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- PDB-7axp: Structural characterisation of WDR5:CS-VIP8 interaction in cis state 2 -

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Basic information

Entry
Database: PDB / ID: 7axp
TitleStructural characterisation of WDR5:CS-VIP8 interaction in cis state 2
Components
  • CS-VIP8
  • WD 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 ...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
WD repeat-containing protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.432 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 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 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 2.0Nov 15, 2023Group: Advisory / Atomic model / Data collection
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / pdbx_validate_polymer_linkage
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id
Revision 2.1Jan 31, 2024Group: Refinement description / Category: 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: CS-VIP8


Theoretical massNumber of molelcules
Total (without water)37,5512
Polymers37,5512
Non-polymers00
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area950 Å2
ΔGint-4 kcal/mol
Surface area11780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.240, 99.240, 98.520
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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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, component of MLL1 methyltransferase complex, chromatin regulator
Source: (gene. exp.) Homo sapiens (human) / Gene: WDR5, BIG3 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P61964
#2: Protein/peptide CS-VIP8


Mass: 915.999 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: cyclic peptide, cyclic strained visible-light photoswitch, WDR5-binder, disrupts MLL1 complex via MLL1-WDR5 inhibition
Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.76 Å3/Da / Density % sol: 67.3 %
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: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.432→64.765 Å / Num. obs: 155702 / % possible obs: 99.7 % / Redundancy: 13.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.086 / Net I/σ(I): 16.5
Reflection shellResolution: 2.432→2.519 Å / Redundancy: 12.8 % / Num. unique obs: 92 / CC1/2: 0.995 / % possible all: 0.998

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Processing

Software
NameVersionClassification
PHENIX1.16refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IAM

6iam


Resolution: 2.432→64.765 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 44.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3307 605 5.01 %
Rwork0.2672 11466 -
obs0.2703 12071 56.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 165.08 Å2 / Biso mean: 67.6577 Å2 / Biso min: 20.47 Å2
Refinement stepCycle: final / Resolution: 2.432→64.765 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2404 0 66 20 2490
Biso mean--65.2 53.89 -
Num. residues----304
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4323-2.67710.546300.5284359
2.6771-3.06450.4025690.4116144129
3.0645-3.86090.38592300.3102432685
3.8609-64.7650.30222760.245264100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.05140.0343-0.06570.0324-0.06710.1214-0.36110.02580.0463-0.229-0.1192-0.1971-0.25510.0065-0.69870.41650.30960.0581-0.1263-0.33610.0645-27.8708-18.1952-7.5868
20.09810.0113-0.03240.04760.02580.0388-0.0202-0.08570.1984-0.16730.0901-0.1099-0.1507-0.10310.0710.75140.2762-0.08020.2029-0.04890.3485-45.7482-20.2314-15.5011
30.0476-0.04130.02670.0627-0.03840.03120.02050.1587-0.1548-0.3754-0.04470.01120.06220.0995-0.04860.74240.23170.1974-0.0609-0.15770.2614-30.0845-32.6115-19.5271
40.04270.02580.01590.0275-0.01060.036-0.0015-0.0701-0.0010.03210.065-0.03040.0086-0.02550.04650.31170.2870.12570.4788-0.0840.5378-36.8683-31.71680.0372
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 30 through 148 )A30 - 148
2X-RAY DIFFRACTION2chain 'A' and (resid 149 through 228 )A149 - 228
3X-RAY DIFFRACTION3chain 'A' and (resid 229 through 333 )A229 - 333
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 7 )B1 - 7

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