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- PDB-7axs: Structural characterisation of WDR5:CS-VIP8 interaction in cis state 1 -

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Basic information

Entry
Database: PDB / ID: 7axs
TitleStructural characterisation of WDR5:CS-VIP8 interaction in cis state 1
Components
  • CS-VIP8, (ALQ)(4FO)R(ABA)(DPN)(EDN)(S7Z)
  • 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 / 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
WD repeat-containing protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 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 2.0Jul 19, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_validate_close_contact / pdbx_validate_polymer_linkage / struct_conf / struct_conn / 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_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.type_symbol / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_label_seq_id / _entity.details / _entity.pdbx_description / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_poly_seq.mon_id / _entity_src_gen.gene_src_common_name / _pdbx_nonpoly_scheme.auth_seq_num / _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 / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg
Revision 3.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / pdbx_validate_polymer_linkage / struct_conn
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 / _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

Downloads & links

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Assembly

Deposited unit
A: WD repeat-containing protein 5
B: CS-VIP8, (ALQ)(4FO)R(ABA)(DPN)(EDN)(S7Z)


Theoretical massNumber of molelcules
Total (without water)37,5792
Polymers37,5792
Non-polymers00
Water5,134285
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-5 kcal/mol
Surface area12870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.022, 47.163, 133.460
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, (ALQ)(4FO)R(ABA)(DPN)(EDN)(S7Z)


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
Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / 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: 1.99 Å3/Da / Density % sol: 38.19 %
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: 1.88→44.51 Å / Num. obs: 22302 / % possible obs: 89.52 % / Redundancy: 1.9 % / Biso Wilson estimate: 21.76 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.02852 / Rpim(I) all: 0.02852 / Rrim(I) all: 0.04034 / Net I/σ(I): 13.12
Reflection shellResolution: 1.88→1.948 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.2242 / Mean I/σ(I) obs: 2.78 / Num. unique obs: 3521 / CC1/2: 0.894 / Rpim(I) all: 0.2242 / Rrim(I) all: 0.3171 / % possible all: 77.66

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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: 1.88→44.468 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2347 1123 5.04 %RANDOM
Rwork0.1996 21174 --
obs0.2013 22297 89.53 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.33 Å2 / Biso mean: 24.978 Å2 / Biso min: 11.92 Å2
Refinement stepCycle: final / Resolution: 1.88→44.468 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2485 0 66 285 2836
Biso mean--30.02 34.46 -
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 (%)
1.8805-1.96610.28731180.2835226078
1.9661-2.06970.28681150.2313236782
2.0697-2.19940.27941380.2174247185
2.1994-2.36920.23181380.2087255787
2.3692-2.60760.24911580.2082262090
2.6076-2.98490.23381410.204283895
2.9849-3.76030.22271680.1846293799
3.7603-44.4680.21031470.1824312499
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)
10.8417-0.20030.09060.2192-0.05150.148-0.0061-0.02830.09010.0271-0.0103-0.0226-0.0314-0.112-0.00060.1696-0.0028-0.00580.1586-0.02370.1841-11.67721.455713.6554
20.6206-0.1268-0.08090.3526-0.09430.2106-0.0417-0.04880.04070.0904-0.02-0.0346-0.0080.1609-00.16430.0004-0.01270.1741-0.02290.16175.8696-7.469912.9322
30.3033-0.1735-0.12880.6722-0.48050.7768-0.0188-0.1122-0.07680.02050.0198-0.04930.0482-0.0119-0.00030.1835-0.004-0.01240.187-0.02060.1749-10.2298-13.948923.7011
40.09850.0488-0.27370.0238-0.13530.75990.0296-0.0046-0.03190.00050.065-0.0039-0.05920.18270.0420.13810.0193-0.06010.30090.05410.2846-12.2227-15.44692.1234
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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