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- PDB-5jqb: Crystal structure of Ebola glycoprotein in complex with ibuprofen -

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Basic information

Entry
Database: PDB / ID: 5jqb
TitleCrystal structure of Ebola glycoprotein in complex with ibuprofen
Components(Envelope glycoprotein ...) x 2
KeywordsVIRAL PROTEIN / Ebola virus / Filoviridae / envelope glycoprotein / protein inhibitor complex / ibuprofen / 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
Similarity search - Function
: / Filoviruses glycoprotein, extracellular domain / Filoviruses glycoprotein / Filovirus glycoprotein / Envelope glycoprotein GP2-like, HR1-HR2
Similarity search - Domain/homology
IBUPROFEN / Envelope glycoprotein
Similarity search - Component
Biological speciesEbola virus - Mayinga
Zaire (virus)
1976
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 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 / 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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.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 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 23, 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 1,Envelope glycoprotein 1,Envelope glycoprotein 1
B: Envelope glycoprotein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,43013
Polymers55,2922
Non-polymers2,13811
Water1,31573
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)172,29139
Polymers165,8766
Non-polymers6,41433
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 area41170 Å2
ΔGint-96 kcal/mol
Surface area52230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.760, 113.760, 306.150
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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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 / Mutation: T42A,T42A,T42A
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 / Production host: Homo sapiens (human) / References: UniProt: Q05320

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Sugars , 2 types, 5 molecules

#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-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 , 3 types, 79 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-IBP / IBUPROFEN / 2-(4-ISOBUTYLPHENYL)PROPIONIC ACID


Mass: 206.281 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H18O2 / Comment: medication*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 3.49 Å3/Da / Density % sol: 64.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
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: 2.68→82.84 Å / Num. obs: 21842 / % possible obs: 99.9 % / Redundancy: 9.8 % / Rmerge(I) obs: 0.129 / Net I/σ(I): 14.7
Reflection shellResolution: 2.68→2.75 Å / Redundancy: 8.3 % / Mean I/σ(I) obs: 1.5 / % 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: 2.68→82.84 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.923 / SU B: 20.159 / SU ML: 0.202 / Cross valid method: THROUGHOUT / ESU R: 0.35 / ESU R Free: 0.253 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1107 5.1 %RANDOM
Rwork0.199 ---
obs0.201 20734 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 73.22 Å2
Baniso -1Baniso -2Baniso -3
1-0.73 Å20.37 Å20 Å2
2--0.73 Å20 Å2
3----2.38 Å2
Refinement stepCycle: LAST / Resolution: 2.68→82.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3025 0 140 73 3238
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0193243
X-RAY DIFFRACTIONr_bond_other_d0.0010.022985
X-RAY DIFFRACTIONr_angle_refined_deg1.2411.9864413
X-RAY DIFFRACTIONr_angle_other_deg0.87136864
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4685382
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.62824.167144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.75815479
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8941517
X-RAY DIFFRACTIONr_chiral_restr0.0670.2507
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213593
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02742
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_it1.5225.4241546
X-RAY DIFFRACTIONr_mcbond_other1.5225.421545
X-RAY DIFFRACTIONr_mcangle_it2.7798.11922
X-RAY DIFFRACTIONr_mcangle_other2.7788.1061923
X-RAY DIFFRACTIONr_scbond_it1.7095.8151697
X-RAY DIFFRACTIONr_scbond_other1.7095.8171698
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0148.6772492
X-RAY DIFFRACTIONr_long_range_B_refined5.97243.6193405
X-RAY DIFFRACTIONr_long_range_B_other5.97143.6313406
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.68→2.75 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 92 -
Rwork0.322 1494 -
obs--100 %
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)
10.5753-0.0986-0.29831.16930.23251.4473-0.0165-0.0291-0.06350.0022-0.0632-0.02770.17380.02120.07980.2114-0.0190.0260.1390.00920.0689-55.166613.0864-19.4579
20.7346-0.208-1.21712.55751.18343.1213-0.17620.0727-0.2017-0.3142-0.0153-0.10470.66570.15780.19140.53040.06710.08390.1698-0.06570.132-46.9915-4.9999-38.6791
30.10210.09510.23930.84250.3740.71120.0111-0.01860.0090.1573-0.0862-0.03060.1723-0.09190.07510.21550.00760.03130.17260.03140.0794-51.938218.08-8.2731
40.2541-0.08770.00141.0813-0.35620.1210.1474-0.03770.0843-0.0151-0.12780.02350.00520.0481-0.01960.55410.0680.00740.30560.03430.0495-50.153631.050536.5147
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A32 - 194
2X-RAY DIFFRACTION2A211 - 477
3X-RAY DIFFRACTION3B502 - 610
4X-RAY DIFFRACTION4B611 - 632

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