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- PDB-6g9b: Crystal structure of Ebolavirus glycoprotein in complex with imip... -

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Basic information

Entry
Database: PDB / ID: 6g9b
TitleCrystal structure of Ebolavirus glycoprotein in complex with imipramine
Components
  • Envelope glycoprotein
  • Envelope glycoprotein,Envelope glycoprotein
KeywordsVIRAL PROTEIN / Ebolavirus Glycoprotein / Imipramine / 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-IXX / Envelope glycoprotein
Similarity search - Component
Biological speciesZaire ebolavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.26 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_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _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.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_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,Envelope glycoprotein
B: Envelope glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,88218
Polymers55,2252
Non-polymers2,65716
Water2,270126
1
A: Envelope glycoprotein,Envelope glycoprotein
B: Envelope glycoprotein
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)173,64654
Polymers165,6756
Non-polymers7,97148
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 area45950 Å2
ΔGint-39 kcal/mol
Surface area48760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.216, 114.216, 305.552
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 / 2 / GP


Mass: 36302.719 Da / Num. of mol.: 1 / Mutation: T42A,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 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


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, 137 molecules

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


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-IXX / 3-(5H-DIBENZO[B,F]AZEPIN-5-YL)-N,N-DIMETHYLPROPAN-1-AMINE / 5-(3-(dimethylamino)propyl)-10,11-dihydro-5H-dibenz[b,f]azepine


Mass: 280.407 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H24N2 / Feature type: SUBJECT OF INVESTIGATION / Comment: antidepressant*YM
#7: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 64.58 %
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: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.26→83 Å / Num. obs: 36357 / % possible obs: 99.9 % / Redundancy: 18.5 % / CC1/2: 1 / Rmerge(I) obs: 0.083 / Net I/σ(I): 18.5
Reflection shellResolution: 2.26→2.3 Å / Redundancy: 11.4 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1787 / CC1/2: 0.71 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
xia2data reduction
xia2data scaling
RefinementResolution: 2.26→60.458 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.57
RfactorNum. reflection% reflection
Rfree0.2249 1886 5.24 %
Rwork0.1959 --
obs0.1974 36003 98.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.26→60.458 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2975 0 174 126 3275
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053224
X-RAY DIFFRACTIONf_angle_d0.9134382
X-RAY DIFFRACTIONf_dihedral_angle_d14.3361840
X-RAY DIFFRACTIONf_chiral_restr0.049493
X-RAY DIFFRACTIONf_plane_restr0.005546
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.26-2.32110.41771390.39012491X-RAY DIFFRACTION95
2.3211-2.38940.39371680.35292511X-RAY DIFFRACTION97
2.3894-2.46650.34231250.3222607X-RAY DIFFRACTION98
2.4665-2.55470.31871520.29562580X-RAY DIFFRACTION99
2.5547-2.6570.30781410.2642608X-RAY DIFFRACTION99
2.657-2.77790.26631520.25282588X-RAY DIFFRACTION99
2.7779-2.92440.26341320.20712631X-RAY DIFFRACTION99
2.9244-3.10760.21681330.19312654X-RAY DIFFRACTION100
3.1076-3.34750.22281780.18542592X-RAY DIFFRACTION100
3.3475-3.68430.19161380.16372673X-RAY DIFFRACTION100
3.6843-4.21730.17061350.15352665X-RAY DIFFRACTION100
4.2173-5.31290.17151440.15652701X-RAY DIFFRACTION100
5.3129-60.47970.24171490.20362816X-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)
13.9813-1.6761.44424.8188-0.89534.4895-0.5388-1.0646-0.57331.20030.9190.73020.2744-1.3751-0.35790.9363-0.01780.15430.72620.03490.5484-59.687113.30630.6542
21.8281-0.8363-0.59192.49890.88192.469-0.1010.0212-0.14980.0605-0.013-0.0450.56450.10740.10870.485-0.05230.07810.29120.03790.3956-55.181112.2073-18.3911
33.5088-1.0204-0.9462.650.43453.7437-0.01550.3445-0.05-0.4276-0.10320.07790.1663-0.16470.09990.5422-0.03520.04710.3409-0.01710.4216-56.016114.1389-30.6707
41.592-0.4693-1.37173.42622.3175.5301-0.24340.465-0.386-0.61450.2168-0.32030.88120.26390.0530.94660.00040.14340.5555-0.05630.6053-48.2482-0.5176-35.9033
50.1230.23140.00480.57140.00630.0171-0.47520.28140.01580.613-0.48590.60831.31560.56940.30142.12850.26740.18660.9727-0.11.2169-47.4088-11.5645-35.6047
62.13681.18091.17863.6384-0.19873.43390.1301-0.2309-0.1720.7031-0.18230.15990.6917-0.09740.08170.68660.02040.09490.4071-0.0080.5375-51.28244.9193-10.3417
70.92142.0474-0.06846.0271-3.15926.00120.47730.7911-0.64261.2189-0.81580.64242.04840.72940.8271.37050.13450.0531.14410.42911.5871-32.239324.9104-11.9678
82.78053.8289-3.19385.4301-4.24723.904-0.1334-0.1461-1.2141.0667-0.5363-2.01140.70982.13890.44160.48510.13380.06630.70.12090.7976-29.993431.6317-18.1028
91.42460.9943-0.09551.5255-0.17821.74220.02210.0142-0.04730.0724-0.1475-0.15350.39660.10480.08560.51560.02260.04010.41840.00570.4751-52.230816.032-14.1497
104.1967-0.936-1.4985.07142.04915.016-0.1766-0.2674-0.48570.3908-0.10270.68110.801-0.50290.20640.47690.00690.00690.40410.03620.4579-59.692726.99250.6859
110.94480.7261-1.20182.519-0.07611.9137-0.516-1.1391-1.14511.36620.3720.66040.0535-1.13860.20921.36510.13760.20171.16770.15450.7725-61.761527.555817.3766
127.5868-0.1639-0.85656.0659-2.67893.16540.84042.75341.88430.0088-0.8625-1.38011.2625-0.8030.2091.4340.0465-0.19992.33690.26281.2793-49.866131.480337.6222
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 31 through 50 )
2X-RAY DIFFRACTION2chain 'A' and (resid 51 through 114 )
3X-RAY DIFFRACTION3chain 'A' and (resid 115 through 176 )
4X-RAY DIFFRACTION4chain 'A' and (resid 177 through 280 )
5X-RAY DIFFRACTION5chain 'A' and (resid 281 through 477 )
6X-RAY DIFFRACTION6chain 'B' and (resid 502 through 520 )
7X-RAY DIFFRACTION7chain 'B' and (resid 521 through 527 )
8X-RAY DIFFRACTION8chain 'B' and (resid 528 through 532 )
9X-RAY DIFFRACTION9chain 'B' and (resid 533 through 583 )
10X-RAY DIFFRACTION10chain 'B' and (resid 584 through 597 )
11X-RAY DIFFRACTION11chain 'B' and (resid 598 through 612 )
12X-RAY DIFFRACTION12chain 'B' and (resid 613 through 631 )

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