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- PDB-6byn: Crystal structure of WDR5-Mb(S4) monobody complex -

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Basic information

Entry
Database: PDB / ID: 6byn
TitleCrystal structure of WDR5-Mb(S4) monobody complex
Components
  • WD repeat-containing protein 5
  • WDR5-binding Monobody, Mb(S4)
KeywordsTRANSCRIPTION / Beta-propeller / fibronectin / MLL1 / inhibitor
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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
WD repeat-containing protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsGupta, A. / Koide, S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)RO1 DA036887 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)RO1 CA194864-01A1 United States
CitationJournal: Nat. Chem. Biol. / Year: 2018
Title: Facile target validation in an animal model with intracellularly expressed monobodies.
Authors: Gupta, A. / Xu, J. / Lee, S. / Tsai, S.T. / Zhou, B. / Kurosawa, K. / Werner, M.S. / Koide, A. / Ruthenburg, A.J. / Dou, Y. / Koide, S.
History
DepositionDec 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
W: WD repeat-containing protein 5
M: WDR5-binding Monobody, Mb(S4)


Theoretical massNumber of molelcules
Total (without water)44,0882
Polymers44,0882
Non-polymers00
Water1,24369
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-6 kcal/mol
Surface area16220 Å2
Unit cell
Length a, b, c (Å)79.078, 48.266, 99.825
Angle α, β, γ (deg.)90.0, 107.741, 90.0
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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


Mass: 33650.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WDR5, BIG3 / Plasmid: pHBT
Details (production host): His6 tag, biotin-acceptor tag and TEV protease containing vector
Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61964
#2: Protein WDR5-binding Monobody, Mb(S4)


Mass: 10437.721 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pHBT
Details (production host): His6 tag, Biotin-acceptor tag and TEV protease site containing plasmid vector
Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.07 Å3/Da / Density % sol: 40.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 28% PEG3350, 0.1 M BisTris pH 5.5

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 23, 2013
RadiationMonochromator: Si (111) Rosenbaum-Rock double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.69→47.54 Å / Num. obs: 10148 / % possible obs: 99.72 % / Redundancy: 6.5 % / Biso Wilson estimate: 36.2 Å2 / Rpim(I) all: 0.049 / Net I/σ(I): 20.9
Reflection shellResolution: 2.69→2.79 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 4 / Num. unique obs: 953 / Rpim(I) all: 0.203 / % possible all: 97.44

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2H9N, 3UYO

2h9n

3uyo


Resolution: 2.69→47.58 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 25.9
RfactorNum. reflection% reflection
Rfree0.2484 489 4.8 %
Rwork0.2156 --
obs0.21718 10144 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 36.16 Å2
Refinement stepCycle: LAST / Resolution: 2.69→47.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3063 0 0 69 3132
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002151609276383166
X-RAY DIFFRACTIONf_angle_d0.6859025601474322
X-RAY DIFFRACTIONf_chiral_restr0.0277190254946492
X-RAY DIFFRACTIONf_plane_restr0.00297785119154537
X-RAY DIFFRACTIONf_dihedral_angle_d11.25975904851095
LS refinement shellResolution: 2.6895→3.0786 Å
RfactorNum. reflection% reflection
Rfree0.3235 161 -
Rwork0.2681 3183 -
obs--99.2 %

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