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- PDB-3smr: Crystal structure of human WD repeat domain 5 with compound -

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Basic information

Entry
Database: PDB / ID: 3smr
TitleCrystal structure of human WD repeat domain 5 with compound
ComponentsWD repeat-containing protein 5
KeywordsTRANSCRIPTION / WDR5 / SGC / Structural Genomics / Structural Genomics Consortium / WD repeat domain 5
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 / positive regulation of gluconeogenesis / methylated histone binding / transcription initiation-coupled chromatin remodeling / skeletal system development / gluconeogenesis / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / mitotic spindle / PKMTs methylate histone lysines / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Neddylation / HATs acetylate histones / 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
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. / WD domain, G-beta repeat / WD40 repeats ...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. / 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
Chem-NP7 / WD repeat-containing protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsDong, A. / Dombrovski, L. / Wasney, G.A. / Tempel, W. / Senisterra, G. / Bolshan, Y. / Smil, D. / Nguyen, K.T. / Hajian, T. / Poda, G. ...Dong, A. / Dombrovski, L. / Wasney, G.A. / Tempel, W. / Senisterra, G. / Bolshan, Y. / Smil, D. / Nguyen, K.T. / Hajian, T. / Poda, G. / Al-Awar, R. / Bountra, C. / Weigelt, J. / Edwards, A.M. / Brown, P.J. / Schapira, M. / Arrowsmith, C.H. / Vedadi, M. / Wu, H. / Structural Genomics Consortium (SGC)
CitationJournal: Biochem. J. / Year: 2013
Title: Small-molecule inhibition of MLL activity by disruption of its interaction with WDR5.
Authors: Senisterra, G. / Wu, H. / Allali-Hassani, A. / Wasney, G.A. / Barsyte-Lovejoy, D. / Dombrovski, L. / Dong, A. / Nguyen, K.T. / Smil, D. / Bolshan, Y. / Hajian, T. / He, H. / Seitova, A. / ...Authors: Senisterra, G. / Wu, H. / Allali-Hassani, A. / Wasney, G.A. / Barsyte-Lovejoy, D. / Dombrovski, L. / Dong, A. / Nguyen, K.T. / Smil, D. / Bolshan, Y. / Hajian, T. / He, H. / Seitova, A. / Chau, I. / Li, F. / Poda, G. / Couture, J.F. / Brown, P.J. / Al-Awar, R. / Schapira, M. / Arrowsmith, C.H. / Vedadi, M.
History
DepositionJun 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2011Provider: repository / Type: Initial release
Revision 1.1May 16, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 13, 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 / pdbx_struct_special_symmetry / 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

Downloads & links

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Assembly

Deposited unit
A: WD repeat-containing protein 5
B: WD repeat-containing protein 5
C: WD repeat-containing protein 5
D: WD repeat-containing protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,08663
Polymers137,1604
Non-polymers2,92759
Water14,808822
1
A: WD repeat-containing protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,16117
Polymers34,2901
Non-polymers87116
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: WD repeat-containing protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,03718
Polymers34,2901
Non-polymers74717
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: WD repeat-containing protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,97513
Polymers34,2901
Non-polymers68512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: WD repeat-containing protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,91315
Polymers34,2901
Non-polymers62314
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)204.171, 93.467, 64.786
Angle α, β, γ (deg.)90.00, 107.24, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-677-

HOH

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Components

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


Mass: 34289.887 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WDR5, BIG3 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): E.coli BL21(DE3) V2RpRARE / References: UniProt: P61964
#2: Chemical
ChemComp-NP7 / 2-chloro-N-[2-(4-methylpiperazin-1-yl)-5-nitrophenyl]benzamide


Mass: 374.821 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H19ClN4O3
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 32 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 822 / 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: 2.15 Å3/Da / Density % sol: 42.85 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 24% PEG3350,9.2M NH4 Acetate, 0.1 Bis Tris pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jun 10, 2011 / Details: VeriMax HR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.82→50 Å / Num. all: 104206 / Num. obs: 104206 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 23.1 Å2 / Rsym value: 0.086 / Net I/σ(I): 25
Reflection shellResolution: 1.82→1.85 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 2.12 / Num. unique all: 5202 / Rsym value: 0.807 / % possible all: 100

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Processing

Software
NameVersionClassification
StructureStudiodata collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2O9K

2o9k


Resolution: 1.82→50 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / SU B: 6.578 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20612 1043 1 %RANDOM
Rwork0.17729 ---
all0.17757 104206 --
obs0.17759 103163 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.61 Å2
Baniso -1Baniso -2Baniso -3
1-2.2 Å20 Å21.52 Å2
2---0.98 Å20 Å2
3----0.32 Å2
Refinement stepCycle: LAST / Resolution: 1.82→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9233 0 228 822 10283
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0229776
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1341.9513280
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.84451233
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.51925.122369
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.264151555
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.2641514
X-RAY DIFFRACTIONr_chiral_restr0.0760.21490
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217286
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.351.56101
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.64529849
X-RAY DIFFRACTIONr_scbond_it0.98833675
X-RAY DIFFRACTIONr_scangle_it1.5674.53431
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.818→1.865 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 85 -
Rwork0.305 7383 -
obs--97.14 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.5264-0.5685-0.38422.16870.3181.3033-0.0561-0.0475-0.03630.1235-0.01170.04950.0917-0.04560.06770.0278-0.00440.00010.0465-0.01640.0118123.576747.364533.0886
21.09610.0105-0.48271.3668-0.13831.1315-0.0182-0.0330.00780.0208-0.0375-0.05610.0651-0.00480.05570.0235-0.02340.00390.0394-0.01270.016120.63790.496932.5156
31.28840.08390.3341.9663-0.29030.83380.10920.07320.1580.1971-0.12370.1487-0.1250.07710.01450.0902-0.02270.0410.03960.00190.0349104.071123.671959.1255
40.9792-0.03170.30951.5245-0.12410.877-0.00380.1152-0.00990.1226-0.0350.0966-0.07680.11080.03880.0605-0.02940.03350.05660.00220.0368104.09669.85759.7434
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A31 - 334
2X-RAY DIFFRACTION1A1000
3X-RAY DIFFRACTION1A500 - 692
4X-RAY DIFFRACTION2B31 - 334
5X-RAY DIFFRACTION2B1000
6X-RAY DIFFRACTION2B500 - 731
7X-RAY DIFFRACTION3C31 - 334
8X-RAY DIFFRACTION3C1000
9X-RAY DIFFRACTION3C500 - 709
10X-RAY DIFFRACTION4D31 - 334
11X-RAY DIFFRACTION4D1000
12X-RAY DIFFRACTION4D500 - 724

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