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- PDB-7axu: Structure of WDR5:CS-VIP8 cocrystal after illumination in situ -

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Basic information

Entry
Database: PDB / ID: 7axu
TitleStructure of WDR5:CS-VIP8 cocrystal after illumination in situ
ComponentsWD repeat-containing protein 5
KeywordsTRANSFERASE / WDR5 / cyclic strained visible-light photoswitches / MLL1 complex disruption / inhibition of hematopoiesis
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
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
Similarity search - Domain/homology
WD repeat-containing protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsWerel, L. / Essen, L.-O.
CitationJournal: Acs Cent.Sci. / Year: 2022
Title: Bistable Photoswitch Allows in Vivo Control of Hematopoiesis.
Authors: Albert, L. / Nagpal, J. / Steinchen, W. / Zhang, L. / Werel, L. / Djokovic, N. / Ruzic, D. / Hoffarth, M. / Xu, J. / Kaspareit, J. / Abendroth, F. / Royant, A. / Bange, G. / Nikolic, K. / ...Authors: Albert, L. / Nagpal, J. / Steinchen, W. / Zhang, L. / Werel, L. / Djokovic, N. / Ruzic, D. / Hoffarth, M. / Xu, J. / Kaspareit, J. / Abendroth, F. / Royant, A. / Bange, G. / Nikolic, K. / Ryu, S. / Dou, Y. / Essen, L.O. / Vazquez, O.
History
DepositionNov 10, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 24, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 15, 2021Group: Database references / Category: citation / citation_author / Item: _citation.title
Revision 1.2Feb 16, 2022Group: 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 / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: WD repeat-containing protein 5


Theoretical massNumber of molelcules
Total (without water)36,6351
Polymers36,6351
Non-polymers00
Water7,062392
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.387, 47.172, 133.499
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 / BMP2-induced 3-kb gene protein


Mass: 36635.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: WDR5, cyclic strained visible-light photoswitches, MLL1 complex disruption, inhibition of hematopoiesis
Source: (gene. exp.) Homo sapiens (human) / Gene: WDR5, BIG3 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P61964
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 392 / 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: 2.04 Å3/Da / Density % sol: 39.6 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 10% (w/v) PEG20000, 20% (v/v) PEG550 MME, 0.02 M sodium formate, 0.02 M ammonium acetate, 0.02 M trisodium citrate, 0.02 M sodium potassium L-tartrate, 0.02 M sodium oxamate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.68→44.7 Å / Num. obs: 34930 / % possible obs: 99.84 % / Redundancy: 2 % / Biso Wilson estimate: 16.1 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.02835 / Rpim(I) all: 0.02835 / Rrim(I) all: 0.04009 / Net I/σ(I): 15.39
Reflection shellResolution: 1.68→1.74 Å / Redundancy: 2 % / Rmerge(I) obs: 0.1981 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 6864 / CC1/2: 0.922 / Rpim(I) all: 0.1981 / Rrim(I) all: 0.2802 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.16refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IAM

6iam


Resolution: 1.68→44.7 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.81 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.1933 1800 5.1 %RANDOM
Rwork0.15889 ---
obs0.16064 33154 99.76 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.39 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20 Å2
2--0.33 Å2-0 Å2
3----0.26 Å2
Refinement stepCycle: LAST / Resolution: 1.68→44.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2420 0 0 392 2812
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0192512
X-RAY DIFFRACTIONr_bond_other_d0.0010.022302
X-RAY DIFFRACTIONr_angle_refined_deg1.7711.8713415
X-RAY DIFFRACTIONr_angle_other_deg1.1932.9335389
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6435321
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.65125.31994
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.67415436
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.255153
X-RAY DIFFRACTIONr_chiral_restr0.1220.2386
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022779
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02488
X-RAY DIFFRACTIONr_mcbond_it1.991.4881272
X-RAY DIFFRACTIONr_mcbond_other1.981.4861270
X-RAY DIFFRACTIONr_mcangle_it3.0282.2281594
X-RAY DIFFRACTIONr_mcangle_other3.0282.231595
X-RAY DIFFRACTIONr_scbond_it2.7171.7631240
X-RAY DIFFRACTIONr_scbond_other2.7141.7631239
X-RAY DIFFRACTIONr_scangle_other4.0252.5191820
X-RAY DIFFRACTIONr_long_range_B_refined6.27720.0382941
X-RAY DIFFRACTIONr_long_range_B_other5.96818.8652803
LS refinement shellResolution: 1.68→1.723 Å
RfactorNum. reflection% reflection
Rfree0.421 149 -
Rwork0.421 2349 -
obs--98.62 %

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