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- PDB-8q1n: Cyclic peptide binder of the WBM-site of WDR5 -

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Basic information

Entry
Database: PDB / ID: 8q1n
TitleCyclic peptide binder of the WBM-site of WDR5
Components
  • Cyclic peptide inhibitor
  • WD repeat-containing protein 5
KeywordsGENE REGULATION / Inhibitor / WD-Repeat
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: 1.843 Å
AuthorsSchmeing, S. / Chang, J.Y. / t Hart, P. / Gasper, R.
Funding support Germany, Taiwan, 2items
OrganizationGrant numberCountry
Other private Germany
Other government Taiwan
CitationJournal: Chem.Commun.(Camb.) / Year: 2023
Title: Macrocyclic peptides as inhibitors of WDR5-lncRNA interactions.
Authors: Chang, J.Y. / Neugebauer, C. / Schmeing, S. / Amrahova, G. / 't Hart, P.
History
DepositionAug 1, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 6, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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
a: Cyclic peptide inhibitor
b: Cyclic peptide inhibitor


Theoretical massNumber of molelcules
Total (without water)73,1094
Polymers73,1094
Non-polymers00
Water7,837435
1
A: WD repeat-containing protein 5
a: Cyclic peptide inhibitor


Theoretical massNumber of molelcules
Total (without water)36,5542
Polymers36,5542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-5 kcal/mol
Surface area14210 Å2
MethodPISA
2
B: WD repeat-containing protein 5
b: Cyclic peptide inhibitor


Theoretical massNumber of molelcules
Total (without water)36,5542
Polymers36,5542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area870 Å2
ΔGint-5 kcal/mol
Surface area13930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.174, 82.174, 201.707
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-592-

HOH

21A-672-

HOH

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Components

#1: Protein WD repeat-containing protein 5


Mass: 35279.004 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WDR5 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61964
#2: Protein/peptide Cyclic peptide inhibitor


Mass: 1275.315 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 435 / 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: 2.33 Å3/Da / Density % sol: 47.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.2M Li3-Citrate, 20 w/v% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.843→42.98 Å / Num. obs: 58518 / % possible obs: 96.59 % / Redundancy: 26.7 % / CC1/2: 0.995 / Net I/σ(I): 8.05
Reflection shellResolution: 1.843→1.909 Å / Mean I/σ(I) obs: 0.26 / Num. unique obs: 3960 / CC1/2: 0.361 / % possible all: 66.37

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Processing

Software
NameVersionClassification
PHENIX(1.20.1-4487_4487: ???)refinement
DIALSdata scaling
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.843→42.98 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2432 3022 5.16 %
Rwork0.1978 --
obs0.2002 58518 96.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.843→42.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5105 0 0 435 5540
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011
X-RAY DIFFRACTIONf_angle_d1.243
X-RAY DIFFRACTIONf_dihedral_angle_d7.793712
X-RAY DIFFRACTIONf_chiral_restr0.073826
X-RAY DIFFRACTIONf_plane_restr0.009902
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.843-1.870.402500.40711059X-RAY DIFFRACTION41
1.87-1.90.39361290.39292169X-RAY DIFFRACTION86
1.9-1.940.39981360.38092537X-RAY DIFFRACTION99
1.94-1.970.36231260.37182581X-RAY DIFFRACTION100
1.97-2.010.37121290.34082570X-RAY DIFFRACTION100
2.01-2.050.3741360.31412579X-RAY DIFFRACTION100
2.05-2.090.35271370.29832566X-RAY DIFFRACTION100
2.09-2.140.33781370.27462561X-RAY DIFFRACTION100
2.14-2.20.32791480.24852581X-RAY DIFFRACTION100
2.2-2.260.27361390.24482582X-RAY DIFFRACTION100
2.26-2.320.30071420.25022581X-RAY DIFFRACTION100
2.32-2.40.30911380.25022593X-RAY DIFFRACTION100
2.4-2.480.29361490.24612595X-RAY DIFFRACTION100
2.48-2.580.30691570.25592575X-RAY DIFFRACTION100
2.58-2.70.28791640.23732580X-RAY DIFFRACTION100
2.7-2.840.27711380.22192626X-RAY DIFFRACTION100
2.84-3.020.30031370.2162611X-RAY DIFFRACTION100
3.02-3.250.25661340.20742654X-RAY DIFFRACTION100
3.25-3.580.20911380.16782655X-RAY DIFFRACTION100
3.58-4.10.20341360.15052669X-RAY DIFFRACTION100
4.1-5.160.17451510.12932706X-RAY DIFFRACTION100
5.16-42.980.1941710.16662866X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -10.1294 Å / Origin y: -30.6504 Å / Origin z: 26.2009 Å
111213212223313233
T0.2053 Å20.0364 Å20.008 Å2-0.382 Å20.0187 Å2--0.2315 Å2
L0.9603 °20.5151 °20.0507 °2-1.7655 °2-0.2155 °2--0.3267 °2
S0.0384 Å °0.0203 Å °-0.1074 Å °-0.0314 Å °-0.0831 Å °-0.0231 Å °0.0646 Å °0.116 Å °0.04 Å °
Refinement TLS groupSelection details: all

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