[English] 日本語
Yorodumi
- PDB-6f6n: CRYSTAL STRUCTURE OF EBOLAVIRUS GLYCOPROTEIN IN COMPLEX WITH SERT... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6f6n
TitleCRYSTAL STRUCTURE OF EBOLAVIRUS GLYCOPROTEIN IN COMPLEX WITH SERTRALINE
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 / symbiont-mediated-mediated suppression of host tetherin activity / entry receptor-mediated virion attachment to host cell / host cell cytoplasm / symbiont-mediated suppression of host innate immune response / membrane raft / symbiont entry into host cell / fusion of virus membrane with host endosome membrane ...host cell endoplasmic reticulum / viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / symbiont-mediated-mediated suppression of host tetherin activity / entry receptor-mediated virion attachment to host cell / host cell cytoplasm / symbiont-mediated suppression of host innate immune response / membrane raft / symbiont entry into host cell / fusion of virus membrane with host endosome membrane / lipid binding / viral envelope / host cell plasma membrane / virion membrane / extracellular region / identical protein binding / membrane
Similarity search - Function
: / Filoviruses glycoprotein, extracellular domain / Filoviruses glycoprotein / Filovirus glycoprotein / Envelope glycoprotein GP2-like, HR1-HR2
Similarity search - Domain/homology
Chem-SRE / Envelope glycoprotein / Envelope glycoprotein
Similarity search - Component
Biological speciesZaire ebolavirus
Ebola virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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 5, 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
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.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
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)57,86614
Polymers55,2252
Non-polymers2,64012
Water2,342130
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)173,59742
Polymers165,6756
Non-polymers7,92136
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 area41340 Å2
ΔGint-96 kcal/mol
Surface area51780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.250, 114.250, 306.190
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

-
Components

-
Protein , 2 types, 2 molecules AB

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


Mass: 36302.719 Da / Num. of mol.: 1 / Mutation: T42A,T42A
Source method: isolated from a genetically manipulated source
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 , 2 types, 5 molecules

#3: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#4: 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.: 4
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, 137 molecules

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


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-SRE / (1S,4S)-4-(3,4-dichlorophenyl)-N-methyl-1,2,3,4-tetrahydronaphthalen-1-amine / Sertraline


