[English] 日本語
Yorodumi
- PDB-6hro: Crystal structure of Ebolavirus glycoprotein in complex with inhi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6hro
TitleCrystal structure of Ebolavirus glycoprotein in complex with inhibitor 118a
Components
  • Envelope glycoprotein
  • Envelope glycoprotein,Envelope glycoprotein,Envelope glycoprotein
KeywordsVIRAL PROTEIN / Ebola Glycoprotein / Structure-based In Silico Screening / 118a / Natural compound
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
Similarity search - Function
Filoviruses glycoprotein, extracellular domain / Filoviruses glycoprotein / Filovirus glycoprotein
Similarity search - Domain/homology
Chem-GKZ / Envelope glycoprotein
Similarity search - Component
Biological speciesZaire ebolavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsRen, J. / Zhao, Y. / Stuart, D.I.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
United Kingdom
CitationJournal: J.Med.Chem. / Year: 2019
Title: Structure-Based in Silico Screening Identifies a Potent Ebolavirus Inhibitor from a Traditional Chinese Medicine Library.
Authors: Shaikh, F. / Zhao, Y. / Alvarez, L. / Iliopoulou, M. / Lohans, C. / Schofield, C.J. / Padilla-Parra, S. / Siu, S.W.I. / Fry, E.E. / Ren, J. / Stuart, D.I.
History
DepositionSep 27, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2019Group: Data collection / Structure summary / Category: pdbx_seq_map_depositor_info / struct_keywords
Item: _pdbx_seq_map_depositor_info.one_letter_code_mod / _struct_keywords.pdbx_keywords / _struct_keywords.text
Revision 1.2Apr 10, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc / pdbx_seq_map_depositor_info
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name / _pdbx_seq_map_depositor_info.one_letter_code_mod
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)58,68515
Polymers55,3102
Non-polymers3,37513
Water2,486138
1
A: Envelope glycoprotein,Envelope glycoprotein,Envelope glycoprotein
B: Envelope glycoprotein
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)176,05645
Polymers165,9306
Non-polymers10,12639
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 area43260 Å2
ΔGint-93 kcal/mol
Surface area53960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.120, 115.120, 308.860
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,Envelope glycoprotein / GP1 / 2 / GP


Mass: 36387.824 Da / Num. of mol.: 1 / Mutation: T42A,T42A,T42A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zaire ebolavirus (strain Mayinga-76), (gene. exp.) Zaire ebolavirus
Strain: Mayinga-76 / Gene: GP / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q05320
#2: Protein Envelope glycoprotein / GP1 / 2 / GP


Mass: 18922.320 Da / Num. of mol.: 1 / Mutation: H613A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zaire ebolavirus (strain Mayinga-76) / Strain: Mayinga-76 / Gene: GP / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q05320

-
Sugars , 2 types, 6 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-Acetylglucosamine


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, 145 molecules

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


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-GKZ / 1-[2-[4-[4-(4-chlorophenyl)-3-methyl-1~{H}-pyrazol-5-yl]-3-oxidanyl-phenoxy]ethyl]piperidin-1-ium-4-carboxamide


