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- PDB-7cfq: Crystal structure of WDR5 in complex with H3K4me3Q5ser peptide -

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Basic information

Entry
Database: PDB / ID: 7cfq
TitleCrystal structure of WDR5 in complex with H3K4me3Q5ser peptide
Components
  • H3K4me3Q5ser peptide
  • WD repeat-containing protein 5
KeywordsGENE REGULATION / Histone modification
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 / histone acetyltransferase complex / positive regulation of gluconeogenesis / methylated histone binding / transcription initiation-coupled chromatin remodeling / 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
SEROTONIN / WD repeat-containing protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsZhao, J. / Zhang, X. / Zang, J.
CitationJournal: Sci Adv / Year: 2021
Title: Structural insights into the recognition of histone H3Q5 serotonylation by WDR5.
Authors: Zhao, J. / Chen, W. / Pan, Y. / Zhang, Y. / Sun, H. / Wang, H. / Yang, F. / Liu, Y. / Shen, N. / Zhang, X. / Mo, X. / Zang, J.
History
DepositionJun 27, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 19, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: WD repeat-containing protein 5
B: H3K4me3Q5ser peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4625
Polymers38,1312
Non-polymers3303
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-3 kcal/mol
Surface area11840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.356, 98.377, 80.338
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-668-

HOH

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#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
Source: (gene. exp.) Homo sapiens (human) / Gene: WDR5, BIG3 / Production host: Escherichia coli (E. coli) / References: UniProt: P61964
#2: Protein/peptide H3K4me3Q5ser peptide


Mass: 1495.704 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 4 types, 182 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-SRO / SEROTONIN / 3-(2-AMINOETHYL)-1H-INDOL-5-OL


Mass: 176.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12N2O / Comment: neurotransmitter*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.02 Å3/Da / Density % sol: 39.16 %
Crystal growTemperature: 295 K / Method: vapor diffusion
Details: 0.15M ammonium sulfate, 0.1M MES pH 5.5, 25% PEG 4000, 2% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 41189 / % possible obs: 100 % / Redundancy: 13.1 % / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.023 / Rrim(I) all: 0.082 / Χ2: 0.999 / Net I/σ(I): 6.9 / Num. measured all: 538967
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2
1.6-1.6312.80.27520390.9730.080.2870.737
1.63-1.6613.40.26220230.9740.0740.2730.807
1.66-1.6913.30.24620250.9760.070.2550.865
1.69-1.7213.20.22420390.9820.0640.2330.907
1.72-1.7613.10.20420270.9830.0590.2130.952
1.76-1.812.50.19120410.9810.0560.21.095
1.8-1.8512.60.16920450.9860.0490.1761.092
1.85-1.913.30.15120470.9910.0430.1571.084
1.9-1.9513.60.13620440.9920.0380.1411.092
1.95-2.0213.40.12420350.9930.0350.1291.016
2.02-2.0913.10.11720540.9920.0330.1211.082
2.09-2.1712.50.10520540.9940.0310.1091.056
2.17-2.2712.80.10120450.9940.0290.1051.002
2.27-2.3913.60.09220550.9950.0260.0961.067
2.39-2.5413.50.08320670.9960.0230.0861.061
2.54-2.7413.10.07620670.9970.0220.0791.074
2.74-3.0112.80.06720740.9980.0190.071.078
3.01-3.4513.70.0620850.9980.0170.0620.918
3.45-4.3412.60.05221040.9980.0150.0540.961
4.34-5012.80.05222190.9970.0150.0551.029

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2gnq

2gnq


Resolution: 1.6→49.24 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.946 / SU B: 1.245 / SU ML: 0.045 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.081 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1896 2086 5.1 %RANDOM
Rwork0.1631 ---
obs0.1645 39078 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 71.56 Å2 / Biso mean: 13.319 Å2 / Biso min: 7.28 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å2-0 Å2
2--0.4 Å20 Å2
3----0.53 Å2
Refinement stepCycle: final / Resolution: 1.6→49.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2421 0 10 179 2610
Biso mean--21.56 21.13 -
Num. residues----311
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0132510
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172322
X-RAY DIFFRACTIONr_angle_refined_deg1.4171.6393404
X-RAY DIFFRACTIONr_angle_other_deg1.3951.5965423
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2935317
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.55124.14199
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.34615436
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.751155
X-RAY DIFFRACTIONr_chiral_restr0.0680.2335
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022752
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02501
LS refinement shellResolution: 1.6→1.642 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.233 152 -
Rwork0.173 2781 -
all-2933 -
obs--96.83 %

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