[English] 日本語
Yorodumi
- PDB-6f6s: CRYSTAL STRUCTURE OF EBOLAVIRUS GLYCOPROTEIN IN COMPLEX WITH benz... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6f6s
TitleCRYSTAL STRUCTURE OF EBOLAVIRUS GLYCOPROTEIN IN COMPLEX WITH benztropine
Components
  • Envelope glycoprotein
  • Envelope glycoprotein,Envelope glycoprotein,GP1
KeywordsVIRAL PROTEIN / EBOLA VIRUS / FILOVIRIDAE / ENVELOPE GLYCOPROTEIN / PROTEIN INHIBITOR COMPLEX / IBUPROFEN / benztropine / bepridil / paroxetine / sertraline / TOREMIFENE
Function / homology
Function and homology information


host cell endoplasmic reticulum / viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / suppression by virus of host tetherin activity / host cell cytoplasm / entry receptor-mediated virion attachment to host cell / symbiont entry into host cell / membrane raft / fusion of virus membrane with host endosome membrane / viral envelope ...host cell endoplasmic reticulum / viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / suppression by virus of host tetherin activity / host cell cytoplasm / entry receptor-mediated virion attachment to host cell / symbiont entry into host cell / membrane raft / fusion of virus membrane with host endosome membrane / viral envelope / lipid binding / host cell plasma membrane / virion membrane / extracellular region / identical protein binding / membrane
Similarity search - Function
Filoviruses glycoprotein, extracellular domain / Filoviruses glycoprotein / Filovirus glycoprotein
Similarity search - Domain/homology
benztropine / Envelope glycoprotein / Envelope glycoprotein
Similarity search - Component
Biological speciesZaire ebolavirus
Ebola virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsRen, J. / Zhao, Y. / Fry, E.E. / Stuart, D.I.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
UKMR/N00065X/1 United Kingdom
Citation
Journal: J. Med. Chem. / Year: 2018
Title: Target Identification and Mode of Action of Four Chemically Divergent Drugs against Ebolavirus Infection.
Authors: Ren, J. / Zhao, Y. / Fry, E.E. / Stuart, D.I.
#1: Journal: Nature / Year: 2016
Title: Toremifene interacts with and destabilizes the Ebola virus glycoprotein.
Authors: Zhao, Y. / Ren, J. / Harlos, K. / Jones, D.M. / Zeltina, A. / Bowden, T.A. / Padilla-Parra, S. / Fry, E.E. / Stuart, D.I.
History
DepositionDec 6, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 3, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation / Item: _citation.title / _citation.year
Revision 1.2Feb 21, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_special_symmetry / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Envelope glycoprotein,Envelope glycoprotein,GP1
B: Envelope glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,33727
Polymers55,1402
Non-polymers3,19725
Water1,26170
1
A: Envelope glycoprotein,Envelope glycoprotein,GP1
B: Envelope glycoprotein
hetero molecules

A: Envelope glycoprotein,Envelope glycoprotein,GP1
B: Envelope glycoprotein
hetero molecules

A: Envelope glycoprotein,Envelope glycoprotein,GP1
B: Envelope glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,01181
Polymers165,4206
Non-polymers9,59175
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area48440 Å2
ΔGint-40 kcal/mol
Surface area49410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.379, 114.379, 305.749
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11B-710-

DMS

-
Components

-
Protein , 2 types, 2 molecules AB

#1: Protein Envelope glycoprotein,Envelope glycoprotein,GP1 / GP1 / 2 / GP


Mass: 36217.613 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: mutation T42A,mutation T42A,mutation T42A
Source: (gene. exp.) Zaire ebolavirus (strain Mayinga-76), (gene. exp.) Ebola virus
Strain: Mayinga-76 / Gene: GP / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q05320
#2: Protein Envelope glycoprotein


Mass: 18922.320 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: mutation, H613A / Source: (gene. exp.) Ebola virus
Gene: GP, DF49_53415gpGP, DF49_53416gpGP, DF49_53417gpGP, DF49_53418gpGP, DF49_53419gpGP, DF49_53420gpGP, DF49_53421gpGP, DF49_53422gpGP, DF49_53423gpGP, DF49_53424gpGP, DF49_53425gpGP, DF49_53426gpGP
Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: A0A0U3BWW0, UniProt: Q05320*PLUS

-
Sugars , 1 types, 5 molecules

#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 4 types, 90 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CXQ / benztropine


Mass: 307.429 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H25NO / Comment: medication, antipsychotic*YM
#6: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.83 Å3/Da / Density % sol: 67.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.2
Details: 9% (W/V) PEG 6000 AND 0.1 M SODIUM CITRATE TRIBASIC DIHYDRATE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.29→60.515 Å / Num. obs: 35081 / % possible obs: 100 % / Redundancy: 18.4 % / CC1/2: 1 / Rmerge(I) obs: 0.063 / Net I/σ(I): 21.9
Reflection shellResolution: 2.29→2.33 Å / Redundancy: 10.8 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1727 / CC1/2: 0.795 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(dev_2940: ???)refinement
xia2data reduction
xia2data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5jq3

