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- PDB-6f5u: CRYSTAL STRUCTURE OF EBOLAVIRUS GLYCOPROTEIN IN COMPLEX WITH BEPRIDIL -

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Basic information

Entry
Database: PDB / ID: 6f5u
TitleCRYSTAL STRUCTURE OF EBOLAVIRUS GLYCOPROTEIN IN COMPLEX WITH BEPRIDIL
Components
  • Envelope glycoprotein
  • Envelope glycoprotein,Envelope glycoprotein,GP1
KeywordsVIRAL PROTEIN / EBOLA VIRUS / FILOVIRIDAE / ENVELOPE GLYCOPROTEIN / PROTEIN INHIBITOR COMPLEX / IBUPROFEN / benztropine / bepridil / paroxetine and 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 / 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
Bepridil / Envelope glycoprotein
Similarity search - Component
Biological speciesZaire ebolavirus
Ebola virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsRen, J. / Zhao, Y. / Fry, E.E. / Stuart, D.I.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
UKMR/N00065X/1 United Kingdom
CitationJournal: 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.
History
DepositionDec 3, 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,Envelope glycoprotein,GP1
B: Envelope glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,24616
Polymers54,5512
Non-polymers2,69514
Water2,666148
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)171,73748
Polymers163,6526
Non-polymers8,08542
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 area42020 Å2
ΔGint-89 kcal/mol
Surface area51930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.050, 114.050, 307.180
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: 35628.434 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zaire ebolavirus (strain Mayinga-76), (gene. exp.) Ebola virus
Strain: Mayinga-76, MAYINGA, ZAIRE, 1976 / Gene: GP / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q05320
#2: Protein Envelope glycoprotein / GP1 / 2 / GP


Mass: 18922.320 Da / Num. of mol.: 1
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): 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 / 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, 157 molecules

#5: 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
#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-CQN / Bepridil / Bepridil


Mass: 366.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H34N2O / Feature type: SUBJECT OF INVESTIGATION / Comment: channel blocker*YM
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 148 / 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: Jul 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.07→83.08 Å / Num. obs: 47246 / % possible obs: 99.9 % / Redundancy: 33.6 % / CC1/2: 1 / Rmerge(I) obs: 0.104 / Net I/σ(I): 21.2
Reflection shellResolution: 2.07→2.11 Å / Redundancy: 20.4 % / Num. unique obs: 2339 / CC1/2: 0.53 / % 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: 5jq7

5jq7


Resolution: 2.07→52.168 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23
RfactorNum. reflection% reflection
Rfree0.2002 2350 4.98 %
Rwork0.1867 --
obs0.1874 47232 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.07→52.168 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2974 0 175 148 3297
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033226
X-RAY DIFFRACTIONf_angle_d0.7254390
X-RAY DIFFRACTIONf_dihedral_angle_d19.611872
X-RAY DIFFRACTIONf_chiral_restr0.049502
X-RAY DIFFRACTIONf_plane_restr0.004548
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.07-2.11230.35491310.33742633X-RAY DIFFRACTION100
2.1123-2.15820.31271350.29592577X-RAY DIFFRACTION100
2.1582-2.20840.27681430.27472618X-RAY DIFFRACTION100
2.2084-2.26360.31381360.24782596X-RAY DIFFRACTION100
2.2636-2.32480.2521430.23292625X-RAY DIFFRACTION100
2.3248-2.39320.23151270.21842629X-RAY DIFFRACTION100
2.3932-2.47050.24051310.22082614X-RAY DIFFRACTION100
2.4705-2.55880.28361230.2192638X-RAY DIFFRACTION100
2.5588-2.66120.21691340.20082625X-RAY DIFFRACTION100
2.6612-2.78230.21391430.20482618X-RAY DIFFRACTION100
2.7823-2.9290.18141470.19072635X-RAY DIFFRACTION100
2.929-3.11250.22381390.19322623X-RAY DIFFRACTION100
3.1125-3.35280.20841320.19632655X-RAY DIFFRACTION100
3.3528-3.69010.18591460.17952646X-RAY DIFFRACTION100
3.6901-4.22390.19511580.15922646X-RAY DIFFRACTION100
4.2239-5.32080.13541350.1472700X-RAY DIFFRACTION100
5.3208-52.18420.20981470.19262804X-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)
10.05950.08170.06640.08130.04390.02510.1179-0.868-0.56080.8390.27930.15490.5083-0.6848-0.00080.8429-0.03870.05310.57590.04480.5511-57.114111.48940.7645
20.1776-0.20650.24140.63450.09290.3956-0.1021-0.17030.02070.35630.1795-0.18220.55280.207-00.612-0.00880.02010.4760.02760.4805-54.690516.3795-1.9051
31.1452-0.6693-0.68341.56640.24530.9252-0.03040.13370.0045-0.186-0.12480.00570.2074-0.11100.5556-0.02480.03930.4099-0.01740.4535-56.09212.2831-29.1198
40.1796-0.2399-0.15721.1234-0.25770.3854-0.07530.09460.0558-0.06490.0622-0.36750.36820.465-00.53590.05940.04830.5356-0.03320.5465-47.88499.5443-21.418
50.1392-0.14690.12970.2998-0.04890.1264-0.02850.0756-0.1019-0.5432-0.15350.19210.50990.0073-0.00020.9418-0.078-0.00320.6412-0.12080.6751-56.68120.2449-40.7214
60.4671-0.00680.04550.760.38450.4348-0.38440.159-0.3463-0.41130.092-0.04370.9798-0.20070.00011.08780.04510.16840.5659-0.06120.591-44.8357-5.9675-42.8326
70.15320.1756-0.0730.1579-0.08110.0370.2053-0.0063-0.3845-0.05870.1870.3647-0.00860.03390.00031.15510.159-0.04310.5742-0.06940.8797-47.0181-12.7828-32.7892
80.30540.2070.38930.38050.08740.41460.1448-0.3047-0.10770.5964-0.18280.04670.49580.066-0.00010.76520.00520.13580.49030.02120.5586-51.55354.1334-10.2189
91.38821.71851.01882.12731.37141.4916-0.2019-0.3911-0.33370.83220.0745-0.43391.02990.35640.07010.52450.06790.00370.58710.12141.2966-33.669426.3305-12.8892
100.19640.3031-0.00320.3750.39650.94150.016-0.00550.00180.0644-0.1157-0.01470.28520.0187-00.45730.02280.02220.40460.05970.4965-50.779116.952-14.4379
110.2297-0.27250.11230.3889-0.00570.1354-0.119-0.295-0.41650.4664-0.07370.46050.3882-0.801300.66040.01420.05560.60850.05770.5062-60.465627.18718.2437
120.14240.1122-0.06370.055-0.01250.02340.02570.7460.1482-0.3584-0.3409-0.74770.02880.0706-0.00021.5703-0.0353-0.07531.4276-0.15121.0596-50.119431.890338.4943
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 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 277 )
7X-RAY DIFFRACTION7chain 'A' and (resid 278 through 311 )
8X-RAY DIFFRACTION8chain 'B' and (resid 502 through 519 )
9X-RAY DIFFRACTION9chain 'B' and (resid 520 through 529 )
10X-RAY DIFFRACTION10chain 'B' and (resid 530 through 583 )
11X-RAY DIFFRACTION11chain 'B' and (resid 584 through 612 )
12X-RAY DIFFRACTION12chain 'B' and (resid 613 through 632 )

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