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- PDB-6g95: Crystal structure of Ebolavirus glycoprotein in complex with thio... -

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Basic information

Entry
Database: PDB / ID: 6g95
TitleCrystal structure of Ebolavirus glycoprotein in complex with thioridazine
Components(Envelope glycoprotein) x 2
KeywordsVIRAL PROTEIN / Ebolavirus Glycoprotein / Thioridazine / Protein drug complex
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-RTZ / Envelope glycoprotein
Similarity search - Component
Biological speciesZaire ebolavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.31 Å
AuthorsZhao, Y. / Ren, J. / Fry, E.E. / Xiao, J. / Townsend, A.R. / Stuart, D.I.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom) United Kingdom
CitationJournal: J. Med. Chem. / Year: 2018
Title: Structures of Ebola Virus Glycoprotein Complexes with Tricyclic Antidepressant and Antipsychotic Drugs.
Authors: Zhao, Y. / Ren, J. / Fry, E.E. / Xiao, J. / Townsend, A.R. / Stuart, D.I.
History
DepositionApr 10, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)57,83215
Polymers55,2252
Non-polymers2,60713
Water1,69394
1
A: Envelope glycoprotein
B: Envelope glycoprotein
hetero molecules

A: Envelope glycoprotein
B: Envelope glycoprotein
hetero molecules

A: Envelope glycoprotein
B: Envelope glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,49645
Polymers165,6756
Non-polymers7,82139
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 area41120 Å2
ΔGint-89 kcal/mol
Surface area51800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.970, 113.970, 305.660
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 / GP1 / 2 / GP


Mass: 36302.719 Da / Num. of mol.: 1 / Mutation: T42A
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): HEK293 / 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): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q05320

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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


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-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, 102 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-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Chemical ChemComp-RTZ / 10-{2-[(2R)-1-methylpiperidin-2-yl]ethyl}-2-(methylsulfanyl)-10H-phenothiazine


