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- PDB-7cfp: Crystal structure of WDR5 in complex with a H3Q5ser peptide -

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Basic information

Entry
Database: PDB / ID: 7cfp
TitleCrystal structure of WDR5 in complex with a H3Q5ser peptide
Components
  • H3Q5ser peptide
  • WD repeat-containing protein 5
KeywordsGENE REGULATION / complex / histone modification / reader
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 / Formation of WDR5-containing histone-modifying complexes / regulation of cell division / 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
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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: WD repeat-containing protein 5
B: H3Q5ser peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3073
Polymers38,1312
Non-polymers1761
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-6 kcal/mol
Surface area11800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.748, 99.411, 80.615
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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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
Source: (gene. exp.) Homo sapiens (human) / Gene: WDR5, BIG3 / Production host: Escherichia coli (E. coli) / References: UniProt: P61964
#2: Protein/peptide H3Q5ser peptide


Mass: 1495.704 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-SRO / SEROTONIN / 3-(2-AMINOETHYL)-1H-INDOL-5-OL / Serotonin


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


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

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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 Å3/Da / Density % sol: 38.5 %
Crystal growTemperature: 295 K / Method: vapor diffusion
Details: 0.1% Octylglucoside, 0.1M Sodium citrate tribasic dihydrate pH 5.5, 22% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 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: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 42035 / % possible obs: 100 % / Redundancy: 12.5 % / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.023 / Rrim(I) all: 0.082 / Χ2: 0.91 / Net I/σ(I): 5.5 / Num. measured all: 523644
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2
1.6-1.6312.10.61220890.9470.1830.6390.55
1.63-1.6612.80.5620560.9470.1620.5840.594
1.66-1.6912.80.53620660.9430.1540.5580.618
1.69-1.7212.70.46220730.9430.1340.4810.683
1.72-1.7612.60.40121030.9390.1170.4180.754
1.76-1.812.40.35820560.9540.1060.3740.813
1.8-1.8511.90.30120780.9680.090.3140.974
1.85-1.911.80.25520890.9740.0770.2671.02
1.9-1.9512.20.21720840.9820.0640.2261.101
1.95-2.02130.18820950.9850.0540.1951.062
2.02-2.0912.90.14920870.9930.0430.1550.913
2.09-2.1712.80.11820960.9950.0350.1230.816
2.17-2.2712.60.12820930.9950.0380.1331.104
2.27-2.3911.80.09520920.9960.0290.10.965
2.39-2.5412.40.08521220.9960.0250.0890.9
2.54-2.7413.20.07320900.9980.0210.0761.032
2.74-3.0112.90.06521380.9970.0190.0680.956
3.01-3.4511.90.05621140.9970.0170.0591.075
3.45-4.3412.60.04821520.9990.0140.051.062
4.34-5011.90.05322620.9960.0160.0551.192

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Processing

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

2gnq


Resolution: 1.6→49.06 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.665 / SU ML: 0.057 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.084 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1994 2046 4.9 %RANDOM
Rwork0.1743 ---
obs0.1755 39965 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 76.75 Å2 / Biso mean: 21.097 Å2 / Biso min: 13.38 Å2
Baniso -1Baniso -2Baniso -3
1-1.11 Å20 Å2-0 Å2
2--0.58 Å20 Å2
3----1.69 Å2
Refinement stepCycle: final / Resolution: 1.6→49.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2421 0 0 179 2600
Biso mean---27.12 -
Num. residues----311
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132497
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172295
X-RAY DIFFRACTIONr_angle_refined_deg1.5111.6393391
X-RAY DIFFRACTIONr_angle_other_deg1.3781.5955361
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4015315
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.06824.4998
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.64715431
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.26154
X-RAY DIFFRACTIONr_chiral_restr0.0740.2335
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022750
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02496
LS refinement shellResolution: 1.6→1.642 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 153 -
Rwork0.222 2907 -
all-3060 -
obs--99.87 %

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