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- PDB-7axq: Structure of the cryo-trapped WDR5:CS-VIP8 cocrystal after illumi... -

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Basic information

Entry
Database: PDB / ID: 7axq
TitleStructure of the cryo-trapped WDR5:CS-VIP8 cocrystal after illumination at 405 nm and 180 K
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


histone H3Q5ser reader activity / histone H3K4me1 reader activity / Epigenetic regulation of gene expression by MLL3 and MLL4 complexes / MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / Cardiogenesis ...histone H3Q5ser reader activity / histone H3K4me1 reader activity / Epigenetic regulation of gene expression by MLL3 and MLL4 complexes / MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / Cardiogenesis / Formation of WDR5-containing histone-modifying complexes / histone methyltransferase complex / regulation of cell division / MLL1 complex / regulation of embryonic development / histone acetyltransferase complex / positive regulation of gluconeogenesis / transcription initiation-coupled chromatin remodeling / gluconeogenesis / skeletal system development / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / PKMTs methylate histone lysines / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / mitotic spindle / HATs acetylate histones / Neddylation / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / 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
WDR5 beta-propeller domain / 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. / 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: 1.562 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 2.0Mar 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_validate_rmsd_angle / struct_conf / struct_conn / struct_ref / struct_ref_seq
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _entity.details / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_poly.pdbx_strand_id / _entity_poly_seq.mon_id / _entity_src_gen.gene_src_common_name / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_poly_seq_scheme.pdb_strand_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_seq_id
Revision 3.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_label_atom_id
Revision 3.1Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 4.0Jul 10, 2024Group: Data collection / Derived calculations ...Data collection / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / entity / struct_conn
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: WD repeat-containing protein 5
C: CS-VIP8


Theoretical massNumber of molelcules
Total (without water)37,5792
Polymers37,5792
Non-polymers00
Water4,252236
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint-5 kcal/mol
Surface area12800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.000, 47.250, 133.620
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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, 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: 943.966 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,cyclic peptide, cyclic strained visible-light photoswitch, WDR5-binder, ...Details: cyclic peptide, cyclic strained visible-light photoswitch, WDR5-binder, disrupts MLL1 complex via MLL1-WDR5 inhibition,cyclic peptide, cyclic strained visible-light photoswitch, WDR5-binder, disrupts MLL1 complex via MLL1-WDR5 inhibition,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


Mass: 18.015 Da / Num. of mol.: 236 / 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: 2 Å3/Da / Density % sol: 38.35 %
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: 1.56→44.59 Å / Num. obs: 42057 / % possible obs: 97.56 % / Redundancy: 6.4 % / Biso Wilson estimate: 20.92 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.0902 / Net I/σ(I): 10.78
Reflection shellResolution: 1.562→1.618 Å / Rmerge(I) obs: 1.096 / Mean I/σ(I) obs: 1.34 / Num. unique obs: 3264 / CC1/2: 0.552

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Processing

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

6iam


Resolution: 1.562→44.547 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2002 2187 5.2 %RANDOM
Rwork0.1674 39870 --
obs0.1691 42057 97.48 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 95.06 Å2 / Biso mean: 23.1909 Å2 / Biso min: 10.71 Å2
Refinement stepCycle: final / Resolution: 1.562→44.547 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2485 0 66 236 2787
Biso mean--22.19 31.15 -
Num. residues----313
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.562-1.59570.2582780.2565155862
1.5957-1.63280.27941540.2582249899
1.6328-1.67360.28251450.23652509100
1.6736-1.71890.24961520.22682480100
1.7189-1.76950.25791500.21972516100
1.7695-1.82660.24731180.21512537100
1.8266-1.89190.29381720.2012508100
1.8919-1.96760.20791480.17452535100
1.9676-2.05720.20321300.16762519100
2.0572-2.16560.20561310.16582540100
2.1656-2.30130.20631250.16782572100
2.3013-2.4790.23371400.17572564100
2.479-2.72840.23561140.17392565100
2.7284-3.12310.22151420.17242604100
3.1231-3.93440.17141390.14692637100
3.9344-44.5470.13461490.13342728100

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