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- PDB-6f6i: CRYSTAL STRUCTURE OF EBOLAVIRUS GLYCOPROTEIN IN COMPLEX WITH PARO... -

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Basic information

Entry
Database: PDB / ID: 6f6i
TitleCRYSTAL STRUCTURE OF EBOLAVIRUS GLYCOPROTEIN IN COMPLEX WITH PAROXETINE
Components
  • Envelope glycoprotein
  • Envelope glycoprotein,GP,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 / membrane => GO:0016020 / 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 / membrane => GO:0016020 / 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 / membrane / identical protein binding
Similarity search - Function
Filoviruses glycoprotein, extracellular domain / Filoviruses glycoprotein / Filovirus glycoprotein
Similarity search - Domain/homology
Paroxetine / GP / Envelope glycoprotein / Envelope glycoprotein / Envelope glycoprotein
Similarity search - Component
Biological speciesEbola virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)57,72714
Polymers55,2252
Non-polymers2,50112
Water1,856103
1
A: Envelope glycoprotein,GP,GP1
B: Envelope glycoprotein
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)173,18042
Polymers165,6756
Non-polymers7,50436
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 area40320 Å2
ΔGint-122 kcal/mol
Surface area51290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.680, 113.680, 306.260
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,GP,GP1


Mass: 36302.719 Da / Num. of mol.: 1 / Mutation: T42A,T42A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ebola virus / Gene: GP, DH33_45402gpGP / Cell line (production host): HEK293T / Production host: Homo sapiens (human)
References: UniProt: A0A0E3NBB1, UniProt: A0A0D5W976, UniProt: Q05320*PLUS
#2: Protein Envelope glycoprotein


Mass: 18922.320 Da / Num. of mol.: 1 / Mutation: H613A
Source method: isolated from a genetically manipulated source
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-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...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: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-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 / N-Acetylglucosamine


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, 110 molecules

#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-8PR / Paroxetine / (3S,4R)-3-[(1,3-benzodioxol-5-yloxy)methyl]-4-(4-fluorophenyl)piperidine / Paroxetine


Mass: 329.365 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H20FNO3 / Comment: antidepressant, inhibitor*YM
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 3.48 Å3/Da / Density % sol: 64.67 %
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: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.4→60.44 Å / Num. obs: 30184 / % possible obs: 99.8 % / Redundancy: 37.2 % / Biso Wilson estimate: 62 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.094 / Net I/σ(I): 28.9
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 13.6 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1446 / CC1/2: 0.697 / % possible all: 96.9

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Processing

Software
NameVersionClassification
PHENIX(dev_2940: ???)refinement
xia2data reduction
xia2data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JQ7

5jq7


Resolution: 2.4→52.008 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.76
RfactorNum. reflection% reflection
Rfree0.2118 1520 5.04 %
Rwork0.1921 --
obs0.1931 30173 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.4→52.008 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2987 0 164 103 3254
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033301
X-RAY DIFFRACTIONf_angle_d0.6494501
X-RAY DIFFRACTIONf_dihedral_angle_d19.5481918
X-RAY DIFFRACTIONf_chiral_restr0.045517
X-RAY DIFFRACTIONf_plane_restr0.004563
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.47750.38111420.32762546X-RAY DIFFRACTION98
2.4775-2.5660.29741310.2652546X-RAY DIFFRACTION100
2.566-2.66880.2611390.23332558X-RAY DIFFRACTION100
2.6688-2.79020.26231380.22312600X-RAY DIFFRACTION100
2.7902-2.93730.25371480.19822565X-RAY DIFFRACTION100
2.9373-3.12130.24611440.20982582X-RAY DIFFRACTION100
3.1213-3.36230.23141580.20052580X-RAY DIFFRACTION100
3.3623-3.70060.22941250.1792627X-RAY DIFFRACTION100
3.7006-4.23580.191400.1682609X-RAY DIFFRACTION100
4.2358-5.33580.15071260.15992661X-RAY DIFFRACTION100
5.3358-52.01990.20941290.20612779X-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)
11.8783-0.3041-2.76458.81740.32434.3858-0.0594-0.311-0.62071.35530.0720.07640.9402-0.39720.07930.7026-0.03460.08270.73350.03720.5256-58.791715.7573.5367
21.9166-0.6692-0.6562.9190.88242.7473-0.050.2211-0.1801-0.2289-0.08550.06790.4241-0.09970.12070.549-0.03820.06530.36070.00580.4243-55.319512.4012-27.0111
32.6565-1.2529-1.62195.10284.63587.1062-0.27350.06830.10540.03640.3212-0.50580.67210.8573-0.04420.57750.08530.01780.40080.05680.5271-47.88819.1913-22.1387
44.2407-1.9846-0.50177.30631.30215.6809-0.55620.3105-0.5471-0.36150.2308-0.0111.08110.17970.32151.1768-0.03060.14610.6186-0.08590.5773-47.7776-4.322-42.2413
50.0152-0.2582-0.49883.14615.33389.2928-0.49010.1933-0.17890.8472-0.18120.63592.5030.37560.5461.77140.18270.1191.0072-0.00531.1502-47.5741-12.4499-35.6302
67.24635.6288-1.6237.167-2.92044.7166-0.03380.0405-0.61370.7055-0.0499-0.33210.6627-0.1710.05570.81770.02310.09820.4885-0.02080.5757-50.91994.8333-10.4631
77.28733.99692.69744.2664-0.89053.6890.6607-1.2021-0.41321.8863-0.90260.2620.68050.3630.15521.08210.11830.14081.4054-0.06051.3529-32.649226.469-13.4086
81.24210.7746-0.13861.03040.38121.3952-0.00140.0512-0.03970.208-0.1569-0.1880.34980.09250.16560.56080.01340.02470.46830.03640.5273-50.843916.7687-14.4291
95.1217-0.0296-0.37915.82783.72927.7342-0.0807-0.9052-0.3341.0583-0.350.72361.1749-1.05710.42860.70680.00170.07660.62230.0650.5219-60.344827.11998.2641
101.0339-0.1-0.76850.84870.11554.56810.27690.65890.7071-0.2346-0.9534-0.4741.2616-1.63590.80481.90880.0625-0.08542.09040.01821.0758-49.692231.765438.2374
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 31 through 59 )
2X-RAY DIFFRACTION2chain 'A' and (resid 60 through 176 )
3X-RAY DIFFRACTION3chain 'A' and (resid 177 through 223 )
4X-RAY DIFFRACTION4chain 'A' and (resid 224 through 277 )
5X-RAY DIFFRACTION5chain 'A' and (resid 278 through 477 )
6X-RAY DIFFRACTION6chain 'B' and (resid 502 through 520 )
7X-RAY DIFFRACTION7chain 'B' and (resid 521 through 530 )
8X-RAY DIFFRACTION8chain 'B' and (resid 531 through 583 )
9X-RAY DIFFRACTION9chain 'B' and (resid 584 through 612 )
10X-RAY DIFFRACTION10chain 'B' and (resid 613 through 632 )

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