5jq3


Resolution: 2.29→60.515 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.28
RfactorNum. reflection% reflection
Rfree0.2328 1755 5.06 %
Rwork0.2069 --
obs0.2083 34650 98.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.29→60.515 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2973 0 198 70 3241
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023243
X-RAY DIFFRACTIONf_angle_d0.5574401
X-RAY DIFFRACTIONf_dihedral_angle_d18.9981843
X-RAY DIFFRACTIONf_chiral_restr0.047494
X-RAY DIFFRACTIONf_plane_restr0.003547
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.29-2.35190.42351510.40852365X-RAY DIFFRACTION95
2.3519-2.42110.39141200.37642466X-RAY DIFFRACTION97
2.4211-2.49930.39511150.35362483X-RAY DIFFRACTION97
2.4993-2.58860.38611540.31722476X-RAY DIFFRACTION98
2.5886-2.69230.31371270.28612496X-RAY DIFFRACTION99
2.6923-2.81480.3181470.25482494X-RAY DIFFRACTION99
2.8148-2.96320.28251310.22212536X-RAY DIFFRACTION99
2.9632-3.14880.25651380.21652536X-RAY DIFFRACTION100
3.1488-3.39190.21791090.19732577X-RAY DIFFRACTION100
3.3919-3.73320.21161350.17412557X-RAY DIFFRACTION100
3.7332-4.27330.19131200.16852602X-RAY DIFFRACTION100
4.2733-5.38340.20651350.16782615X-RAY DIFFRACTION100
5.3834-60.53590.20761730.2132692X-RAY DIFFRACTION100
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)
18.1913-1.81613.88459.0336-1.53477.9086-0.0319-1.1441-0.52581.1250.22140.22291.0764-0.7804-0.30640.7543-0.03080.16670.53190.01540.4338-60.278513.49750.6927
22.0250.1208-0.45547.89756.52638.4812-0.1934-0.3446-0.07190.31860.3875-0.43920.72710.8839-0.02360.52020.0724-0.00460.45470.06820.468-52.727516.2369-3.242
33.3851-0.5062-0.11183.29531.03134.6119-0.0390.4357-0.1647-0.6582-0.17690.15420.3625-0.22540.21210.7428-0.04280.05070.3927-0.00250.4261-56.633212.539-29.0349
41.9617-0.902-0.90786.60854.20367.5325-0.19880.2976-0.0923-0.25680.1623-0.53220.50570.5368-0.05640.57660.06330.09010.36220.03520.4894-48.71719.4732-21.9165
52.7028-4.14650.10316.80490.25424.6455-0.28680.2494-0.6863-0.7417-0.06870.26231.3759-0.26840.24171.4417-0.13320.11510.7461-0.12270.6466-54.1867-1.7484-40.5239
62.8740.65921.06965.8199-0.68125.3563-0.38680.1779-0.5655-0.66350.0065-0.54161.39060.12860.38511.5720.12140.32490.7166-0.11810.8509-44.6256-7.8346-38.3066
71.00450.2718-1.26921.61170.35612.1888-1.1688-0.0959-0.21021.10380.11371.21310.59770.50410.85711.99620.1561-0.02991.0258-0.12591.4319-46.7161-14.2031-47.8982
83.29854.2121-3.58436.7357-4.95185.89550.3701-0.1758-0.2240.8055-0.4042-0.14680.3601-0.2061-0.02720.76240.03650.03740.4138-0.05330.5499-49.33857.6824-10.4952
94.71073.7939-5.23445.0991-1.34462.00880.08910.2864-0.6588-0.116-0.0339-0.36260.4760.9351-0.22010.79950.13180.08050.8931-0.02670.9696-32.136628.0837-21.6812
101.1105-0.01210.18212.7628-0.21593.9304-0.0969-0.1309-0.11130.2671-0.1123-0.29390.62680.01820.15520.5777-0.04090.04760.2995-0.01990.4985-54.916210.6677-10.5743
112.2216-1.53630.60224.6174-5.19876.7303-0.51690.10430.8072-0.5611-1.38740.7552-0.56851.09422.05950.9753-0.2004-0.09580.71090.01950.971-62.962929.4028-16.7117
125.82960.1459-0.34277.47553.59797.2291-0.3065-1.0461-0.32691.1126-0.35380.76220.7202-1.31940.49440.6175-0.00920.06720.57040.07380.5127-60.93327.49158.7912
138.7188-6.2653-7.0368.8361.55918.6251-0.7449-1.93711.35811.20172.2265-1.693-1.415-3.0772-0.56282.09790.8043-0.13212.2944-0.16411.6345-50.248130.005533.3394
141.97363.72983.07017.02985.78454.7554-0.6563-0.46490.3013-2.21610.09671.3862-2.30961.93650.89992.2037-0.5516-0.15631.83660.11982.0281-49.807235.70448.7607
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 31 through 50 )
2X-RAY DIFFRACTION2chain 'A' and (resid 51 through 73 )
3X-RAY DIFFRACTION3chain 'A' and (resid 74 through 176 )
4X-RAY DIFFRACTION4chain 'A' and (resid 177 through 223 )
5X-RAY DIFFRACTION5chain 'A' and (resid 224 through 249 )
6X-RAY DIFFRACTION6chain 'A' and (resid 250 through 305 )
7X-RAY DIFFRACTION7chain 'A' and (resid 306 through 477 )
8X-RAY DIFFRACTION8chain 'B' and (resid 502 through 526 )
9X-RAY DIFFRACTION9chain 'B' and (resid 527 through 541 )
10X-RAY DIFFRACTION10chain 'B' and (resid 542 through 575 )
11X-RAY DIFFRACTION11chain 'B' and (resid 576 through 583 )
12X-RAY DIFFRACTION12chain 'B' and (resid 584 through 612 )
13X-RAY DIFFRACTION13chain 'B' and (resid 613 through 625 )
14X-RAY DIFFRACTION14chain 'B' and (resid 626 through 632 )

+
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