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- PDB-6g9i: Crystal structure of Ebolavirus glycoprotein in complex with clom... -

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Basic information

Entry
Database: PDB / ID: 6g9i
TitleCrystal structure of Ebolavirus glycoprotein in complex with clomipramine
Components(Envelope glycoprotein,Envelope ...) x 2
KeywordsVIRAL PROTEIN / Ebolavirus Glycoprotein / Clomipramine / 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 / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell plasma membrane / virion membrane / extracellular region / identical protein binding
Similarity search - Function
Filoviruses glycoprotein, extracellular domain / Filoviruses glycoprotein / Filovirus glycoprotein / Fibritin C-terminal / Fibritin C-terminal region
Similarity search - Domain/homology
Chem-CXX / Envelope glycoprotein / Envelope glycoprotein
Similarity search - Component
Biological speciesEbola virus - Mayinga
Zaire
1976
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.19 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,Envelope glycoprotein
B: Envelope glycoprotein,Envelope glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,54212
Polymers55,2252
Non-polymers2,31710
Water2,234124
1
A: Envelope glycoprotein,Envelope glycoprotein
B: Envelope glycoprotein,Envelope glycoprotein
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)172,62536
Polymers165,6756
Non-polymers6,95030
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 area41010 Å2
ΔGint-108 kcal/mol
Surface area50580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.206, 114.206, 306.426
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,Envelope ... , 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,T42A,T42A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ebola virus - Mayinga, Zaire, 1976 / Gene: GP / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q05320
#2: Protein Envelope glycoprotein,Envelope glycoprotein / GP1 / 2 / GP


Mass: 18922.320 Da / Num. of mol.: 1 / Mutation: H613A,H613A,H613A,H613A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ebola virus - Mayinga, Zaire, 1976, (gene. exp.) Human immunodeficiency virus 1
Gene: GP / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q05320, UniProt: M1E1E4

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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-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 , 3 types, 129 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-CXX / 3-(3-CHLORO-5H-DIBENZO[B,F]AZEPIN-5-YL)-N,N-DIMETHYLPROPAN-1-AMINE / 3-chloro-5-(3-(dimethylamino)propyl)-10,11-dihydro-5H-dibenz[b,f]azepine / Clomipramine


