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- PDB-5jq7: Crystal structure of Ebola glycoprotein in complex with toremifene -

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Basic information

Entry
Database: PDB / ID: 5jq7
TitleCrystal structure of Ebola glycoprotein in complex with toremifene
Components(Envelope glycoprotein ...) x 2
KeywordsVIRAL PROTEIN / Ebola virus / Filoviridae / envelope glycoprotein / protein inhibitor complex / ibuprofen / 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 / 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
Toremifene / Envelope glycoprotein
Similarity search - Component
Biological speciesEbola virus - Mayinga
Zaire
1976
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsZhao, Y. / Ren, J. / Stuart, D.I.
CitationJournal: 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
DepositionMay 4, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2016Group: Database references
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 / pdbx_struct_special_symmetry / 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 / _pdbx_struct_special_symmetry.label_asym_id / _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 10, 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 1,Envelope glycoprotein 1,Envelope glycoprotein 1
B: Envelope glycoprotein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,59411
Polymers55,2922
Non-polymers2,3029
Water95553
1
A: Envelope glycoprotein 1,Envelope glycoprotein 1,Envelope glycoprotein 1
B: Envelope glycoprotein 2
hetero molecules

A: Envelope glycoprotein 1,Envelope glycoprotein 1,Envelope glycoprotein 1
B: Envelope glycoprotein 2
hetero molecules

A: Envelope glycoprotein 1,Envelope glycoprotein 1,Envelope glycoprotein 1
B: Envelope glycoprotein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,78233
Polymers165,8766
Non-polymers6,90527
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 area37690 Å2
ΔGint-86 kcal/mol
Surface area55690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.450, 113.450, 306.870
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11B-820-

HOH

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Components

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Envelope glycoprotein ... , 2 types, 2 molecules AB

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


Mass: 36302.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ebola virus - Mayinga, Zaire, 1976 / Gene: GP / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q05320
#2: Protein Envelope glycoprotein 2 / GP1 / 2 / GP


Mass: 18989.391 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ebola virus - Mayinga, Zaire, 1976 / Gene: GP / Cell line (production host): HEK293T / 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


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


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, 57 molecules

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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Chemical ChemComp-T0R / Toremifene


Mass: 405.960 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H28ClNO / Comment: medication*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 64.6 %
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: 0.97 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.69→51.15 Å / Num. obs: 21539 / % possible obs: 99.9 % / Redundancy: 9.8 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 20
Reflection shellResolution: 2.69→2.76 Å / Redundancy: 8.6 % / Mean I/σ(I) obs: 1.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
xia2data reduction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JQ3

5jq3


Resolution: 2.69→51.15 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.918 / SU B: 20.978 / SU ML: 0.209 / Cross valid method: THROUGHOUT / ESU R: 0.365 / ESU R Free: 0.267 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.245 1090 5.1 %RANDOM
Rwork0.203 ---
obs0.205 20449 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 92.64 Å2
Baniso -1Baniso -2Baniso -3
1-2.47 Å21.23 Å20 Å2
2--2.47 Å20 Å2
3----8 Å2
Refinement stepCycle: LAST / Resolution: 2.69→51.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3034 0 151 53 3238
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0193268
X-RAY DIFFRACTIONr_bond_other_d0.0010.023004
X-RAY DIFFRACTIONr_angle_refined_deg1.2861.9924448
X-RAY DIFFRACTIONr_angle_other_deg0.86736910
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1735382
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.17324.11146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.31815485
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2291518
X-RAY DIFFRACTIONr_chiral_restr0.0650.2507
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213618
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02756
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7796.1791546
X-RAY DIFFRACTIONr_mcbond_other1.7786.1751545
X-RAY DIFFRACTIONr_mcangle_it3.2299.2331922
X-RAY DIFFRACTIONr_mcangle_other3.2299.2381923
X-RAY DIFFRACTIONr_scbond_it2.0376.6961722
X-RAY DIFFRACTIONr_scbond_other2.0366.7011723
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5089.9722527
X-RAY DIFFRACTIONr_long_range_B_refined6.45649.4233392
X-RAY DIFFRACTIONr_long_range_B_other6.45549.4393393
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.69→2.76 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 88 -
Rwork0.3 1502 -
obs--99.94 %
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)
10.8661-0.1770.45112.02420.39453.2696-0.1196-0.0139-0.08890.0614-0.06820.08570.5259-0.21620.18780.1625-0.02530.0870.0203-0.00420.3222-55.580613.1695-19.6225
20.40450.0457-0.78344.09952.98414.063-0.42670.0602-0.27580.0090.2319-0.34481.26040.2080.19481.00750.19550.15080.1592-0.09430.4377-46.6782-5.4402-38.8177
30.29870.04740.39681.1580.25872.2358-0.0078-0.0463-0.0340.2444-0.0926-0.05990.482-0.06430.10030.1718-0.01320.03790.01610.04230.379-51.836417.9591-8.2679
41.0915-0.11910.16240.3693-0.04290.03140.4039-0.06780.11460.2349-0.3979-0.12510.09330.0299-0.0061.1702-0.1982-0.12930.4870.0810.32-50.038430.976936.4189
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A30 - 190
2X-RAY DIFFRACTION2A211 - 477
3X-RAY DIFFRACTION3B502 - 610
4X-RAY DIFFRACTION4B611 - 632

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