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

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Basic information

Entry
Database: PDB / ID: 7ssr
TitleCrystal Structure of Ebola zaire Envelope glycoprotein GP in complex with compound ARN0075093
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-ZTL / Envelope glycoprotein
Similarity search - Component
Biological speciesZaire ebolavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 ARN0075093
Authors: Abendroth, J. / 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)57,32011
Polymers55,1402
Non-polymers2,1809
Water2,936163
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)171,96033
Polymers165,4206
Non-polymers6,54127
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 area36610 Å2
ΔGint-89 kcal/mol
Surface area47310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.070, 114.070, 308.090
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: 36217.613 Da / Num. of mol.: 1
Fragment: 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 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


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, 167 molecules

#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-ZTL / (1R,2s,3S,5s,7s)-N-[(1r,4r)-4-(aminomethyl)cyclohexyl]-5-phenyladamantane-2-carboxamide


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


Mass: 18.015 Da / Num. of mol.: 163 / 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: 3.37 Å3/Da / Density % sol: 63.5 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 4.3
Details: Optimization condition around ProPlex screen, condition E1: 100mM sodium acetate / hydrochloride pH 4.3, 8.07% (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 4.3, 8.07% (w/V) PEG 8000, 100mM magnesium chloride: EbzaA.19907.a.HE11.PD38458 at 14.4mg/ml + 1mM BSI110988 / ARN00075093: tray 322831c7: cryo: 25% EG + 1mM compound: puck sni3-1

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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: 2.5→50 Å / Num. obs: 26682 / % possible obs: 98.2 % / Redundancy: 4.711 % / Biso Wilson estimate: 63.04 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.056 / Rrim(I) all: 0.062 / Χ2: 0.935 / Net I/σ(I): 16.24
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.5-2.564.7390.6192.3419720.8570.69599.5
2.56-2.644.7610.4633.1519190.9170.51999.3
2.64-2.714.7450.3534.2318680.9490.39699
2.71-2.84.7890.2785.3217990.9640.31198.9
2.8-2.894.7820.1987.3417410.9810.22299
2.89-2.994.7520.1519.2817080.9870.1798.7
2.99-3.14.7550.1211.6416140.990.13598.2
3.1-3.234.7720.09714.2915720.9910.10998.5
3.23-3.374.7380.07816.9915230.9940.08798.1
3.37-3.544.7110.06220.9514350.9960.0798.6
3.54-3.734.6990.05123.9213790.9970.05798
3.73-3.954.6780.04926.4813130.9970.05498
3.95-4.234.6730.04428.4312200.9980.04998.1
4.23-4.564.6140.04130.9311530.9980.04698.3
4.56-54.6450.0431.2110480.9980.04497.7
5-5.594.6430.03930.389710.9980.04498.2
5.59-6.454.6270.03630.888560.9980.0497.5
6.45-7.914.6010.03432.147170.9980.03896.2
7.91-11.184.5820.03334.415640.9980.03693.8
11.18-504.1610.03232.483100.9980.03787.3