Mass: 314.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C19H23ClN2 / Feature type: SUBJECT OF INVESTIGATION / Comment: antidepressant*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 64.68 %
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: Aug 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.19→60.6 Å / Num. obs: 40019 / % possible obs: 100 % / Redundancy: 38.9 % / CC1/2: 1 / Rmerge(I) obs: 0.08 / Net I/σ(I): 26.9
Reflection shellResolution: 2.19→2.23 Å / Redundancy: 33.4 % / Mean I/σ(I) obs: 2.6 / Num. unique obs: 1962 / CC1/2: 0.94 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
xia2data reduction
xia2data scaling
RefinementResolution: 2.19→52.095 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.3
RfactorNum. reflection% reflection
Rfree0.2084 2035 5.12 %
Rwork0.19 --
obs0.191 39766 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.19→52.095 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2977 0 152 124 3253
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063264
X-RAY DIFFRACTIONf_angle_d0.7454451
X-RAY DIFFRACTIONf_dihedral_angle_d12.5142303
X-RAY DIFFRACTIONf_chiral_restr0.05513
X-RAY DIFFRACTIONf_plane_restr0.004558
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.19-2.2410.34791220.33812480X-RAY DIFFRACTION98
2.241-2.2970.34691150.30172460X-RAY DIFFRACTION98
2.297-2.35910.27281400.27582456X-RAY DIFFRACTION99
2.3591-2.42850.25781300.25882487X-RAY DIFFRACTION99
2.4285-2.50690.27751480.24592434X-RAY DIFFRACTION99
2.5069-2.59650.26731650.22262492X-RAY DIFFRACTION99
2.5965-2.70050.22431530.20012473X-RAY DIFFRACTION99
2.7005-2.82330.2311380.20452497X-RAY DIFFRACTION100
2.8233-2.97220.24531200.19082513X-RAY DIFFRACTION100
2.9722-3.15840.25711060.19172562X-RAY DIFFRACTION100
3.1584-3.40220.22121360.19542532X-RAY DIFFRACTION100
3.4022-3.74450.19061370.16912524X-RAY DIFFRACTION100
3.7445-4.28610.15421310.15562560X-RAY DIFFRACTION100
4.2861-5.39910.1571350.15482591X-RAY DIFFRACTION100
5.3991-52.10970.2211590.20222670X-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)
12.1534-0.9090.41574.2197-0.11711.0551-0.1521-0.7972-0.61461.18890.43190.4770.513-0.2969-0.25170.74810.00130.16340.58020.00320.4584-60.354214.0021.9062
21.4169-0.5352-0.59193.271.79473.238-0.1418-0.0036-0.17480.2290.2271-0.13740.67030.3696-0.00120.461-0.05220.08460.26070.08090.4028-55.931711.4807-12.8653
32.003-0.9063-0.70842.75950.39712.9074-0.0210.2709-0.0825-0.3403-0.09850.01450.249-0.09680.09420.4447-0.03220.04330.3305-0.02210.3814-55.559813.9473-29.1874
41.523-0.6515-1.37033.89491.70824.8776-0.25250.0969-0.0102-0.0130.225-0.46740.58290.8498-0.03440.37510.08980.01270.39130.01570.461-48.15719.406-21.394
55.2664-3.411-2.25654.70941.35616.1743-0.590.0918-0.3141-0.45610.20760.28450.8827-0.35320.55090.9776-0.13090.04530.5334-0.10690.5437-57.01840.3397-40.6528
63.39620.1641-0.88863.81780.08516.4821-0.5620.0371-0.38790.05240.2329-0.02470.97960.26860.44491.04680.09110.18840.4903-0.03740.6172-44.9091-5.5691-39.0937
74.76860.8264-0.93742.9394-0.67443.9753-0.6650.0913-0.658-0.83530.542-0.79250.9252-0.11160.25821.622-0.05430.25720.7884-0.16040.6219-46.4584-8.3865-48.1344
80.04720.1066-0.05621.23131.31941.5277-0.25360.2635-0.27770.3347-0.19160.31231.3360.280.20761.6920.16630.10650.7989-0.15831.1481-47.6018-11.5346-34.4694
93.41491.2250.43313.9749-0.76283.51680.0379-0.1666-0.26830.5361-0.08450.20360.7141-0.2451-0.03130.6450.02940.08040.3815-0.0120.4546-51.35714.9335-10.4416
101.33911.79531.06187.16031.36397.4715-0.7317-0.374-1.79681.4942-0.24630.69761.0125-0.46820.79720.80590.23240.02251.01130.20251.3419-32.63226.9007-13.2636
111.55991.9079-0.64784.4535-0.78361.4537-0.03790.2558-0.26850.1710.0999-0.49630.1671-0.07040.22010.39250.0758-0.01370.47150.05170.484-36.950219.8059-17.9048
121.88340.0522-0.11363.2326-0.54862.3316-0.1203-0.1214-0.04050.17060.09760.20970.3141-0.30130.07040.4018-0.0330.04710.3207-0.04720.3647-60.005115.0649-12.3056
134.5895-0.74370.33084.7691.06288.2046-0.2318-1.0989-0.50611.3120.01130.65550.9906-1.08350.17620.72060.03780.07770.63490.08480.501-60.656527.22588.1639
146.3019-2.1255-2.15981.71552.61174.5840.44881.90140.6567-0.7796-0.3224-0.87671.4048-1.852-0.4282.37340.32430.16332.43020.1511.3146-50.87228.637929.5981
153.0355-1.8377-3.9055.54020.44555.96271.14170.78941.52321.1599-0.0762-1.00641.5686-0.72-0.50221.6714-0.2077-0.35971.818-0.05231.719-49.472333.417343.2162
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 32 through 50 )
2X-RAY DIFFRACTION2chain 'A' and (resid 51 through 89 )
3X-RAY DIFFRACTION3chain 'A' and (resid 90 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 263 )
7X-RAY DIFFRACTION7chain 'A' and (resid 264 through 280 )
8X-RAY DIFFRACTION8chain 'A' and (resid 281 through 477 )
9X-RAY DIFFRACTION9chain 'B' and (resid 502 through 520 )
10X-RAY DIFFRACTION10chain 'B' and (resid 521 through 530 )
11X-RAY DIFFRACTION11chain 'B' and (resid 531 through 550 )
12X-RAY DIFFRACTION12chain 'B' and (resid 551 through 583 )
13X-RAY DIFFRACTION13chain 'B' and (resid 584 through 612 )
14X-RAY DIFFRACTION14chain 'B' and (resid 613 through 620 )
15X-RAY DIFFRACTION15chain 'B' and (resid 621 through 631 )

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