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- PDB-6hs4: Crystal structure of Ebolavirus glycoprotein in complex with inhi... -

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Basic information

Entry
Database: PDB / ID: 6hs4
TitleCrystal structure of Ebolavirus glycoprotein in complex with inhibitor 118
Components
  • Envelope glycoprotein
  • Envelope glycoprotein,GP1,Envelope glycoprotein
KeywordsVIRAL PROTEIN / Ebola Glycoprotein / Structure-based In Silico Screening / compound 118 / compound 118a / Natural compound
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
Chem-GON / Envelope glycoprotein
Similarity search - Component
Biological speciesZaire ebolavirus
Ebola virus - Mayinga
Zaire (virus)
1976
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsRen, J. / Zhao, Y. / Stuart, D.I.
CitationJournal: J.Med.Chem. / Year: 2019
Title: Structure-Based in Silico Screening Identifies a Potent Ebolavirus Inhibitor from a Traditional Chinese Medicine Library.
Authors: Shaikh, F. / Zhao, Y. / Alvarez, L. / Iliopoulou, M. / Lohans, C. / Schofield, C.J. / Padilla-Parra, S. / Siu, S.W.I. / Fry, E.E. / Ren, J. / Stuart, D.I.
History
DepositionSep 28, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc / pdbx_seq_map_depositor_info
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name / _pdbx_seq_map_depositor_info.one_letter_code_mod
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 24, 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
Revision 2.2Nov 20, 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,GP1,Envelope glycoprotein
B: Envelope glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,49414
Polymers55,3102
Non-polymers3,18412
Water2,972165
1
A: Envelope glycoprotein,GP1,Envelope glycoprotein
B: Envelope glycoprotein
hetero molecules

A: Envelope glycoprotein,GP1,Envelope glycoprotein
B: Envelope glycoprotein
hetero molecules

A: Envelope glycoprotein,GP1,Envelope glycoprotein
B: Envelope glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,48342
Polymers165,9306
Non-polymers9,55336
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 area42080 Å2
ΔGint-74 kcal/mol
Surface area52260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.160, 114.160, 305.458
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,GP1,Envelope glycoprotein / GP1 / 2 / GP


Mass: 36387.824 Da / Num. of mol.: 1 / Mutation: T42A,T42A,T42A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zaire ebolavirus (strain Mayinga-76), (gene. exp.) Ebola virus - Mayinga, Zaire, 1976
Strain: Mayinga-76 / 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 / Mutation: H613A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zaire ebolavirus / 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, 6 molecules

#3: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[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: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-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.: 5
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, 171 molecules

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


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-GON / 1-[2-[3-oxidanyl-4-(4-phenyl-1~{H}-pyrazol-5-yl)phenoxy]ethyl]piperidine-4-carboxamide


Mass: 406.478 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H26N4O3
#7: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 3.47 Å3/Da / Density % sol: 64.52 %
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 6M / Detector: PIXEL / Date: Dec 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.05→57.08 Å / Num. obs: 47703 / % possible obs: 98.4 % / Redundancy: 15.8 % / Biso Wilson estimate: 42.3 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.063 / Net I/σ(I): 21.1
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 6 % / Mean I/σ(I) obs: 1.1 / CC1/2: 0.435 / % possible all: 90.4

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
DIALSdata reduction
DIALSdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6F5U

