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- PDB-2gnq: Structure of wdr5 -

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Basic information

Entry
Database: PDB / ID: 2gnq
TitleStructure of wdr5
ComponentsWD-repeat protein 5
KeywordsTRANSCRIPTION / h3k4me2 binding protein / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


histone H3Q5ser reader activity / histone H3K4me1 reader activity / Epigenetic regulation of gene expression by MLL3 and MLL4 complexes / MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / Cardiogenesis ...histone H3Q5ser reader activity / histone H3K4me1 reader activity / Epigenetic regulation of gene expression by MLL3 and MLL4 complexes / MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / Cardiogenesis / Formation of WDR5-containing histone-modifying complexes / histone methyltransferase complex / regulation of cell division / MLL1 complex / regulation of embryonic development / histone acetyltransferase complex / positive regulation of gluconeogenesis / transcription initiation-coupled chromatin remodeling / gluconeogenesis / skeletal system development / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / PKMTs methylate histone lysines / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / mitotic spindle / Neddylation / HATs acetylate histones / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / histone binding / regulation of cell cycle / 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 / nucleoplasm / nucleus
Similarity search - Function
WDR5 beta-propeller domain / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / 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. / WD40 repeats ...WDR5 beta-propeller domain / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / 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. / 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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMin, J. / Schuetz, A. / Allali-Hassani, A. / Loppnau, P. / Vedadi, M. / Weigelt, J. / Sundstrom, M. / Edwards, A.M. / Arrowsmith, C.H. / Bochkarev, A. ...Min, J. / Schuetz, A. / Allali-Hassani, A. / Loppnau, P. / Vedadi, M. / Weigelt, J. / Sundstrom, M. / Edwards, A.M. / Arrowsmith, C.H. / Bochkarev, A. / Plotnikov, A.N. / Structural Genomics Consortium (SGC)
CitationJournal: Embo J. / Year: 2006
Title: Structural basis for molecular recognition and presentation of histone H3 By WDR5.
Authors: Schuetz, A. / Allali-Hassani, A. / Loppnau, P. / Vedadi, M. / Bochkarev, A. / Plotnikov, A.N. / Arrowsmith, C.H. / Min, J.
History
DepositionApr 10, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: WD-repeat protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8152
Polymers36,7801
Non-polymers351
Water8,719484
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.045, 55.323, 124.308
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein WD-repeat protein 5 / BMP2-induced 3-kb gene protein


Mass: 36779.566 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WDR5, BIG3 / Production host: Escherichia coli (E. coli) / References: UniProt: P61964
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 484 / 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: 2.34 Å3/Da / Density % sol: 47.4 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20%peg5k mme, bis-tris 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Mar 8, 2006
RadiationMonochromator: varimax / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→62.14 Å / Num. all: 30580 / Num. obs: 30580 / % possible obs: 93 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.8→1.86 Å / % possible all: 62.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CrystalClear(MSC/RIGAKU)data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VYH

1vyh


Resolution: 1.8→62.14 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.933 / SU B: 1.853 / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.118 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.192 1544 5 %RANDOM
Rwork0.149 ---
all0.151 29046 --
obs0.151 29046 93.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.759 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å20 Å2
2--0.49 Å20 Å2
3----0.32 Å2
Refinement stepCycle: LAST / Resolution: 1.8→62.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2485 0 1 484 2970
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222540
X-RAY DIFFRACTIONr_angle_refined_deg1.2771.9433451
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1525322
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.60125.25897
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.18815442
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.691154
X-RAY DIFFRACTIONr_chiral_restr0.0930.2388
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021877
X-RAY DIFFRACTIONr_nbd_refined0.1950.21176
X-RAY DIFFRACTIONr_nbtor_refined0.2960.21743
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2377
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1960.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1270.237
X-RAY DIFFRACTIONr_mcbond_it0.6281.51636
X-RAY DIFFRACTIONr_mcangle_it1.03622584
X-RAY DIFFRACTIONr_scbond_it1.82431055
X-RAY DIFFRACTIONr_scangle_it2.9374.5867
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 71 -
Rwork0.194 1379 -
obs--60.49 %

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