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- PDB-4gm9: Crystal structure of human WD repeat domain 5 with compound MM-401 -

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Basic information

Entry
Database: PDB / ID: 4gm9
TitleCrystal structure of human WD repeat domain 5 with compound MM-401
Components
  • MM-401
  • WD repeat-containing protein 5
KeywordsTRANSCRIPTION/TRANSCRIPTION INHIBITOR / MLL1 / histone methyltransferase / WD40 / TRANSCRIPTION-TRANSCRIPTION INHIBITOR complex
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
MM-401 / WD repeat-containing protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKaratas, H. / Townsend, E.C. / Chen, Y. / Bernard, D. / Liu, L. / Dou, Y. / Lei, M. / Wang, S.
CitationJournal: To be Published
Title: Crystal structure of human WD repeat domain 5 with compound MM-401
Authors: Karatas, H. / Townsend, E.C. / Chen, Y. / Bernard, D. / Liu, L. / Dou, Y. / Lei, M. / Wang, S.
History
DepositionAug 15, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _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
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_torsion / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_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
E: MM-401
F: MM-401


Theoretical massNumber of molelcules
Total (without water)69,9934
Polymers69,9934
Non-polymers00
Water9,422523
1
A: WD repeat-containing protein 5
E: MM-401


Theoretical massNumber of molelcules
Total (without water)34,9972
Polymers34,9972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: WD repeat-containing protein 5
F: MM-401


Theoretical massNumber of molelcules
Total (without water)34,9972
Polymers34,9972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.904, 47.242, 68.896
Angle α, β, γ (deg.)88.50, 89.50, 74.53
Int Tables number1
Space group name H-MP1

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Components

#1: Protein WD repeat-containing protein 5 / WDR5 / BMP2-induced 3-kb gene protein


Mass: 34390.992 Da / Num. of mol.: 2 / Fragment: UNP residues 22-334
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WDR5, BIG3 / Plasmid: PET28b-sumo / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61964
#2: Protein/peptide MM-401


Type: Peptide-like / Class: Inhibitor / Mass: 605.750 Da / Num. of mol.: 2 / Source method: obtained synthetically / References: MM-401
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 523 / 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: 2.1 Å3/Da / Density % sol: 41.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% PEG4000, 0.2 M magnesium chloride, 0.1 M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.00K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 25, 2012
RadiationMonochromator: Diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.1→100 Å / Num. all: 33182 / Num. obs: 32452 / % possible obs: 97.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 1.9 % / Rsym value: 0.06 / Net I/σ(I): 14.2
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsRsym valueDiffraction-ID% possible all
2.1-2.181.73.80.167194.9
2.18-2.26197.2
2.26-2.37197.7
2.37-2.49197.8
2.49-2.65197.9
2.65-2.85198.3
2.85-3.14198.6
3.14-3.59198.7
3.59-4.52198.8
4.52-100197.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2H14

2h14


Resolution: 2.1→37.822 Å / SU ML: 0.23 / σ(F): 2 / Phase error: 20.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2078 1634 5.04 %RANDOM
Rwork0.1589 ---
obs0.1613 32442 97.51 %-
all-33182 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.205 Å2 / ksol: 0.397 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.5254 Å22.3117 Å21.0077 Å2
2--5.1816 Å2-0.1892 Å2
3----4.6562 Å2
Refinement stepCycle: LAST / Resolution: 2.1→37.822 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4877 0 0 523 5400
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045002
X-RAY DIFFRACTIONf_angle_d0.9196789
X-RAY DIFFRACTIONf_dihedral_angle_d14.4241789
X-RAY DIFFRACTIONf_chiral_restr0.065766
X-RAY DIFFRACTIONf_plane_restr0.003840
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.16170.25241260.18782414X-RAY DIFFRACTION92
2.1617-2.23140.24771380.17742592X-RAY DIFFRACTION97
2.2314-2.31120.25031410.1782524X-RAY DIFFRACTION97
2.3112-2.40370.21131210.16712583X-RAY DIFFRACTION98
2.4037-2.51310.24181610.16512568X-RAY DIFFRACTION98
2.5131-2.64550.21211400.16942563X-RAY DIFFRACTION98
2.6455-2.81120.21641270.16662579X-RAY DIFFRACTION98
2.8112-3.02820.21621320.16662615X-RAY DIFFRACTION99
3.0282-3.33280.20251390.15172613X-RAY DIFFRACTION99
3.3328-3.81460.19571550.14312572X-RAY DIFFRACTION99
3.8146-4.80450.15721280.13122602X-RAY DIFFRACTION99
4.8045-37.82780.19691260.1672583X-RAY DIFFRACTION97

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