Mass: 455.957 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H28ClN4O3
#7: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / 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 / Water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 3.56 Å3/Da / Density % sol: 65.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.2
Details: CRYSTALLIZATION CONDITIONS: 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: I04 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 2.3→83.76 Å / Num. obs: 35437 / % possible obs: 100 % / Redundancy: 91 % / Biso Wilson estimate: 65.2 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.098 / Net I/σ(I): 36.5
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 16.8 % / Mean I/σ(I) obs: 1.4 / CC1/2: 0.751 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
xia2data reduction
xia2data scaling
REFMACphasing
RefinementResolution: 2.3→83.759 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.49
RfactorNum. reflection% reflection
Rfree0.212 1696 4.79 %
Rwork0.1801 --
obs0.1818 35410 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→83.759 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3022 0 223 138 3383
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033340
X-RAY DIFFRACTIONf_angle_d0.6344558
X-RAY DIFFRACTIONf_dihedral_angle_d21.2761929
X-RAY DIFFRACTIONf_chiral_restr0.044521
X-RAY DIFFRACTIONf_plane_restr0.005566
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.36770.28521210.27542780X-RAY DIFFRACTION100
2.3677-2.44410.2941360.2522761X-RAY DIFFRACTION100
2.4441-2.53150.30071390.23742775X-RAY DIFFRACTION100
2.5315-2.63280.26641200.22192814X-RAY DIFFRACTION100
2.6328-2.75270.27051360.21312778X-RAY DIFFRACTION100
2.7527-2.89780.28181270.21232799X-RAY DIFFRACTION100
2.8978-3.07940.24561360.20272794X-RAY DIFFRACTION100
3.0794-3.31710.23551540.19392806X-RAY DIFFRACTION100
3.3171-3.6510.20291430.17352790X-RAY DIFFRACTION100
3.651-4.17930.18781500.15612832X-RAY DIFFRACTION100
4.1793-5.26530.16431870.1452815X-RAY DIFFRACTION100
5.2653-83.81450.23161470.19032970X-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)
12.90450.67890.85445.66691.90984.6041-0.0027-0.6291-0.02210.92190.0140.07610.72-0.29770.04880.73380.03330.06770.56690.06010.4787-56.35315.1028-1.488
21.3006-0.866-0.36462.56620.84593.1066-0.04110.3246-0.146-0.3163-0.13560.06230.4762-0.11260.1610.6214-0.03270.07520.4211-0.00550.4708-56.526512.4546-28.24
34.3243-1.3315-1.04724.44821.95019.4770.01830.3735-0.0343-0.29330.6331-1.32720.41622.07-0.56690.62610.09010.06190.37960.01470.8203-44.6878.0335-23.8551
43.3871-4.0062-0.72774.81230.25334.4029-0.38-0.0968-0.5499-0.37140.10060.36620.7197-0.0990.20641.2582-0.1680.11250.7868-0.14290.7342-54.0557-2.2998-40.9182
52.71951.6719-2.62647.1146-1.06832.6264-0.7336-0.0376-1.4565-0.18660.0756-1.3010.85731.7470.1191.22830.30170.21020.9184-0.01440.9274-40.3171-6.4724-38.3846
67.63652.2198-1.41172.6541-0.25278.1137-0.15980.6671-1.4025-1.15690.0644-1.0740.7524-0.12270.17641.5105-0.05740.25470.7362-0.270.7738-46.9148-9.6152-46.8889
70.12280.43290.64861.77223.10545.7651-0.4260.06140.03260.62330.14810.21951.90760.68360.27511.80930.40980.04271.0296-0.02241.2523-46.0264-12.5484-36.5023
83.42273.98612.81326.09980.55127.83750.32550.1366-0.21611.4297-0.31050.3571.333-0.38130.02951.1502-0.13410.1890.51830.02380.6851-56.4030.4727-8.3472
95.0614.7461-3.83964.4209-3.97164.06220.067-0.4196-0.1361-0.0205-0.542-0.77490.19250.70780.4920.52150.135-0.00110.70420.11320.6966-36.07123.27-17.4553
101.82743.9425-1.45379.6574-4.98524.2694-0.0931-0.12-0.27460.5289-0.2427-0.66790.6080.31380.1940.83180.0876-0.00370.66360.17440.7418-41.00339.0874-11.1906
110.8102-1.6261.41126.5206-1.63748.91380.3599-0.3229-0.42530.3868-0.277-0.24631.4730.0473-0.02020.9245-0.02750.10830.41040.02040.6211-54.47645.3311-6.5666
123.2201-1.23770.41812.6546-0.34234.5014-0.1538-0.20580.28310.16320.17740.55090.0179-0.6430.08210.536-0.03150.05520.5385-0.02770.5808-64.498821.9344-16.4787
135.5602-1.7656-2.11659.78346.01583.87410.0871-0.3574-0.55850.8122-0.13090.58570.6064-0.44830.08530.5546-0.02110.02360.46690.04680.5275-60.152227.11450.6864
142.13961.6192-1.77722.5315-2.55832.6235-0.4646-0.949-0.87961.1897-0.15080.80780.9554-1.40720.48441.33840.01820.16731.45190.1231.0678-62.168627.78217.594
158.9227-7.0453-2.22765.57481.75560.55550.52431.43871.0866-0.8006-0.3962-0.8986-0.3515-0.4174-0.04862.06450.33980.27322.59040.39181.7955-51.512129.082929.9938
161.49211.52721.30241.54451.32821.1270.62081.2082-0.27231.0051-0.848-1.52810.18860.84910.17561.9934-0.2499-0.15432.5666-0.00132.0026-49.760833.66843.7968
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 30 through 73 )
2X-RAY DIFFRACTION2chain 'A' and (resid 74 through 185 )
3X-RAY DIFFRACTION3chain 'A' and (resid 186 through 223 )
4X-RAY DIFFRACTION4chain 'A' and (resid 224 through 249 )
5X-RAY DIFFRACTION5chain 'A' and (resid 250 through 263 )
6X-RAY DIFFRACTION6chain 'A' and (resid 264 through 282 )
7X-RAY DIFFRACTION7chain 'A' and (resid 283 through 478 )
8X-RAY DIFFRACTION8chain 'B' and (resid 502 through 514 )
9X-RAY DIFFRACTION9chain 'B' and (resid 515 through 542 )
10X-RAY DIFFRACTION10chain 'B' and (resid 543 through 550 )
11X-RAY DIFFRACTION11chain 'B' and (resid 551 through 564 )
12X-RAY DIFFRACTION12chain 'B' and (resid 565 through 583 )
13X-RAY DIFFRACTION13chain 'B' and (resid 584 through 597 )
14X-RAY DIFFRACTION14chain 'B' and (resid 598 through 612 )
15X-RAY DIFFRACTION15chain 'B' and (resid 613 through 620 )
16X-RAY DIFFRACTION16chain 'B' and (resid 621 through 631 )

+
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