[English] 日本語
Yorodumi
- PDB-8b1s: co-crystal of SUDV VP40 with salicylic acid -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8b1s
Titleco-crystal of SUDV VP40 with salicylic acid
ComponentsMatrix protein VP40
KeywordsVIRAL PROTEIN / Ebola virus / SUDV / VP40 / matrix protein / dimer / co-crystallization / ligand / drug discovery
Function / homology
Function and homology information


host cell endomembrane system / host cell late endosome membrane / viral budding via host ESCRT complex / structural constituent of virion / symbiont-mediated suppression of host innate immune response / ribonucleoprotein complex / host cell plasma membrane / virion membrane / RNA binding / membrane
Similarity search - Function
EV matrix protein, C-terminal / EV matrix protein / EV matrix domain superfamily / EV matrix protein, N-terminal / Matrix protein VP40
Similarity search - Domain/homology
2-HYDROXYBENZOIC ACID / Matrix protein VP40
Similarity search - Component
Biological speciesSudan ebolavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsWerner, A.-D. / Krapoth, N. / Norris, M.J. / Heine, A. / Klebe, G. / Ollmann Saphire, E. / Becker, S.
Funding support Germany, 1items
OrganizationGrant numberCountry
LOEWE Center DRUID Germany
CitationJournal: Acs Omega / Year: 2024
Title: Development of a Crystallographic Screening to Identify Sudan Virus VP40 Ligands.
Authors: Werner, A.D. / Krapoth, N. / Norris, M.J. / Heine, A. / Klebe, G. / Saphire, E.O. / Becker, S.
History
DepositionSep 12, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2024Group: Structure summary / Category: audit_author
Revision 1.2Jul 31, 2024Group: 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.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3Aug 14, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Matrix protein VP40
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7422
Polymers32,6041
Non-polymers1381
Water2,396133
1
A: Matrix protein VP40
hetero molecules

A: Matrix protein VP40
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,4834
Polymers65,2072
Non-polymers2762
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area2390 Å2
ΔGint-4 kcal/mol
Surface area21690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.100, 90.623, 48.189
Angle α, β, γ (deg.)90.000, 94.255, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

-
Components

#1: Protein Matrix protein VP40 / Membrane-associated protein VP40


Mass: 32603.617 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sudan ebolavirus / Gene: VP40, DF49_53412gpVP40, DH33_45403gpVP40, SEBOVgp3 / Production host: Escherichia coli (E. coli) / References: UniProt: B0LPL6
#2: Chemical ChemComp-SAL / 2-HYDROXYBENZOIC ACID / SALICYLIC ACID


Mass: 138.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 2.08 Å3/Da / Density % sol: 40.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM HEPES 40 mM MgCl2 10% (v/v) PEG400 salicylic acid

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.999998 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999998 Å / Relative weight: 1
ReflectionResolution: 1.6→48.06 Å / Num. obs: 33883 / % possible obs: 97.7 % / Redundancy: 6.9 % / Biso Wilson estimate: 24.27 Å2 / CC1/2: 0.99 / Net I/σ(I): 21.8
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 3.8 / Num. unique obs: 1474 / CC1/2: 0.97 / % possible all: 86.7

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LD8

4ld8


Resolution: 1.6→45.31 Å / SU ML: 0.1882 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.8674
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.207 1621 4.79 %
Rwork0.1889 32221 -
obs0.1898 33842 97.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.95 Å2
Refinement stepCycle: LAST / Resolution: 1.6→45.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1844 0 10 133 1987
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00341922
X-RAY DIFFRACTIONf_angle_d0.71982636
X-RAY DIFFRACTIONf_chiral_restr0.0489324
X-RAY DIFFRACTIONf_plane_restr0.0051334
X-RAY DIFFRACTIONf_dihedral_angle_d12.2906700
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.650.29041390.23712495X-RAY DIFFRACTION91.11
1.65-1.710.2561320.21462663X-RAY DIFFRACTION97.18
1.71-1.770.23751380.20652681X-RAY DIFFRACTION97.75
1.77-1.840.21571440.19042683X-RAY DIFFRACTION98.23
1.84-1.920.22281430.19422664X-RAY DIFFRACTION97.91
1.92-2.020.25971100.19342682X-RAY DIFFRACTION95.98
2.02-2.150.23021400.19752689X-RAY DIFFRACTION98.43
2.15-2.310.21771400.20122730X-RAY DIFFRACTION99.07
2.31-2.550.21541520.20352717X-RAY DIFFRACTION99.07
2.55-2.920.22421400.20452656X-RAY DIFFRACTION96.81
2.92-3.670.19191170.18852802X-RAY DIFFRACTION99.69
3.67-45.310.1791260.16782759X-RAY DIFFRACTION98.4
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)
11.534087557891.78853770614-0.1531064505283.04334215086-0.3370162517840.842541174717-0.0364033499193-0.0230426570457-0.102566301849-0.1164157409780.01073068290440.005569796078710.158752110546-0.00166977719511-0.003544643414230.2760483604580.01013274003430.003698020700710.199848383280.001793869091760.199642883319-8.8859815189-23.104419117617.351274626
21.404035939430.9228944908250.2427255907492.826372901560.3564310949560.893035329523-0.00136319028402-0.01184625082570.0620301884983-0.0997222473183-0.03368248440920.3396597860550.0809287230416-0.1592719277520.04358885605140.2485023923-0.00659503347742-0.01079989134030.2080344194790.003901945130120.209374000293-16.1297864816-18.442012238217.5296408774
34.19943746787-0.5903667401451.69762887644.69631721626-1.901614228383.07774000181-0.141561526733-0.603546819070.1061450628240.0293847868260.265598034380.68356096480.0351883318041-0.696886869559-0.2247695848990.3678279760730.0258373020677-0.02841256030850.4094204287150.03358776708260.285127130624-19.646041474-4.553116566234.41285799582
42.8841306202-1.623858451581.931583234365.59346612017-2.494696740083.841941239720.1226691261160.2522399007650.291593002883-0.605443709038-0.0368757039330.1921245969110.437248067991-0.172622219013-0.06072166456530.394087524908-0.0285051516612-0.01791827325550.3355575238860.04636075516030.252353323928-15.2596339666-3.50252811771-3.82069146946
54.26501376621-1.150624264460.7796455045973.8640008818-2.990894487693.584991222230.204009271061-0.1056002600110.0517896281695-0.270091157369-0.02326830255470.2882734446860.318019428065-0.216199576261-0.1390692344660.522419086911-0.0568424318583-0.02764669078720.372946089493-0.0142963855180.239151384666-17.0138147229-8.52422519510.44480432832
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 45 through 94 )
2X-RAY DIFFRACTION2chain 'A' and (resid 95 through 185 )
3X-RAY DIFFRACTION3chain 'A' and (resid 186 through 235 )
4X-RAY DIFFRACTION4chain 'A' and (resid 236 through 272 )
5X-RAY DIFFRACTION5chain 'A' and (resid 273 through 311 )

+
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://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