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- PDB-8f87: Crystal structure of Ebola Zaire envelope glycoprotein GP in comp... -

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Basic information

Entry
Database: PDB / ID: 8f87
TitleCrystal structure of Ebola Zaire envelope glycoprotein GP in complex with compound ARN75092
Components
  • GP1
  • GP2
KeywordsVIRAL PROTEIN / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE
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-XJ5 / Envelope glycoprotein
Similarity search - Component
Biological speciesEbola virus - Mayinga
Zaire (virus)
1976
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
National Institutes of Health/Office of the DirectorOD030394 United States
CitationJournal: To be Published
Title: Crystal structure of Ebola Zaire envelope glycoprotein GP in complex with compound ARN75092
Authors: Liu, L. / Battaile, K.P. / Lovell, S.
History
DepositionNov 21, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)53,5009
Polymers51,2322
Non-polymers2,2687
Water19811
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)160,50027
Polymers153,6956
Non-polymers6,80521
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 area36200 Å2
ΔGint-84 kcal/mol
Surface area46840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.199, 113.199, 306.021
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 GP1


Mass: 32309.303 Da / Num. of mol.: 1 / Fragment: EbzaA.19907.a.HE11 proteolyzed N-terminal domain / Mutation: T42A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ebola virus - Mayinga, Zaire, 1976 / Gene: GP / Plasmid: EBZAA.19907.A.HE11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q05320
#2: Protein 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.) Ebola virus - Mayinga, Zaire, 1976 / Gene: GP / Plasmid: EBZAA.19907.A.HE11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q05320

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Sugars , 2 types, 5 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-ROHGlycam 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
[][D-1-deoxy-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.: 4 / Source method: obtained synthetically / 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, 13 molecules

#5: Chemical ChemComp-XJ5 / [(4S)-4-amino-3,3-dimethylpiperidin-1-yl][(1S,3R,5R,7S)-3-methyl-5-phenyladamantan-1-yl]methanone


Mass: 380.566 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H36N2O / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 3.68 Å3/Da / Density % sol: 66.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5
Details: Proplex E2: 8% PEG8000, 0.1 M citrate, pH 5.0, 6.9 mg/mL EbzaA.19907.a.HE11.PD38351, plate: 12752-well E2 drop 2, Puck: PSL-1001, cryoprotectant: 16% PEG8000, 20% glycerol, 0.08 M citrate, ...Details: Proplex E2: 8% PEG8000, 0.1 M citrate, pH 5.0, 6.9 mg/mL EbzaA.19907.a.HE11.PD38351, plate: 12752-well E2 drop 2, Puck: PSL-1001, cryoprotectant: 16% PEG8000, 20% glycerol, 0.08 M citrate, pH 5.0, originally obtained from the complex with ARN75231, crystals were soaked in 5 mM ARN75092, 16% PEG8000, 0.1 M citrate, pH 5.0 for 24 hours before freezing

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Data collection

DiffractionMean temperature: 291 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.97949 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Aug 11, 2022
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.6→93.36 Å / Num. obs: 23674 / % possible obs: 100 % / Redundancy: 21.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.022 / Rrim(I) all: 0.103 / Χ2: 1 / Net I/σ(I): 22.2 / Num. measured all: 505303
Reflection shellResolution: 2.6→2.67 Å / % possible obs: 100 % / Redundancy: 21.2 % / Rmerge(I) obs: 1.406 / Num. measured all: 36486 / Num. unique obs: 1722 / CC1/2: 0.928 / Rpim(I) all: 0.312 / Rrim(I) all: 1.44 / Χ2: 0.97 / Net I/σ(I) obs: 2.4

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6NAE

6nae


Resolution: 2.6→51 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2282 1113 4.71 %
Rwork0.2176 --
obs0.2181 23620 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2710 0 151 11 2872
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042947
X-RAY DIFFRACTIONf_angle_d0.5814030
X-RAY DIFFRACTIONf_dihedral_angle_d15.3211094
X-RAY DIFFRACTIONf_chiral_restr0.048466
X-RAY DIFFRACTIONf_plane_restr0.007504
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.720.35321410.3162767X-RAY DIFFRACTION100
2.72-2.860.3071380.26532772X-RAY DIFFRACTION100
2.86-3.040.29821250.26572787X-RAY DIFFRACTION100
3.04-3.280.34381360.27482793X-RAY DIFFRACTION100
3.28-3.610.25291380.22812802X-RAY DIFFRACTION100
3.61-4.130.20521300.20122813X-RAY DIFFRACTION100
4.13-5.20.18751330.1742855X-RAY DIFFRACTION100
5.2-510.20121720.21682918X-RAY DIFFRACTION99
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)
12.43221.59473.19877.70762.34274.3994-0.0457-0.5487-0.05770.93680.1794-0.24330.6868-0.1306-0.0340.69770.0510.07040.53340.12160.5032-54.674114.6225-1.678
22.5932-0.52170.07692.53390.9082.8571-0.03090.2282-0.1971-0.3312-0.11740.10250.43880.01820.14240.5893-0.03610.09530.37920.01480.4587-55.558712.1268-29.0591
30.8603-0.6153-1.20313.8323.00885.8015-0.2280.2081-0.2538-0.28010.0478-0.13931.24710.28450.14070.99950.05780.1470.51890.00080.6165-47.6167-1.3628-34.9267
45.44073.4137-0.51012.7622-0.64717.3998-0.06710.3855-0.41871.37620.0593-0.05641.2007-0.16860.0090.95720.0720.16360.44450.04460.6397-49.96044.6386-10.6463
55.4325-0.17271.46084.3033.93455.76160.4995-0.5471-1.66473.1446-1.03580.52382.10171.56920.44871.32010.2638-0.06961.02780.06511.1463-31.710626.8312-12.7851
61.68070.8369-0.14012.1802-0.41951.94210.0386-0.0694-0.13570.3058-0.1904-0.09920.34880.0610.16650.56320.02560.04370.4372-0.01210.4461-50.471416.6716-14.3486
74.4006-2.2546-1.92985.96515.89425.8249-0.131-0.4583-0.22830.9352-0.21210.60281.3217-0.51010.29570.70650.02310.0460.5320.04820.6006-58.989326.33981.0085
84.84883.0065-5.28473.0542-4.74497.6252-0.66150.1218-0.51681.08490.42940.75031.1082-0.78220.22251.3351-0.00680.19991.0867-0.04740.9561-61.106627.261817.0961
98.4357-1.8237-4.64023.98982.87543.52510.40841.23941.54110.07511.2704-0.05531.010.5127-1.48771.84920.4470.23362.32820.21731.5103-50.114129.228827.944
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 32 through 73 )
2X-RAY DIFFRACTION2chain 'A' and (resid 74 through 176 )
3X-RAY DIFFRACTION3chain 'A' and (resid 177 through 292 )
4X-RAY DIFFRACTION4chain 'B' and (resid 502 through 520 )
5X-RAY DIFFRACTION5chain 'B' and (resid 521 through 530 )
6X-RAY DIFFRACTION6chain 'B' and (resid 531 through 583 )
7X-RAY DIFFRACTION7chain 'B' and (resid 584 through 597 )
8X-RAY DIFFRACTION8chain 'B' and (resid 598 through 612 )
9X-RAY DIFFRACTION9chain 'B' and (resid 613 through 618 )

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