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- PDB-4gmb: Crystal structure of human WD repeat domain 5 with compound MM-402 -

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Basic information

Entry
Database: PDB / ID: 4gmb
TitleCrystal structure of human WD repeat domain 5 with compound MM-402
Components
  • MM-402
  • 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 / transcription factor TFIID complex / RNA polymerase II general transcription initiation factor activity / histone acetyltransferase complex / positive regulation of gluconeogenesis / transcription initiation-coupled chromatin remodeling / methylated histone binding / 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-402 / WD repeat-containing protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.781 Å
AuthorsKaratas, H. / Townsend, E.C. / Chen, Y. / Bernard, D. / Cao, F. / Liu, L. / Lei, M. / Dou, Y. / Wang, S.
CitationJournal: J.Med.Chem. / Year: 2017
Title: Discovery of a Highly Potent, Cell-Permeable Macrocyclic Peptidomimetic (MM-589) Targeting the WD Repeat Domain 5 Protein (WDR5)-Mixed Lineage Leukemia (MLL) Protein-Protein Interaction.
Authors: Karatas, H. / Li, Y. / Liu, L. / Ji, J. / Lee, S. / Chen, Y. / Yang, J. / Huang, L. / Bernard, D. / Xu, J. / Townsend, E.C. / Cao, F. / Ran, X. / Li, X. / Wen, B. / Sun, D. / Stuckey, J.A. / ...Authors: Karatas, H. / Li, Y. / Liu, L. / Ji, J. / Lee, S. / Chen, Y. / Yang, J. / Huang, L. / Bernard, D. / Xu, J. / Townsend, E.C. / Cao, F. / Ran, X. / Li, X. / Wen, B. / Sun, D. / Stuckey, J.A. / Lei, M. / Dou, Y. / Wang, S.
History
DepositionAug 15, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 24, 2022Group: Advisory / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.3Sep 13, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
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 / 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

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Assembly

Deposited unit
A: WD repeat-containing protein 5
E: MM-402


Theoretical massNumber of molelcules
Total (without water)35,0252
Polymers35,0252
Non-polymers00
Water1,08160
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.297, 50.837, 137.845
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-containing protein 5 / WDR5 / BMP2-induced 3-kb gene protein


Mass: 34390.992 Da / Num. of mol.: 1 / 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-402


Type: Peptide-like / Class: Inhibitor / Mass: 633.803 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: MM-402
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.37 Å3/Da / Density % sol: 48.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25% tert-butanol, 0.1 M Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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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: 2.781→100 Å / Num. all: 8827 / Num. obs: 8589 / % possible obs: 97.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.2 % / Rsym value: 0.138 / Net I/σ(I): 14.5
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsRsym valueDiffraction-ID% possible all
2.781-2.96.23.40.488198.8
2.9-3.02196
3.02-3.15195.7
3.15-3.32198
3.32-3.53196.3
3.53-3.8195.9
3.8-4.18196.3
4.18-4.79196.8
4.79-6.03199.2
6.03-100199.7

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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: 2.781→44.737 Å / SU ML: 0.38 / σ(F): 1.35 / Phase error: 22.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2466 406 4.75 %RANDOM
Rwork0.1899 ---
obs0.1925 8552 96.73 %-
all-8827 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 10.591 Å2 / ksol: 0.311 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.5196 Å20 Å20 Å2
2--5.1158 Å2-0 Å2
3---0.4039 Å2
Refinement stepCycle: LAST / Resolution: 2.781→44.737 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2421 0 0 60 2481
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022480
X-RAY DIFFRACTIONf_angle_d0.7233365
X-RAY DIFFRACTIONf_dihedral_angle_d11.009878
X-RAY DIFFRACTIONf_chiral_restr0.05378
X-RAY DIFFRACTIONf_plane_restr0.002415
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.781-3.18310.32721420.22552583X-RAY DIFFRACTION95
3.1831-4.010.23371270.1772667X-RAY DIFFRACTION96
4.01-44.74260.21851370.18412896X-RAY DIFFRACTION99

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