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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: 2.5→31.93 Å / SU ML: 0.2421 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.6252
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.197 2000 7.5 %0
Rwork0.1729 24655 --
obs0.1748 26655 98.22 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 72.9 Å2
Refinement stepCycle: LAST / Resolution: 2.5→31.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2737 0 175 163 3075
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00593045
X-RAY DIFFRACTIONf_angle_d0.75454161
X-RAY DIFFRACTIONf_chiral_restr0.0498485
X-RAY DIFFRACTIONf_plane_restr0.0063528
X-RAY DIFFRACTIONf_dihedral_angle_d12.83741079
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.560.29821500.24741758X-RAY DIFFRACTION99.53
2.56-2.630.24991390.21061749X-RAY DIFFRACTION99.11
2.63-2.710.2411540.20431745X-RAY DIFFRACTION98.96
2.71-2.80.24921550.21131729X-RAY DIFFRACTION98.9
2.8-2.90.25361480.20631756X-RAY DIFFRACTION98.91
2.9-3.010.22331380.19731738X-RAY DIFFRACTION98.43
3.01-3.150.23451400.17541767X-RAY DIFFRACTION98.65
3.15-3.320.2191190.19841776X-RAY DIFFRACTION98.08
3.32-3.520.23871420.19251730X-RAY DIFFRACTION98.27
3.52-3.790.18471340.15831796X-RAY DIFFRACTION98.27
3.79-4.180.14241440.14491745X-RAY DIFFRACTION97.98
4.18-4.780.14231550.12831761X-RAY DIFFRACTION98.01
4.78-6.010.18381420.16191796X-RAY DIFFRACTION97.78
6.01-31.930.21661400.19291809X-RAY DIFFRACTION94.47
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)
10.2959360073420.9676170587070.7890818774677.352122246680.4935259869223.038777323890.0565044812468-0.734093128576-0.1885753155631.25114803774-0.1223803103720.0002481730777040.528442385773-0.5781612709550.1140004867240.6624151432930.01423064318280.1161184568210.5820919003340.007776255957660.514226233985-57.737601984315.40735909323.40655521213
21.99803430498-0.815989461742-0.5291727833343.224661529661.063647177693.56494474651-0.04981158116360.272393915526-0.24580250414-0.324564574242-0.0498841186470.07011828728190.383867068778-0.09684143286510.09607280013950.443040914115-0.04564284124180.05526795403280.334631363886-0.03164082872710.38837007964-55.511234384812.3811629521-27.0004048519
31.52610332848-1.48255913276-2.116626331255.506713394743.409357014475.24342034891-0.1312583768930.242243413938-0.35310517663-0.5714473105910.13184530998-0.2890482620650.670196893410.633718531155-0.01160798087730.7367550946690.07331507359170.08298315265360.49728315611-0.05296112020910.545476597256-48.91619627751.05917293843-33.3142203405
41.029685804831.535161267131.623243372774.816894806143.554648383393.07460884568-0.2226860005090.299340035917-0.324395280711-0.668533585436-0.0194316753138-0.1384023203022.300289566921.001586841980.1847409963851.397213231120.345814620360.1250304576810.651434352434-0.09436770770670.844388469576-45.902380359-7.23545138207-39.3105182004
56.871958124824.002427481371.020537545646.30389727133-1.132194969835.822760915430.0527834239405-0.195773834731-0.3188595559920.899772638466-0.06788381911790.2377699652880.867403947825-0.2060171866180.01381356739940.6155515038680.04322146620460.09223071462580.3113677997560.001926779785980.485772974325-51.4732842154.19246158878-10.2318825203
60.7041538678162.177796185830.651488996676.742155570392.010191043020.6769111951050.755322462805-1.20822399825-0.8473391185391.23861979807-1.13528945148-1.750489111530.7740790211311.353305338380.5999743521560.876467078866-0.107058486476-0.09357801683570.8079286863030.2415096308090.993416812724-34.342636974325.6031918653-12.1884184363
71.265520057980.05944090503680.3285753053151.713444006590.5187107548840.686022013429-0.100227075582-0.171236059002-0.05762534421230.40543920411-0.02183050475770.08698707127050.360124564568-0.09678497180930.1170112782310.4374170637310.01475280133550.02709712023780.3694975146430.03810801518730.371133874804-54.041362818620.4171235737-6.61693507144
81.437359664831.495534223371.768096135663.922784628594.321763009944.7752993221-0.0655845827461.30685277517-0.255265633612-2.59405590952-0.1439586334270.3387417413710.126528004167-0.9064889174850.3526019356881.92178102715-0.2680039563-0.00968731583253.1450151644-0.3352475710040.839733950552-50.531467807330.062924096232.5743759582
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 262 )AA177 - 262146 - 208
44chain 'A' and (resid 263 through 292 )AA263 - 292209 - 231
55chain 'B' and (resid 502 through 519 )BB502 - 5191 - 18
66chain 'B' and (resid 520 through 529 )BB520 - 52919 - 28
77chain 'B' and (resid 530 through 612 )BB530 - 61229 - 111
88chain 'B' and (resid 613 through 626 )BB613 - 626112 - 125

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