[English] 日本語
Yorodumi
- PDB-8t55: Co-crystal structure of the WD-repeat domain of human WDR91 in co... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8t55
TitleCo-crystal structure of the WD-repeat domain of human WDR91 in complex with MR46654
ComponentsWD repeat-containing protein 91
KeywordsTRANSPORT PROTEIN / WD-repeat / WDR / WDR91 / SGC / covalent ligand / Structural Genomics / PSI-2 / Protein Structure Initiative / Structural Genomics Consortium
Function / homology
Function and homology information


phosphatidylinositol 3-kinase inhibitor activity / extrinsic component of endosome membrane / phosphatidylinositol 3-kinase regulator activity / early endosome to late endosome transport / regulation of protein catabolic process / CDC42 GTPase cycle / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / late endosome membrane / early endosome membrane / endosome membrane / cytosol
Similarity search - Function
WD repeat-containing protein 91 / Anaphase-promoting complex subunit 4, WD40 domain / Anaphase-promoting complex subunit 4 WD40 domain / 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
Chem-ZI3 / WD repeat-containing protein 91
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsAhmad, H. / Zeng, H. / Dong, A. / Li, Y. / Yen, H. / Seitova, A. / Xu, J. / Feng, J.W. / Brown, P.J. / Santhakumar, V. ...Ahmad, H. / Zeng, H. / Dong, A. / Li, Y. / Yen, H. / Seitova, A. / Xu, J. / Feng, J.W. / Brown, P.J. / Santhakumar, V. / Ackloo, S. / Arrowsmith, C.H. / Edwards, A.M. / Halabelian, L. / Structural Genomics Consortium (SGC)
Funding support Canada, 1items
OrganizationGrant numberCountry
Other private Canada
CitationJournal: J.Med.Chem. / Year: 2023
Title: Discovery of a First-in-Class Small-Molecule Ligand for WDR91 Using DNA-Encoded Chemical Library Selection Followed by Machine Learning.
Authors: Ahmad, S. / Xu, J. / Feng, J.A. / Hutchinson, A. / Zeng, H. / Ghiabi, P. / Dong, A. / Centrella, P.A. / Clark, M.A. / Guie, M.A. / Guilinger, J.P. / Keefe, A.D. / Zhang, Y. / Cerruti, T. / ...Authors: Ahmad, S. / Xu, J. / Feng, J.A. / Hutchinson, A. / Zeng, H. / Ghiabi, P. / Dong, A. / Centrella, P.A. / Clark, M.A. / Guie, M.A. / Guilinger, J.P. / Keefe, A.D. / Zhang, Y. / Cerruti, T. / Cuozzo, J.W. / von Rechenberg, M. / Bolotokova, A. / Li, Y. / Loppnau, P. / Seitova, A. / Li, Y.Y. / Santhakumar, V. / Brown, P.J. / Ackloo, S. / Halabelian, L.
History
DepositionJun 12, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Source and taxonomy / Category: chem_comp_atom / chem_comp_bond / entity_src_gen
Revision 1.2May 1, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: WD repeat-containing protein 91
B: WD repeat-containing protein 91
C: WD repeat-containing protein 91
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,8067
Polymers118,5473
Non-polymers1,2594
Water4,216234
1
A: WD repeat-containing protein 91
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9152
Polymers39,5161
Non-polymers3991
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: WD repeat-containing protein 91
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9773
Polymers39,5161
Non-polymers4612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: WD repeat-containing protein 91
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9152
Polymers39,5161
Non-polymers3991
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.696, 121.618, 132.027
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein WD repeat-containing protein 91


Mass: 39515.785 Da / Num. of mol.: 3 / Fragment: WD repeat domains / Mutation: 15-residue deletion within the WD3 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WDR91, HSPC049 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A4D1P6
#2: Chemical ChemComp-ZI3 / N-[3-(4-chlorophenyl)oxetan-3-yl]-1-propanoyl-1,2,3,4-tetrahydroquinoline-5-carboxamide


