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- PDB-4gm8: Crystal structure of human WD repeat domain 5 with compound MM-102 -

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Basic information

Entry
Database: PDB / ID: 4gm8
TitleCrystal structure of human WD repeat domain 5 with compound MM-102
Components
  • MM-102
  • 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 ...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 / regulation of cell division / Formation of WDR5-containing histone-modifying complexes / MLL1 complex / regulation of embryonic development / 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. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. ...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. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
MM-102 / WD repeat-containing protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.601 Å
AuthorsKaratas, H. / Townsend, E.C. / Chen, Y. / Bernard, D. / Cao, F. / Liu, L. / Lei, M. / Dou, Y. / Wang, S.
CitationJournal: J.Am.Chem.Soc. / Year: 2013
Title: High-affinity, small-molecule peptidomimetic inhibitors of MLL1/WDR5 protein-protein interaction.
Authors: Karatas, H. / Townsend, E.C. / Cao, F. / Chen, Y. / Bernard, D. / Liu, L. / Lei, M. / Dou, Y. / Wang, S.
History
DepositionAug 15, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 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 / _struct_conn.pdbx_leaving_atom_flag
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_rmsd_angle / 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
C: WD repeat-containing protein 5
D: WD repeat-containing protein 5
E: MM-102
F: MM-102
G: MM-102
H: MM-102


Theoretical massNumber of molelcules
Total (without water)140,2478
Polymers140,2478
Non-polymers00
Water5,477304
1
A: WD repeat-containing protein 5
E: MM-102


Theoretical massNumber of molelcules
Total (without water)35,0622
Polymers35,0622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area920 Å2
ΔGint-4 kcal/mol
Surface area11730 Å2
MethodPISA
2
B: WD repeat-containing protein 5
F: MM-102


Theoretical massNumber of molelcules
Total (without water)35,0622
Polymers35,0622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint-4 kcal/mol
Surface area11550 Å2
MethodPISA
3
C: WD repeat-containing protein 5
G: MM-102


Theoretical massNumber of molelcules
Total (without water)35,0622
Polymers35,0622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area920 Å2
ΔGint-4 kcal/mol
Surface area11730 Å2
MethodPISA
4
D: WD repeat-containing protein 5
H: MM-102


Theoretical massNumber of molelcules
Total (without water)35,0622
Polymers35,0622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area920 Å2
ΔGint-4 kcal/mol
Surface area11600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.861, 106.478, 120.719
Angle α, β, γ (deg.)90.00, 90.35, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 35:210 or resseq 213:334 )
211chain B and (resseq 35:210 or resseq 213:334 )
311chain C and (resseq 35:210 or resseq 213:334 )
411chain D and (resseq 35:210 or resseq 213:334 )

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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.: 4 / 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-102


Type: Peptide-like / Class: Inhibitor / Mass: 670.813 Da / Num. of mol.: 4 / Source method: obtained synthetically / References: MM-102
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 304 / 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: 2.24 Å3/Da / Density % sol: 45.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 30% PEG8000, 0.2 M ammonium sulfate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 25, 2011
RadiationMonochromator: Diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.6→100 Å / Num. all: 37980 / Num. obs: 35626 / % possible obs: 93.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.7 % / Rsym value: 0.134 / Net I/σ(I): 12
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsRsym valueDiffraction-ID% possible all
2.6-2.692.33.10.399194.2
2.69-2.8195.4
2.8-2.93196.8
2.93-3.08196.4
3.08-3.28195.5
3.28-3.53194
3.53-3.88193
3.88-4.45191.8
4.45-5.6191.2
5.6-100189.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
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: 2.601→48.86 Å / SU ML: 0.39 / σ(F): 0 / Phase error: 27.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2494 1604 4.99 %RANDOM
Rwork0.1926 ---
all0.1954 37980 --
obs0.1954 32146 84.48 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.844 Å2 / ksol: 0.393 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.0324 Å20 Å21.7924 Å2
2--16.6865 Å20 Å2
3----13.654 Å2
Refinement stepCycle: LAST / Resolution: 2.601→48.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9501 0 0 304 9805
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089729
X-RAY DIFFRACTIONf_angle_d1.213203
X-RAY DIFFRACTIONf_dihedral_angle_d16.5683521
X-RAY DIFFRACTIONf_chiral_restr0.0721475
X-RAY DIFFRACTIONf_plane_restr0.0031615
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2305X-RAY DIFFRACTIONPOSITIONAL
12B2305X-RAY DIFFRACTIONPOSITIONAL0.037
13C2305X-RAY DIFFRACTIONPOSITIONAL0.031
14D2289X-RAY DIFFRACTIONPOSITIONAL0.034
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.601-2.68490.34051250.26572416X-RAY DIFFRACTION74
2.6849-2.78090.30221360.23712596X-RAY DIFFRACTION79
2.7809-2.89220.30771340.22182679X-RAY DIFFRACTION82
2.8922-3.02380.31681470.22092734X-RAY DIFFRACTION84
3.0238-3.18320.2391380.19452790X-RAY DIFFRACTION86
3.1832-3.38260.21761550.18232874X-RAY DIFFRACTION88
3.3826-3.64370.25131480.19352864X-RAY DIFFRACTION87
3.6437-4.01020.23771290.17182919X-RAY DIFFRACTION88
4.0102-4.59010.20881590.14512863X-RAY DIFFRACTION88
4.5901-5.78160.22781630.17792926X-RAY DIFFRACTION89
5.7816-48.86870.22951700.21232881X-RAY DIFFRACTION86

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