Mass: 370.575 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H26N2S2 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 3.46 Å3/Da / Density % sol: 64.44 %
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 PILATUS 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: 2.31→82.9 Å / Num. obs: 33894 / % possible obs: 99.8 % / Redundancy: 35.6 % / CC1/2: 1 / Rmerge(I) obs: 0.083 / Net I/σ(I): 30.8
Reflection shellResolution: 2.31→2.35 Å / Redundancy: 10.5 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1662 / CC1/2: 0.67 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
xia2data reduction
xia2data scaling
RefinementResolution: 2.31→51.971 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.27
RfactorNum. reflection% reflection
Rfree0.2108 1652 4.88 %
Rwork0.1836 --
obs0.185 33886 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.31→51.971 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3001 0 167 94 3262
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063308
X-RAY DIFFRACTIONf_angle_d0.7674509
X-RAY DIFFRACTIONf_dihedral_angle_d21.091921
X-RAY DIFFRACTIONf_chiral_restr0.045517
X-RAY DIFFRACTIONf_plane_restr0.004564
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.31-2.3780.33891290.29032668X-RAY DIFFRACTION99
2.378-2.45480.27741180.24582633X-RAY DIFFRACTION100
2.4548-2.54250.26511370.22332650X-RAY DIFFRACTION100
2.5425-2.64430.27331510.2052649X-RAY DIFFRACTION100
2.6443-2.76460.29751340.21372662X-RAY DIFFRACTION100
2.7646-2.91040.25131480.20022656X-RAY DIFFRACTION100
2.9104-3.09270.25541490.20532648X-RAY DIFFRACTION100
3.0927-3.33140.26361300.19252680X-RAY DIFFRACTION100
3.3314-3.66660.22781340.17462714X-RAY DIFFRACTION100
3.6666-4.1970.15291170.15722717X-RAY DIFFRACTION100
4.197-5.28690.14611360.15082733X-RAY DIFFRACTION100
5.2869-51.98410.2171690.19892824X-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)
15.196-4.88985.51684.6794-5.20295.8398-0.2577-1.1763-1.2151.36090.91680.31390.0881-1.6409-0.44231.01740.05350.04760.76340.00620.6616-57.425811.44270.7621
23.78755.1114-3.67659.2923-1.91167.9948-0.1678-0.9935-1.5031.4363-0.0346-0.53910.79590.03930.09390.72190.01950.15840.57020.04970.7507-59.544719.00295.7536
32.56690.37120.0984.89044.36613.9292-0.1453-0.04370.13780.00060.4414-0.82230.34760.886-0.16920.70860.03460.02080.48460.0790.5536-51.278513.3623-10.9402
42.2557-0.5426-0.67442.64860.92213.223-0.00650.2963-0.1497-0.3835-0.09850.10260.3131-0.1990.10890.5372-0.03610.0340.357-0.01290.3952-56.255312.3192-29.1627
50.607-0.5206-0.9214.65842.55533.0806-0.18720.233-0.0743-0.24670.2309-0.59950.64610.7117-0.17690.51680.10650.00630.5280.01830.5355-48.09519.367-21.424
63.6199-4.4994-3.53236.99472.17427.7771-0.02050.2731-0.2248-0.5007-0.07470.29560.4749-0.31630.37290.9841-0.0472-0.0130.5912-0.0580.5859-56.94320.3606-40.6989
76.6709-0.8726-1.70286.47921.489.2527-0.64090.1119-0.73740.08180.4079-0.22841.21550.24340.17261.06250.05040.16170.5382-0.07140.6361-45.1901-5.6012-38.8769
88.97821.1355-0.76253.46571.49556.4528-1.14060.7449-1.3893-0.80780.3302-1.09341.3188-0.08370.55581.66790.04140.29170.7336-0.24420.8283-46.2553-9.4163-46.5098
90.02810.0245-0.07656.44445.40874.6411-0.31660.177-0.09790.54120.23160.52260.82370.5391-0.0281.67670.17880.02580.8504-0.08570.9693-45.0734-11.802-31.5109
105.88013.3982-1.28485.2239-2.34275.3368-0.07030.0191-0.39330.20410.0931-0.01350.5791-0.2085-0.00840.66260.05440.05540.4706-0.0060.5404-51.37854.8796-10.4647
110.4391-0.27280.5284.39081.77623.37220.4388-0.8275-1.1032.02090.68591.22271.58550.4187-0.80581.02570.25760.03931.26350.32391.7747-33.010526.6172-13.0432
121.720.59980.07511.6667-0.4382.10720.0231-0.0222-0.02750.0719-0.112-0.06940.23930.03160.07270.5250.00420.01790.40860.0010.4408-51.078516.6228-14.2487
135.7045-0.1346-0.11916.11943.87847.3391-0.0463-0.9966-0.38231.1012-0.02390.75360.9546-0.96280.17960.67310.02110.06660.5770.08490.5395-60.521727.22868.1165
142.70551.6444-0.72742.83181.47612.14860.85471.02021.0712-1.1714-1.0917-1.7179-0.2665-2.34160.7631.8650.2541-0.14221.8950.01671.3217-49.78131.497837.3049
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 32 through 45 )
2X-RAY DIFFRACTION2chain 'A' and (resid 46 through 59 )
3X-RAY DIFFRACTION3chain 'A' and (resid 60 through 73 )
4X-RAY DIFFRACTION4chain 'A' and (resid 74 through 176 )
5X-RAY DIFFRACTION5chain 'A' and (resid 177 through 223 )
6X-RAY DIFFRACTION6chain 'A' and (resid 224 through 237 )
7X-RAY DIFFRACTION7chain 'A' and (resid 238 through 262 )
8X-RAY DIFFRACTION8chain 'A' and (resid 263 through 282 )
9X-RAY DIFFRACTION9chain 'A' and (resid 283 through 311 )
10X-RAY DIFFRACTION10chain 'B' and (resid 502 through 520 )
11X-RAY DIFFRACTION11chain 'B' and (resid 521 through 530 )
12X-RAY DIFFRACTION12chain 'B' and (resid 531 through 583 )
13X-RAY DIFFRACTION13chain 'B' and (resid 584 through 612 )
14X-RAY DIFFRACTION14chain 'B' and (resid 613 through 631 )

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