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- PDB-2co0: WDR5 and unmodified Histone H3 complex at 2.25 Angstrom -

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Basic information

Entry
Database: PDB / ID: 2co0
TitleWDR5 and unmodified Histone H3 complex at 2.25 Angstrom
Components
  • (WD-REPEAT PROTEIN 5) x 2
  • HISTONE H3 DIMETHYL-LYSINE 4
KeywordsTRANSCRIPTION / HISTONE PRESENTER / LYSINE METHYLATION / MLL1 / LEUKEMIA / HOX GENE ACTIVATION / TRANSCRIPTION ACTIVATION
Function / homology
Function and homology information


MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / Cardiogenesis / histone methyltransferase complex / regulation of tubulin deacetylation / Formation of WDR5-containing histone-modifying complexes ...MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / Cardiogenesis / histone methyltransferase complex / regulation of tubulin deacetylation / Formation of WDR5-containing histone-modifying complexes / regulation of cell division / regulation of embryonic development / MLL1 complex / histone acetyltransferase complex / Chromatin modifying enzymes / positive regulation of gluconeogenesis / methylated histone binding / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / epigenetic regulation of gene expression / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / transcription initiation-coupled chromatin remodeling / DNA methylation / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / HCMV Late Events / PRC2 methylates histones and DNA / skeletal system development / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / gluconeogenesis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / HDMs demethylate histones / B-WICH complex positively regulates rRNA expression / mitotic spindle / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Neddylation / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / histone binding / gene expression / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / regulation of cell cycle / cadherin binding / protein heterodimerization activity / Amyloid fiber formation / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus
Similarity search - Function
YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold ...YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
WD repeat-containing protein 5 / Histone H3.1 / Histone H3-7
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsRuthenburg, A.J. / Wang, W. / Graybosch, D.M. / Li, H. / Allis, C.D. / Patel, D.J. / Verdine, G.L.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2006
Title: Histone H3 Recognition and Presentation by the Wdr5 Module of the Mll1 Complex
Authors: Ruthenburg, A.J. / Wang, W. / Graybosch, D.M. / Li, H. / Allis, C.D. / Patel, D.J. / Verdine, G.L.
History
DepositionMay 25, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2006Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Other / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3May 23, 2018Group: Data collection / Structure summary / Category: diffrn_detector / struct / Item: _struct.title
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: WD-REPEAT PROTEIN 5
B: HISTONE H3 DIMETHYL-LYSINE 4
C: WD-REPEAT PROTEIN 5
D: HISTONE H3 DIMETHYL-LYSINE 4


Theoretical massNumber of molelcules
Total (without water)72,3204
Polymers72,3204
Non-polymers00
Water5,350297
1
A: WD-REPEAT PROTEIN 5
B: HISTONE H3 DIMETHYL-LYSINE 4


Theoretical massNumber of molelcules
Total (without water)36,1672
Polymers36,1672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: WD-REPEAT PROTEIN 5
D: HISTONE H3 DIMETHYL-LYSINE 4


Theoretical massNumber of molelcules
Total (without water)36,1532
Polymers36,1532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)64.916, 47.030, 101.768
Angle α, β, γ (deg.)90.00, 107.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein WD-REPEAT PROTEIN 5 / BMP2-INDUCED 3-KB GENE PROTEIN


Mass: 34601.203 Da / Num. of mol.: 1 / Fragment: RESIDUES 20-334
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): ROSETTA2 PLYSS / References: UniProt: P61964
#2: Protein/peptide HISTONE H3 DIMETHYL-LYSINE 4


Mass: 1565.797 Da / Num. of mol.: 2 / Fragment: HISTONE TAIL, UNP RESIDUES 2-16 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q5TEC6, UniProt: P68431*PLUS
#3: Protein WD-REPEAT PROTEIN 5 / BMP2-INDUCED 3-KB GENE PROTEIN


Mass: 34587.219 Da / Num. of mol.: 1 / Fragment: RESIDUES 20-334
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): ROSETTA2 PLYSS / References: UniProt: P61964
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 40.12 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU R-AXIS IV / Wavelength: 1.54
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.25→20 Å / Num. obs: 28460 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 6.7 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 15.8
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 3.07 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ERJ

1erj


Resolution: 2.25→20 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2262 1309 4.6 %RANDOM
Rwork0.19 ---
obs0.19 26948 95.4 %-
Solvent computationBsol: 45.39 Å2 / ksol: 0.378881 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.68 Å20 Å2-3.029 Å2
2---0.121 Å20 Å2
3----3.559 Å2
Refinement stepCycle: LAST / Resolution: 2.25→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4795 0 0 297 5092
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005633
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.53419
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2WATER.PARAM
X-RAY DIFFRACTION3ION.PARAM

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