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- PDB-6f6n: CRYSTAL STRUCTURE OF EBOLAVIRUS GLYCOPROTEIN IN COMPLEX WITH SERT... -

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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


symbiont-mediated killing of host cell / 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 / host cell cytoplasm / entry receptor-mediated virion attachment to host cell / symbiont-mediated suppression of host innate immune response / membrane raft / fusion of virus membrane with host endosome membrane ...symbiont-mediated killing of host cell / 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 / host cell cytoplasm / entry receptor-mediated virion attachment to host cell / symbiont-mediated suppression of host innate immune response / membrane raft / fusion of virus membrane with host endosome membrane / viral envelope / lipid binding / symbiont entry into host cell / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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Components

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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

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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: 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

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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
#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

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Details

Has protein modificationY

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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: 3.52 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

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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

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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 )

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