Mass: 306.230 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H17Cl2N / Comment: medication, antidepressant, inhibitor*YM
#7: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.52 Å3/Da / Density % sol: 65.06 %
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 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.15→60.54 Å / Num. obs: 42259 / % possible obs: 100 % / Redundancy: 66 % / CC1/2: 1 / Rmerge(I) obs: 0.11 / Net I/σ(I): 34.2
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 14.2 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2065 / CC1/2: 0.708 / % 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: 2.15→60.54 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.51
RfactorNum. reflection% reflection
Rfree0.2035 1997 4.73 %
Rwork0.1839 --
obs0.1849 42255 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.15→60.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3001 0 171 130 3302
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043259
X-RAY DIFFRACTIONf_angle_d0.6894444
X-RAY DIFFRACTIONf_dihedral_angle_d20.011890
X-RAY DIFFRACTIONf_chiral_restr0.052514
X-RAY DIFFRACTIONf_plane_restr0.005554
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.20380.25881190.27332870X-RAY DIFFRACTION100
2.2038-2.26340.24021440.23112816X-RAY DIFFRACTION100
2.2634-2.330.21251510.20412846X-RAY DIFFRACTION100
2.33-2.40520.24891260.20032848X-RAY DIFFRACTION100
2.4052-2.49110.2091690.21072831X-RAY DIFFRACTION100
2.4911-2.59090.23981270.21172859X-RAY DIFFRACTION100
2.5909-2.70880.23561630.20032821X-RAY DIFFRACTION100
2.7088-2.85160.24621410.20312876X-RAY DIFFRACTION100
2.8516-3.03030.21341500.19012848X-RAY DIFFRACTION100
3.0303-3.26420.21671520.19352872X-RAY DIFFRACTION100
3.2642-3.59270.19811160.17822902X-RAY DIFFRACTION100
3.5927-4.11240.17941400.1582894X-RAY DIFFRACTION100
4.1124-5.18080.16211470.15032932X-RAY DIFFRACTION100
5.1808-60.56790.22351520.20213043X-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)
12.3143-0.67281.56842.4577-1.02953.4303-0.3182-0.7483-0.42351.03250.43220.29870.4661-0.6697-0.14410.71070.01530.05270.4580.05310.4146-58.73813.20811.3016
21.2535-0.16060.31833.71522.22832.7917-0.1418-0.17550.0260.62280.3686-0.28490.64410.5464-0.16940.56840.02980.02180.42450.03280.4775-52.259116.3571-3.2734
31.9125-0.542-0.75192.02870.08662.0658-0.02860.2455-0.1031-0.3025-0.12190.10030.2565-0.12450.13320.4933-0.02450.03260.3622-0.02830.4077-56.212212.44-29.0378
40.8572-0.3383-0.75732.34180.94483.4091-0.12940.1393-0.117-0.0390.0365-0.24130.40270.4230.02210.46420.0670.02830.41030.00650.5213-48.65629.5427-22.124
54.3917-3.6799-1.30353.17450.60224.2256-0.1643-0.1057-0.1383-0.610.15120.1820.6376-0.29810.07591.0407-0.13060.07470.6774-0.09230.6031-56.970.6151-40.67
62.0918-0.0836-1.57841.8767-0.70614.9745-0.4099-0.0605-0.4273-0.22620.04940.07540.99520.10380.36331.0150.05560.1720.5499-0.06220.6404-45.0785-5.3546-38.883
74.17341.1067-0.52094.1492-1.27542.2782-0.23340.4943-1.2263-1.0622-0.0602-0.79480.9529-0.29190.22391.4391-0.00620.23110.6625-0.16070.7907-46.0605-9.164-46.4973
80.14840.1461-0.02330.7891.22342.3207-0.03210.1373-0.1363-0.03040.04690.37180.55750.36620.13411.42510.15250.12230.8145-0.10341.018-45.6816-11.6011-35.2639
92.18920.93160.46133.2273-0.09822.10870.0788-0.1408-0.02880.822-0.17440.21570.4468-0.00870.0160.65120.00960.09670.40160.0060.5201-51.48614.15-10.148
106.17074.2686-0.57654.23171.73123.61520.2008-1.7911-0.06540.7720.00510.49141.22830.53310.01430.44930.1294-0.00120.92590.48431.4322-34.031326.1417-12.785
111.12860.8332-0.47820.82190.15650.83240.0368-0.0261-0.01540.115-0.1309-0.05270.20750.03460.08880.45080.02350.01290.41310.02960.479-50.888916.9908-14.3297
123.0303-0.56620.15713.30241.59575.9206-0.2099-0.8802-0.45990.9166-0.13380.60410.7582-0.7270.45410.5898-0.00410.06560.56790.080.4659-60.594627.24968.5565
131.58850.45180.88730.7719-0.31150.99260.20840.65550.94-0.3561-1.43640.36090.1552-0.19211.33722.1675-0.0812-0.09041.96140.0621.2794-49.955332.090738.687
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 32 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 237 )
6X-RAY DIFFRACTION6chain 'A' and (resid 238 through 262 )
7X-RAY DIFFRACTION7chain 'A' and (resid 263 through 282 )
8X-RAY DIFFRACTION8chain 'A' and (resid 283 through 477 )
9X-RAY DIFFRACTION9chain 'B' and (resid 502 through 519 )
10X-RAY DIFFRACTION10chain 'B' and (resid 520 through 529 )
11X-RAY DIFFRACTION11chain 'B' and (resid 530 through 583 )
12X-RAY DIFFRACTION12chain 'B' and (resid 584 through 612 )
13X-RAY DIFFRACTION13chain 'B' and (resid 613 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://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