6f5u


Resolution: 2.05→57.08 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 25.7
RfactorNum. reflection% reflection
Rfree0.2198 2285 4.83 %
Rwork0.19 --
obs0.1915 47321 97.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.05→57.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3028 0 213 165 3406
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053340
X-RAY DIFFRACTIONf_angle_d0.7994559
X-RAY DIFFRACTIONf_dihedral_angle_d21.2151937
X-RAY DIFFRACTIONf_chiral_restr0.048524
X-RAY DIFFRACTIONf_plane_restr0.004568
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0497-2.09430.39591060.39382493X-RAY DIFFRACTION87
2.0943-2.1430.31491160.36172617X-RAY DIFFRACTION91
2.143-2.19660.31241400.30942653X-RAY DIFFRACTION93
2.1966-2.2560.27141560.26942696X-RAY DIFFRACTION96
2.256-2.32240.29411450.24622800X-RAY DIFFRACTION98
2.3224-2.39730.25471280.23852818X-RAY DIFFRACTION99
2.3973-2.4830.241190.21582896X-RAY DIFFRACTION100
2.483-2.58240.25081350.20722855X-RAY DIFFRACTION99
2.5824-2.70.22681490.19582849X-RAY DIFFRACTION100
2.7-2.84230.23011580.19212857X-RAY DIFFRACTION100
2.8423-3.02040.21931460.18312867X-RAY DIFFRACTION100
3.0204-3.25360.20241440.18492892X-RAY DIFFRACTION100
3.2536-3.58090.19371680.18212866X-RAY DIFFRACTION100
3.5809-4.0990.18031550.15772899X-RAY DIFFRACTION100
4.099-5.16380.17461390.14582949X-RAY DIFFRACTION100
5.1638-57.10210.25381810.19453029X-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)
10.37721.0803-0.56716.27760.60312.45490.0393-0.3773-0.14371.0283-0.0007-0.08390.2837-0.29250.07390.59210.01130.0850.43370.0280.4002-58.265915.7862.6655
21.32-0.3974-0.64121.87030.48292.104-0.0510.1884-0.1254-0.2532-0.06550.00640.3234-0.03180.1080.3949-0.02210.04680.2628-0.01820.289-55.696112.4993-26.913
31.3909-0.3714-1.17773.77973.00797.2798-0.16740.2803-0.1465-0.33910.0187-0.10090.4970.15210.13780.4990.02040.05570.27220.00090.4111-51.39766.1007-28.728
42.9512-0.6747-1.78144.04261.7777.9989-0.45390.2998-0.4076-0.1120.2482-0.07391.13390.25350.21830.92270.07820.16080.4671-0.05860.5811-45.0048-5.6981-39.0313
54.03240.3011.12864.1641.92255.678-0.12590.2148-0.6559-0.52640.2435-0.54060.9320.1292-0.04711.3544-0.06290.22660.6176-0.19290.6852-46.6435-9.2641-46.5651
60.0031-0.0889-0.13372.35283.61865.5305-0.32360.356-0.13170.62-0.0994-0.13991.56510.33260.35311.27360.17550.08570.6802-0.05670.8321-45.0594-10.615-25.7027
72.8323-1.3182-2.88928.25640.70173.0273-0.09880.5255-0.6727-0.68140.13470.57060.11440.45570.12681.69130.11760.12130.7207-0.14840.9611-47.3745-14.2849-48.4524
84.7613.334-0.7834.6999-1.99232.65860.0382-0.3449-0.3380.272-0.12570.0140.5118-0.04670.05310.52170.02310.06070.3085-0.00610.3546-51.33414.8979-10.4518
93.88754.74441.32655.8221.64760.53370.7389-1.3508-0.06041.6958-0.85270.48610.34240.4751-0.25080.64040.02570.05341.14360.11741.0473-32.468925.7556-12.1605
101.39292.3691-0.92435.4486-1.23750.6932-0.05430.2422-0.24240.04490.0541-0.58450.0806-0.10010.05240.34390.0750.00580.49750.07310.4755-36.979119.7713-17.9013
112.1711-0.32210.93813.2372-1.19372.9322-0.0512-0.1374-0.08640.0253-0.0220.03590.3986-0.21570.07080.2907-0.02990.06520.2259-0.03540.2384-59.990915.0527-12.2713
125.9572-3.3615-4.04214.76184.98025.28390.1163-0.1609-0.52720.462-0.19030.53840.5666-0.98090.17520.3427-0.0305-0.00190.3250.02440.3182-59.66426.88060.6659
132.24150.4248-0.31239.556-3.089.2994-0.0904-0.9295-0.60140.9322-0.1560.60781.0999-0.85250.3490.88020.04510.14390.94220.09820.5453-61.69427.630917.3141
145.1518-5.9559-2.37557.05052.16563.44980.3579-0.68630.2770.27150.2308-0.804-0.1957-0.2908-0.44571.8443-0.0450.12221.78490.16711.586-50.955928.806229.4119
153.28350.90261.30170.24840.36030.5170.2140.51140.37880.55-0.1765-0.68150.35020.88640.01381.6376-0.075-0.11231.74610.01431.6991-49.257233.376543.1445
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 30 through 59 )
2X-RAY DIFFRACTION2chain 'A' and (resid 60 through 176 )
3X-RAY DIFFRACTION3chain 'A' and (resid 177 through 237 )
4X-RAY DIFFRACTION4chain 'A' and (resid 238 through 263 )
5X-RAY DIFFRACTION5chain 'A' and (resid 264 through 282 )
6X-RAY DIFFRACTION6chain 'A' and (resid 283 through 305 )
7X-RAY DIFFRACTION7chain 'A' and (resid 306 through 478 )
8X-RAY DIFFRACTION8chain 'B' and (resid 502 through 520 )
9X-RAY DIFFRACTION9chain 'B' and (resid 521 through 530 )
10X-RAY DIFFRACTION10chain 'B' and (resid 531 through 550 )
11X-RAY DIFFRACTION11chain 'B' and (resid 551 through 583 )
12X-RAY DIFFRACTION12chain 'B' and (resid 584 through 597 )
13X-RAY DIFFRACTION13chain 'B' and (resid 598 through 612 )
14X-RAY DIFFRACTION14chain 'B' and (resid 613 through 620 )
15X-RAY DIFFRACTION15chain 'B' and (resid 621 through 631 )

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