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- PDB-7ssq: Crystal Structure of Ebola zaire Envelope glycoprotein GP in comp... -

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Basic information

Entry
Database: PDB / ID: 7ssq
TitleCrystal Structure of Ebola zaire Envelope glycoprotein GP in complex with compound ARN0075231
Components
  • GP1
  • GP2
KeywordsVIRAL PROTEIN/INHIBITOR / SSGCID / Envelope glycoprotein / Zaire ebolavirus / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / VIRAL PROTEIN / VIRAL PROTEIN-INHIBITOR 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
ACETATE ION / Chem-ZQH / Envelope glycoprotein
Similarity search - Component
Biological speciesZaire ebolavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700059C United States
CitationJournal: to be published
Title: Crystal Structure of Ebola zaire Envelope glycoprotein GP in complex with compound ARN0075231
Authors: Abendroth, J. / Fox III, D. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionNov 11, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GP1
B: GP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,70311
Polymers55,0552
Non-polymers2,6489
Water3,423190
1
A: GP1
B: GP2
hetero molecules

A: GP1
B: GP2
hetero molecules

A: GP1
B: GP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,10833
Polymers165,1646
Non-polymers7,94327
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 area38760 Å2
ΔGint-71 kcal/mol
Surface area47960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.940, 113.940, 308.490
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein GP1 / Envelope glycoprotein GP1


Mass: 36132.508 Da / Num. of mol.: 1
Fragment: EbzaA.19907.a.HE11,EbzaA.19907.a.HE11,EbzaA.19907.a.HE11,EbzaA.19907.a.HE11,EbzaA.19907.a.HE11
Mutation: T42A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zaire ebolavirus / Strain: Mayinga-76 / Gene: GP / Plasmid: EbzaA.19907.a.HE11 / Production host: Homo sapiens (human) / Strain (production host): HEK-293 / References: UniProt: Q05320
#2: Protein GP2 / Envelope glycoprotein GP2


Mass: 18922.320 Da / Num. of mol.: 1 / Fragment: EbzaA.19907.a.HE11 proteolyzed C-terminal domain / Mutation: H613A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zaire ebolavirus / Strain: Mayinga-76 / Gene: GP / Plasmid: EbzaA.19907.a.HE11 / Production host: Homo sapiens (human) / Strain (production host): HEK-293 / References: UniProt: Q05320

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Sugars , 2 types, 5 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1114.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-1/a4-b1_b4-c1_c3-d1_c6-e1_e2-f1WURCSPDB2Glycan 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]{[(2+1)][b-D-GlcpNAc]{}}}}}}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, 194 molecules

#5: Chemical ChemComp-ZQH / [(4R)-4-amino-3,3-dimethylpiperidin-1-yl][(1S,3R,5R,6Z,7S)-3-phenyl-6-(2-phenylethylidene)adamantan-1-yl]methanone


Mass: 468.673 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H40N2O / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Sequence detailsResidues in the C-terminal portion of chain A were difficult to identify, and so were modeled as ...Residues in the C-terminal portion of chain A were difficult to identify, and so were modeled as UNK. The actual sequence for chain A is: ETGRSIPLGVIHNSALQVSDVDKLVCRDKLSSTNQLRSVGLNLEGNGVATDVPSATKRWGFRSGVPPKVVNYEAGEWAENCYNLEIKKPDGSECLPAAPDGIRGFPRCRYVHKVSGTGPCAGDFAFHKEGAFFLYDRLASTVIYRGTTFAEGVVAFLILPQAKKDFFSSHPLREPVNATEDPSSGYYSTTIRYQATGFGTNETEYLFEVDNLTYVQLESRFTPQFLLQLNETIYTSGKRSNTTGKLIWKVNPEIDTTIGEWAFWETKKNLTRKIRSEELSFTVVSTHHQDTGEESASSGKLGLITNTIAGVAGLITGGRRTRR. This is consistent with PDB entry 5JQ3 and subsequent depositions.

