.212, 50.105, 85.949
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Transcription initiation factor TFIID subunit 3 / 140 kDa TATA box-binding protein-associated factor / TBP-associated factor 3 / Transcription ...140 kDa TATA box-binding protein-associated factor / TBP-associated factor 3 / Transcription initiation factor TFIID 140 kDa subunit / TAFII140


Mass: 7347.350 Da / Num. of mol.: 4 / Fragment: PHD finger domain, UNP residues 853-915
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TAF3 / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5VWG9
#2: Protein/peptide
H3 peptide


Mass: 1190.416 Da / Num. of mol.: 4 / Source method: obtained synthetically
Details: chemically synthesized H3 peptide 1-10 with K4Cme3 modification
Source: (synth.) synthetic construct (others) / References: UniProt: P68431*PLUS
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.83 Å3/Da / Density % sol: 32.83 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.03M magnesium chloride, 0.03M calcium chloride, 0.1M MES, 0.1M imidazole, PH6.5, 15% PEGMME 550, 15% PEG 20K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 16, 2014 / Details: mirrors
RadiationMonochromator: double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 15064 / % possible obs: 99.6 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.123 / Χ2: 2.097 / Net I/av σ(I): 17.129 / Net I/σ(I): 7.1 / Num. measured all: 54999
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.1-2.143.70.6697461.542100
2.14-2.183.70.5587771.672100
2.18-2.223.70.5527131.607100
2.22-2.263.70.4387641.65899.9
2.26-2.313.70.4237641.66499.9
2.31-2.373.70.3987291.66100
2.37-2.423.70.3367411.84599.7
2.42-2.493.70.2947591.68499.7
2.49-2.563.70.3127381.83599.9
2.56-2.653.70.2657711.79499.9
2.65-2.743.70.2217621.97999.9
2.74-2.853.70.2017242.051100
2.85-2.983.70.1617592.07299.6
2.98-3.143.70.1327652.29499.9
3.14-3.333.60.1157532.46499.6
3.33-3.593.60.0897382.64599.6
3.59-3.953.30.0847463.34997.3
3.95-4.523.50.0587702.81499.6
4.52-5.73.50.0497602.61999.3
5.7-503.50.0547853.02898.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.101→32.62 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2796 760 5.07 %Random selection
Rwork0.2217 14241 --
obs0.2248 15001 99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 127.34 Å2 / Biso mean: 37.3714 Å2 / Biso min: 13.47 Å2
Refinement stepCycle: final / Resolution: 2.101→32.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2108 0 8 78 2194
Biso mean--25.83 37.7 -
Num. residues----260
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142184
X-RAY DIFFRACTIONf_angle_d1.5572984
X-RAY DIFFRACTIONf_chiral_restr0.07280
X-RAY DIFFRACTIONf_plane_restr0.01384
X-RAY DIFFRACTIONf_dihedral_angle_d16.894796
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1014-2.26370.33211200.24482845296598
2.2637-2.49140.28131570.24392830298799
2.4914-2.85170.30211570.236728292986100
2.8517-3.59210.2831560.21952869302599
3.5921-32.62380.25861700.20492868303898

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