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- PDB-5sxm: WDR5 in complex with MLL Win motif peptidomimetic -

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Basic information

Entry
Database: PDB / ID: 5sxm
TitleWDR5 in complex with MLL Win motif peptidomimetic
Components
  • ACE-ALA-ARG-THR-GLU-VAL-TYR-NH2
  • WD repeat-containing protein 5
KeywordsTRANSCRIPTION / beta propeller / WD40 repeat / transcription regulator / scaffold
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
WD repeat-containing protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsAlicea-Velazquez, N.L. / Shinsky, S.A. / Cosgrove, M.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)5R01CA140522-07 United States
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Targeted Disruption of the Interaction between WD-40 Repeat Protein 5 (WDR5) and Mixed Lineage Leukemia (MLL)/SET1 Family Proteins Specifically Inhibits MLL1 and SETd1A Methyltransferase Complexes.
Authors: Alicea-Velazquez, N.L. / Shinsky, S.A. / Loh, D.M. / Lee, J.H. / Skalnik, D.G. / Cosgrove, M.S.
History
DepositionAug 9, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2016Group: Database references
Revision 1.2Nov 23, 2016Group: Database references
Revision 1.3Sep 13, 2017Group: Advisory / Author supporting evidence / Database references
Category: citation / pdbx_audit_support / pdbx_unobs_or_zero_occ_atoms
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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
D: ACE-ALA-ARG-THR-GLU-VAL-TYR-NH2
C: ACE-ALA-ARG-THR-GLU-VAL-TYR-NH2


Theoretical massNumber of molelcules
Total (without water)70,6504
Polymers70,6504
Non-polymers00
Water4,900272
1
A: WD repeat-containing protein 5
C: ACE-ALA-ARG-THR-GLU-VAL-TYR-NH2


Theoretical massNumber of molelcules
Total (without water)35,3252
Polymers35,3252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-7 kcal/mol
Surface area11680 Å2
MethodPISA
2
B: WD repeat-containing protein 5
D: ACE-ALA-ARG-THR-GLU-VAL-TYR-NH2


Theoretical massNumber of molelcules
Total (without water)35,3252
Polymers35,3252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-7 kcal/mol
Surface area11640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.938, 74.938, 93.544
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and (resseq 32:334 )
21chain B and (resseq 32:334 )

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: CYS / End label comp-ID: CYS / Auth seq-ID: 32 - 334 / Label seq-ID: 13 - 315

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain A and (resseq 32:334 )AA
2chain B and (resseq 32:334 )BB

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Components

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


Mass: 34562.148 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WDR5, BIG3 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta II (DE3) pLys / References: UniProt: P61964
#2: Protein/peptide ACE-ALA-ARG-THR-GLU-VAL-TYR-NH2


Mass: 762.855 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: MLL Win motif-derived peptidomimetic / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 272 / 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: 2.21 Å3/Da / Density % sol: 44.43 % / Description: Hollow-looking needles
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1M sodium citrate pH 5.6, 15% 2-propanol, and 17% PEG 4000, and 10mM ATP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.977 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 26, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 1.9→37.945 Å / Num. obs: 45994 / % possible obs: 100 % / Redundancy: 8 % / Biso Wilson estimate: 26.61 Å2 / Rmerge(I) obs: 0.123 / Net I/av σ(I): 28.556 / Net I/σ(I): 7.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
1.9-1.975.40.8252.40.7381100
1.97-2.057.40.6264.20.871100
2.05-2.148.30.466.40.9321100
2.14-2.258.50.3788.40.9581100
2.25-2.398.50.30510.50.971100
2.39-2.588.50.23114.60.9811100
2.58-2.848.50.16322.30.991100
2.84-3.258.50.11733.30.9941100
3.25-4.098.40.08251.60.9961100
4.09-508.10.07164.20.997199.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIX1.7.2_869refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2H14

2h14


Resolution: 2→37.945 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 28.15
RfactorNum. reflection% reflection
Rfree0.2434 1955 4.93 %
Rwork0.2139 --
obs0.2154 39660 99.94 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Bsol: 42.567 Å2 / ksol: 0.395 e/Å3
Displacement parametersBiso max: 74.39 Å2 / Biso mean: 32.94 Å2 / Biso min: 15.23 Å2
Baniso -1Baniso -2Baniso -3
1-3.6354 Å20 Å20 Å2
2--3.6354 Å20 Å2
3----7.2708 Å2
Refinement stepCycle: final / Resolution: 2→37.945 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4817 0 0 272 5089
Biso mean---37.53 -
Num. residues----623
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034996
X-RAY DIFFRACTIONf_angle_d0.8846787
X-RAY DIFFRACTIONf_chiral_restr0.06763
X-RAY DIFFRACTIONf_plane_restr0.003843
X-RAY DIFFRACTIONf_dihedral_angle_d12.0431777
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2347X-RAY DIFFRACTIONPOSITIONAL0.005
12B2347X-RAY DIFFRACTIONPOSITIONAL0.005
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2-2.050.36271580.304126392797
2.05-2.10550.2651360.271627452881
2.1055-2.16740.27981120.254426982810
2.1674-2.23740.34591320.250127072839
2.2374-2.31730.28521400.268626822822
2.3173-2.41010.3141200.260827382858
2.4101-2.51970.33371470.269526592806
2.5197-2.65260.26541340.27127062840
2.6526-2.81870.27591650.243326512816
2.8187-3.03620.26391180.241127372855
3.0362-3.34160.2641600.213126752835
3.3416-3.82480.23481260.181927062832
3.8248-4.81730.15541480.144326792827
4.8173-37.95130.2051590.181526832842
Refinement TLS params.Method: refined / Origin x: 13.8723 Å / Origin y: -2.4656 Å / Origin z: 11.3321 Å
111213212223313233
T0.2145 Å20.0711 Å20.0819 Å2-0.0683 Å2-0.0381 Å2--0.0322 Å2
L0.9137 °2-0.0737 °20.942 °2-0.6436 °2-1.2371 °2--0.5365 °2
S0.0042 Å °0.5158 Å °0.0925 Å °0.1729 Å °-0.2709 Å °0.0501 Å °0.0058 Å °0.04 Å °-0.0154 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA31 - 334
2X-RAY DIFFRACTION1allB32 - 334
3X-RAY DIFFRACTION1allD0 - 7
4X-RAY DIFFRACTION1allC0 - 7
5X-RAY DIFFRACTION1allS1 - 265
6X-RAY DIFFRACTION1allS266 - 272

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