Mass: 398.883 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C22H23ClN2O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.65 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 12% (w/v) PEG3350, 0.2 M KCl, 0.1 M MES pH 6.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 62021 / % possible obs: 97.9 % / Redundancy: 7.7 % / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.032 / Rrim(I) all: 0.086 / Χ2: 0.922 / Net I/σ(I): 6.2 / Num. measured all: 478836
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.2-2.248.21.01430750.8260.9510.3751.0830.72498.4
2.24-2.2880.84330950.8820.9680.3140.9010.75798.6
2.28-2.3280.71630950.9180.9780.2670.7650.71798.7
2.32-2.377.90.61630650.9360.9830.2320.6590.73398.9
2.37-2.427.70.55330880.9430.9850.2110.5930.73398.9
2.42-2.487.40.45131210.9580.9890.1760.4850.7598.8
2.48-2.547.40.35928420.9750.9940.1370.3860.75291
2.54-2.618.20.31330880.9820.9950.1150.3340.76799.1
2.61-2.698.30.25631220.990.9970.0930.2730.79499
2.69-2.778.30.19731110.9930.9980.0720.210.79899.1
2.77-2.878.20.15731220.9950.9990.0580.1680.80699
2.87-2.998.10.13531360.9960.9990.050.1440.83499.6
2.99-3.127.90.09831170.9970.9990.0370.1050.8699.2
3.12-3.297.70.07931390.99810.030.0850.93399.4
3.29-3.497.20.06331730.99910.0260.0681.0299.1
3.49-3.767.10.05928620.99810.0240.0641.1390.5
3.76-4.147.60.05431660.99810.0210.0581.17299.1
4.14-4.7470.0531950.99810.0220.0551.35398.9
4.74-5.976.80.04831900.9980.9990.0210.0531.3598.1
5.97-507.20.05232190.99910.020.0561.65794.2

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-3000data scaling
PHASERphasing
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→38.78 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.94 / SU B: 14.599 / SU ML: 0.179 / Cross valid method: THROUGHOUT / ESU R: 0.271 / ESU R Free: 0.226 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28777 1207 1.9 %RANDOM
Rwork0.24466 ---
obs0.2455 60770 97.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.441 Å2
Baniso -1Baniso -2Baniso -3
1--1.21 Å2-0 Å20 Å2
2--0.78 Å2-0 Å2
3---0.43 Å2
Refinement stepCycle: 1 / Resolution: 2.2→38.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7238 0 4 234 7476
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0137462
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176616
X-RAY DIFFRACTIONr_angle_refined_deg1.271.65110155
X-RAY DIFFRACTIONr_angle_other_deg1.1791.58715291
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4085968
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.99922.368321
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.187151117
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8731536
X-RAY DIFFRACTIONr_chiral_restr0.0520.2993
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028469
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021563
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2232.9643890
X-RAY DIFFRACTIONr_mcbond_other1.2232.9643889
X-RAY DIFFRACTIONr_mcangle_it2.0494.4394852
X-RAY DIFFRACTIONr_mcangle_other2.0484.4394853
X-RAY DIFFRACTIONr_scbond_it1.4133.0833572
X-RAY DIFFRACTIONr_scbond_other1.4133.0833573
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2824.5735297
X-RAY DIFFRACTIONr_long_range_B_refined5.09333.7777418
X-RAY DIFFRACTIONr_long_range_B_other5.07633.5717380
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.492 72 -
Rwork0.406 4424 -
obs--97.21 %
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)
12.9512-0.5079-0.07122.7479-0.66231.6135-0.1166-0.0840.1878-0.06620.0998-0.08370.16050.16050.01680.04630.0054-0.02320.0623-0.03420.072481.935937.80412.1056
22.87230.56420.20712.8029-0.69271.6827-0.10350.0769-0.17420.09560.1139-0.1022-0.22690.1607-0.01040.07530.00670.01380.0644-0.03750.081481.813422.981253.894
35.209-0.82111.59740.8067-0.84793.7680.1191-0.0338-0.72810.10010.05910.25850.1645-0.2625-0.17820.47880.0505-0.00730.77560.00010.812746.835220.676528.6401
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A394 - 729
2X-RAY DIFFRACTION2B394 - 801
3X-RAY DIFFRACTION3C395 - 728

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more