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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: 3.36 Å3/Da / Density % sol: 63.4 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 4.8
Details: Optimization condition around ProPlex screen, condition E1: 100mM sodium acetate / hydrochloride pH 4.8, 7.49% (w/V) PEG 8000, 100mM magnesium chloride: EbzaA.19907.a.HE11.PD38458 at 14. ...Details: Optimization condition around ProPlex screen, condition E1: 100mM sodium acetate / hydrochloride pH 4.8, 7.49% (w/V) PEG 8000, 100mM magnesium chloride: EbzaA.19907.a.HE11.PD38458 at 14.4mg/ml + 1mM BSI111592 / ARN00075231: tray 322840 h3: cryo: 25% EG + 1mM compound: puck sni3-8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 8, 2021 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 36679 / % possible obs: 99.1 % / Redundancy: 4.94 % / Biso Wilson estimate: 56.829 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Rrim(I) all: 0.056 / Χ2: 0.946 / Net I/σ(I): 17.81
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.25-2.313.2080.6061.6624780.730.7191.8
2.31-2.373.620.492.2825740.7960.56797.4
2.37-2.444.4780.4263.2325360.8890.48299.4
2.44-2.525.2150.3734.2524950.9230.415100
2.52-2.65.3330.2715.9524430.9620.399.9
2.6-2.695.3640.2057.923040.9780.22799.9
2.69-2.795.3390.1569.9722740.9860.173100
2.79-2.95.3280.11213.4621780.9920.124100
2.9-3.035.3260.08816.720810.9940.097100
3.03-3.185.3190.06920.8520180.9960.077100
3.18-3.355.3050.05824.3119120.9970.06599.9
3.35-3.565.2390.04829.1618120.9980.05399.9
3.56-3.85.220.04133.1217170.9980.04599.9
3.8-4.115.2120.03835.8415780.9980.04299.9
4.11-4.55.1530.03438.9714810.9980.03899.9
4.5-5.035.1720.03440.1213230.9980.038100
5.03-5.815.1310.03338.9111980.9990.037100
5.81-7.125.0870.03139.7210190.9990.03499.9
7.12-10.064.9190.0341.848030.9990.03399.6
10.06-504.510.02941.424550.9980.03394.6

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.20rc1refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 6f5u

