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- PDB-6nae: Crystal Structure of Ebola zaire GP protein with bound ARN0074898 -

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Basic information

Entry
Database: PDB / ID: 6nae
TitleCrystal Structure of Ebola zaire GP protein with bound ARN0074898
Components
  • Envelope glycoprotein
  • Envelope glycoprotein,Envelope glycoprotein,Envelope glycoprotein
KeywordsVIRAL PROTEIN / SSGCID / Ebola zaire / glycoprotein / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
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-mediated suppression of host innate immune response / symbiont entry into host cell / membrane raft / 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 / suppression by virus of host tetherin activity / host cell cytoplasm / entry receptor-mediated virion attachment to host cell / symbiont-mediated suppression of host innate immune response / symbiont entry into host cell / membrane raft / fusion of virus membrane with host endosome membrane / lipid binding / viral envelope / 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-KHG / Envelope glycoprotein
Similarity search - Component
Biological speciesZaire ebolavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.75 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Acs Med.Chem.Lett. / Year: 2020
Title: Discovery of Adamantane Carboxamides as Ebola Virus Cell Entry and Glycoprotein Inhibitors.
Authors: Plewe, M.B. / Sokolova, N.V. / Gantla, V.R. / Brown, E.R. / Naik, S. / Fetsko, A. / Lorimer, D.D. / Dranow, D.M. / Smutney, H. / Bullen, J. / Sidhu, R. / Master, A. / Wang, J. / Kallel, E.A. ...Authors: Plewe, M.B. / Sokolova, N.V. / Gantla, V.R. / Brown, E.R. / Naik, S. / Fetsko, A. / Lorimer, D.D. / Dranow, D.M. / Smutney, H. / Bullen, J. / Sidhu, R. / Master, A. / Wang, J. / Kallel, E.A. / Zhang, L. / Kalveram, B. / Freiberg, A.N. / Henkel, G. / McCormack, K.
History
DepositionDec 5, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Category: citation / citation_author / Item: _citation.journal_abbrev / _citation.title
Revision 1.2Jul 1, 2020Group: Data collection / Database references / Category: chem_comp / citation / citation_author
Item: _chem_comp.type / _citation.country ..._chem_comp.type / _citation.country / _citation.journal_abbrev / _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 / _citation_author.name
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 / _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 2.1Oct 11, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)57,84813
Polymers55,2252
Non-polymers2,62311
Water1,58588
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)173,54339
Polymers165,6756
Non-polymers7,86833
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 area38220 Å2
ΔGint-74 kcal/mol
Surface area46430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.250, 113.250, 307.210
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

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Protein , 2 types, 2 molecules AB

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


Mass: 36302.719 Da / Num. of mol.: 1
Fragment: EbzaA.19907.a.HE11,EbzaA.19907.a.HE11,EbzaA.19907.a.HE11,EbzaA.19907.a.HE11,EbzaA.19907.a.HE11,EbzaA.19907.a.HE11,EbzaA.19907.a.HE11,EbzaA.19907.a.HE11,EbzaA.19907.a.HE11
Mutation: T42A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zaire ebolavirus (strain Mayinga-76) / Strain: Mayinga-76 / Gene: GP / Plasmid: EbzaA.19907.a.HE11 / Production host: Homo sapiens (human) / Strain (production host): HEK-293 / 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 / Plasmid: EbzaA.19907.a.HE11 / Production host: Homo sapiens (human) / Strain (production host): HEK-293 / References: UniProt: Q05320

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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: obtained synthetically / 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

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Non-polymers , 3 types, 94 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-KHG / (1S,3R,5R,7S)-N-(trans-4-aminocyclohexyl)-3-methyl-5-phenyltricyclo[3.3.1.1~3,7~]decane-1-carboxamide


Mass: 366.540 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C24H34N2O
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.47 Å3/Da / Density % sol: 64.55 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.1
Details: EbzaA.19907.a.HE11.PD38326 at 6.01 mg /ml and mixed 1:1 with an opt screen based on JCSG+(b8): 11 % (w/v) PEG-8000, 0.1 M Tris base/ HCl, pH = 7.1, 200 mM MgCl2, Crystals were soaked with 1 ...Details: EbzaA.19907.a.HE11.PD38326 at 6.01 mg /ml and mixed 1:1 with an opt screen based on JCSG+(b8): 11 % (w/v) PEG-8000, 0.1 M Tris base/ HCl, pH = 7.1, 200 mM MgCl2, Crystals were soaked with 1 mM ARN0074898 for 4 hours and cryoprotected with 20% glyerol. Tray: 303411b4, puck: jvo4-3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 5, 2018 / Details: Beryllium Lenses
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.75→49.554 Å / Num. obs: 20154 / % possible obs: 100 % / Redundancy: 7.409 % / Biso Wilson estimate: 57.765 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Rrim(I) all: 0.07 / Χ2: 1.038 / Net I/σ(I): 23.09 / Num. measured all: 149327
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.75-2.827.5370.5284.1514910.9470.567100
2.82-2.97.540.4175.2314220.9620.448100
2.9-2.987.5430.336.4713960.9790.355100
2.98-3.077.5360.2538.0413350.9870.27299.9
3.07-3.187.5320.2159.5213140.9860.231100
3.18-3.297.5330.1711.6912800.9930.183100
3.29-3.417.5310.12714.912270.9960.137100
3.41-3.557.4540.09619.2611840.9970.103100
3.55-3.717.4420.07624.1611350.9970.082100
3.71-3.897.4710.06627.2610990.9980.07100
3.89-4.17.4250.0513210330.9990.054100
4.1-4.357.3970.04337.189880.9990.046100
4.35-4.657.4210.03743.029220.9990.04100
4.65-5.027.330.03941.948730.9990.042100
5.02-5.57.2920.03941.178040.9990.042100
5.5-6.157.230.03741.197360.9990.04100
6.15-7.17.1760.03443.556550.9990.037100
7.1-8.77.0290.02951.885580.9990.031100
8.7-12.36.7150.02456.784420.9990.026100
12.3-49.5545.8460.02553.462600.9990.02896.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6f5u

6f5u


Resolution: 2.75→49.554 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.98
RfactorNum. reflection% reflection
Rfree0.2398 2076 10.31 %
Rwork0.1927 --
obs0.1974 20139 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 168.95 Å2 / Biso mean: 65.2952 Å2 / Biso min: 26.28 Å2
Refinement stepCycle: final / Resolution: 2.75→49.554 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2647 0 209 88 2944
Biso mean--100.14 55.22 -
Num. residues----348
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.75-2.8140.27691370.216411841321
2.814-2.88440.3441280.216712021330
2.8844-2.96230.25841270.199811931320
2.9623-3.04950.29341460.219311711317
3.0495-3.14790.30671520.220611761328
3.1479-3.26040.3161470.216911751322
3.2604-3.39090.25471560.205911711327
3.3909-3.54520.2441240.191412071331
3.5452-3.7320.20851430.182611901333
3.732-3.96580.21221410.176311941335
3.9658-4.27180.21511370.158112121349
4.2718-4.70140.17481470.152612031350
4.7014-5.3810.22831360.182212271363
5.381-6.77670.29181280.204212411369
6.7767-49.56170.2391270.226213171444

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