6f5u


Resolution: 2.25→31.92 Å / SU ML: 0.2335 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.8238
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2033 2075 5.66 %0
Rwork0.1796 34588 --
obs0.181 36663 99.07 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.34 Å2
Refinement stepCycle: LAST / Resolution: 2.25→31.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2752 0 203 190 3145
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00873075
X-RAY DIFFRACTIONf_angle_d0.90714204
X-RAY DIFFRACTIONf_chiral_restr0.0537493
X-RAY DIFFRACTIONf_plane_restr0.0076529
X-RAY DIFFRACTIONf_dihedral_angle_d15.56271092
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.30.32261260.26412089X-RAY DIFFRACTION91.26
2.3-2.360.26161350.24992233X-RAY DIFFRACTION97.17
2.36-2.420.26671530.23262253X-RAY DIFFRACTION98.85
2.42-2.490.25081410.22312313X-RAY DIFFRACTION100
2.49-2.580.2181290.19362285X-RAY DIFFRACTION99.96
2.58-2.670.1891280.17212326X-RAY DIFFRACTION99.84
2.67-2.770.19731390.17992317X-RAY DIFFRACTION99.96
2.77-2.90.22871150.1852328X-RAY DIFFRACTION99.96
2.9-3.050.23241400.19662293X-RAY DIFFRACTION100
3.05-3.240.22051390.19372329X-RAY DIFFRACTION99.96
3.24-3.490.22751590.18652315X-RAY DIFFRACTION99.96
3.49-3.850.18171400.16042320X-RAY DIFFRACTION99.96
3.85-4.40.1681520.14532354X-RAY DIFFRACTION99.92
4.4-5.540.17531420.15622367X-RAY DIFFRACTION99.96
5.54-31.920.20761370.19922466X-RAY DIFFRACTION99.24
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)
11.206011578190.699447692922.415817874977.51663674663-1.236855605666.179430858670.149567917172-0.681770587625-0.3524342701311.22751470937-0.031049449643-0.08207337058740.777261581179-0.567745102099-0.0887953335920.570364869894-0.009467767333680.1163713937380.4292625960360.02520304608870.383435951899-57.159555672815.2080151143.58348656257
21.71778814196-0.465914248649-0.3300996961382.397893328860.514264634443.3178200796-0.05120989268130.304048775674-0.202567009725-0.296062429382-0.03505083145730.03416178193120.359081420089-0.03976574157330.08708967355430.42889524994-0.02812943607670.03989473052760.323986009058-0.03402121840510.365259862331-55.447115003412.4258587226-26.9274144477
31.23623883628-0.851832146532-0.7871590044853.679063072752.749770992076.38112291899-0.07207057957730.341952366368-0.373951587017-0.4883020649380.0477152495323-0.1337771568840.8661306696610.594960858101-0.0521985764920.8311874388670.059902485120.09894330035040.511389078486-0.07176732220170.597307739553-48.0485717087-0.695241160278-34.6226285982
42.686547485133.774512156461.616798212477.13466076915-0.4281885540785.015030622650.173393796414-0.0607068049313-0.08763596732060.70247464531-0.03561997502360.4128152620820.765645359417-0.201427817915-0.1720221801620.5498357287380.03692256385520.1115086828490.3586255875350.002200809811470.470221452448-50.92180965514.83131658891-10.362698995
58.065531780666.22370692793.072898101697.49135959327-0.5779534298284.396460281942.40258713269-0.7543435495040.3909455228111.9779458262-1.710574348630.5091124759840.6411223788380.821162840422-0.7439517383430.872822157893-0.1322713070550.06071161229570.796264956010.034244267411.16958726579-33.381105112226.0201389257-12.424078438
60.8996672080180.692387747765-0.5616516582882.07050998674-0.3018894580561.247854246180.0410932968734-0.033556254388-0.1704467905290.132529839376-0.148088759927-0.08332471291350.2547986834080.1255474613770.1076182213510.4140755857320.02953874465950.002067800692120.3922090279750.003837198509350.386787367449-50.961417935816.8389994383-14.3129494412
77.19302413518-1.50955248022-0.3404216167066.242278855822.057635276937.00525511121-0.0806769259054-0.965770286265-0.3425099544161.1070242895-0.03959618223070.6948551888410.711867964426-1.038741639250.1080527624810.531733431823-0.03348336362420.04545002440160.4744239684420.04953266438190.415800741662-60.3269044627.14611645598.13815638309
80.806857425051-0.9477104435471.764193435846.22560857303-0.7836515396374.197740245510.791957492249-2.344646183840.4688689236670.597086407815-0.447030183538-0.714100458647-1.067400401330.181333910147-0.1813488463781.80400409048-0.170733941325-0.1496455027782.59553710894-0.1893662689561.07749469893-50.284782411730.27626695634.0943008661
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 32 through 59 )AA32 - 591 - 28
22chain 'A' and (resid 60 through 176 )AA60 - 17629 - 145
33chain 'A' and (resid 177 through 292 )AA177 - 292146 - 231
44chain 'B' and (resid 502 through 520 )BB502 - 5201 - 19
55chain 'B' and (resid 521 through 530 )BB521 - 53020 - 29
66chain 'B' and (resid 531 through 583 )BB531 - 58330 - 82
77chain 'B' and (resid 584 through 612 )BB584 - 61283 - 111
88chain 'B' and (resid 613 through 628 )BB613 - 628112 - 127

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