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

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Basic information

Entry
Database: PDB / ID: 7lyy
TitleCrystal Structure of Ebola zaire Envelope glycoprotein GP in complex with compound ARN0075164
Components
  • GP1
  • GP2
KeywordsVIRAL PROTEIN / SSGCID / Envelope glycoprotein / Zaire ebolavirus / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
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
Chem-YPM / Envelope glycoprotein
Similarity search - Component
Biological speciesZaire ebolavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of Ebola zaire Envelope glycoprotein GP in complex with compound ARN0075164
Authors: Abendroth, J. / Horanyi, P.S. / Lorimer, D.D. / Edwards, T.E.
History
DepositionMar 8, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GP1
B: GP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,39511
Polymers51,1472
Non-polymers2,2489
Water1,40578
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)160,18533
Polymers153,4406
Non-polymers6,74527
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 area36220 Å2
ΔGint-58 kcal/mol
Surface area47220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.400, 114.400, 307.890
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
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


Mass: 32224.197 Da / Num. of mol.: 1 / Fragment: proteolyzed EbzaA.19907.a.HE11 N-terminal domain / 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: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q05320
#2: Protein GP2


Mass: 18922.320 Da / Num. of mol.: 1 / Fragment: proteolyzed EbzaA.19907.a.HE11 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: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / 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
[][D-1-deoxy-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 , 3 types, 82 molecules

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


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-YPM / (1s,3R,5S,7s)-N-[(1r,4r)-4-aminocyclohexyl]-3,5-diphenyladamantane-1-carboxamide


Mass: 428.609 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H36N2O
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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

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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: 3.38 Å3/Da / Density % sol: 63.7 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 5
Details: Molecular Dimensions / Calibre Proplex screen e2: 100mM sodium citrate pH 5.0, 8% (w/V) PEG 8000: EbzaA.19907.a.HE11.PD38351 at 10.61 mg/ml + 1mM compound AN75164/BSI110991: tray 313199e2, ...Details: Molecular Dimensions / Calibre Proplex screen e2: 100mM sodium citrate pH 5.0, 8% (w/V) PEG 8000: EbzaA.19907.a.HE11.PD38351 at 10.61 mg/ml + 1mM compound AN75164/BSI110991: tray 313199e2, cryo: 20% EG + 5mM compound: puck puk2-8

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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: Feb 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: 2.75→50 Å / Num. obs: 20588 / % possible obs: 99.9 % / Redundancy: 5.511 % / Biso Wilson estimate: 66.76 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.6
Reflection shellResolution: 2.75→2.82 Å / Redundancy: 5.66 % / Rmerge(I) obs: 0.597 / Mean I/σ(I) obs: 2.84 / Num. unique obs: 1504 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 6F5U

6f5u


Resolution: 2.75→47.16 Å / SU ML: 0.349 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.117
Stereochemistry target values: GEOSTD + MONOMER LIBRARY + CDL V1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.225 2085 10.14 %0
Rwork0.183 ---
obs0.188 20572 99.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 79.7 Å2
Refinement stepCycle: LAST / Resolution: 2.75→47.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2704 0 150 78 2932
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052925
X-RAY DIFFRACTIONf_angle_d0.6673990
X-RAY DIFFRACTIONf_dihedral_angle_d12.6081017
X-RAY DIFFRACTIONf_chiral_restr0.065473
X-RAY DIFFRACTIONf_plane_restr0.006501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.810.28341350.24991214X-RAY DIFFRACTION100
2.81-2.880.26371420.23071215X-RAY DIFFRACTION100
2.88-2.960.31671370.23481205X-RAY DIFFRACTION100
2.96-3.050.36831230.25521240X-RAY DIFFRACTION100
3.05-3.150.25831460.21361189X-RAY DIFFRACTION100
3.15-3.260.26251330.20721231X-RAY DIFFRACTION100
3.26-3.390.2521490.20021212X-RAY DIFFRACTION100
3.39-3.540.23821200.19531239X-RAY DIFFRACTION100
3.55-3.730.23531120.19531260X-RAY DIFFRACTION100
3.73-3.970.22811510.16711221X-RAY DIFFRACTION100
3.97-4.270.18551390.14861219X-RAY DIFFRACTION100
4.27-4.70.1641540.13711242X-RAY DIFFRACTION100
4.7-5.380.2051460.15481229X-RAY DIFFRACTION100
5.38-6.770.21481390.1881272X-RAY DIFFRACTION100
6.78-47.160.23681590.19711299X-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)
19.2569-1.23456.2792.3466-2.95676.7381-0.3312-1.6921-0.79921.66190.5636-0.23481.1777-1.1915-0.29911.18550.07760.02840.70350.03050.549-57.438911.52070.7755
21.34291.09211.72082.72922.82563.33410.0034-0.5729-1.23941.59930.22020.2791.7248-0.9712-0.2811.1763-0.06480.17450.90910.10831.0437-58.243119.81276.179
32.9386-0.5783-0.20273.47410.89684.3033-0.02220.246-0.2191-0.3165-0.09890.0180.5389-0.02930.12140.5036-0.03750.0810.2907-0.02170.394-55.859712.4704-27.1143
41.5843-1.1804-1.49465.78824.44013.5461-0.30870.11940.0003-0.15480.2369-0.31020.54651.09990.09080.63140.06690.07850.50950.04480.4959-49.3349.5944-22.0118
56.0677-2.4707-0.58215.62141.77775.4043-0.49020.5529-0.9489-0.61860.1994-0.0481.11640.07970.25221.38910.11820.17290.6179-0.12390.6483-49.0674-3.5299-39.8302
60.76831.21842.01236.6622-0.13249.1055-0.5815-0.0876-0.346-0.083-0.00920.04642.49170.79240.58421.51380.22930.3110.7886-0.10631.0145-46.7526-6.9348-40.1368
73.89345.4726-0.52339.5999-4.19686.8603-0.02510.5285-0.45130.39250.25170.13211.0745-0.1844-0.29930.80590.08330.06910.41340.00010.5593-51.87534.0446-10.22
83.14962.0705-4.66498.5254-3.49766.97981.4755-2.5121-1.47061.2611-2.1707-0.43851.22751.98720.5181.1288-0.1447-0.08880.92550.34621.1573-33.76926.1898-12.8638
91.25710.7729-0.25351.8879-0.15962.57110.0936-0.1151-0.08810.1282-0.2486-0.13550.51010.22710.14340.58930.04710.03090.4313-0.00750.4995-51.049116.8854-14.2934
106.1181-4.8461-4.20188.08775.72734.2263-0.1718-0.4383-0.83330.7912-0.14670.47911.1072-0.23420.26420.6049-0.044-0.03830.36750.03470.4926-59.754626.88280.5357
116.4272-0.1597-2.89983.141-2.43593.3826-0.661-0.2746-1.11112.0842-0.12230.55510.791-0.81360.74071.4099-0.04170.08041.04730.02840.8981-61.866727.763217.2566
120.62661.5421.47614.26514.1133.96370.7998-1.62321.12041.1393-1.1420.04252.9077-6.21820.4941.9638-0.06850.3762.6456-0.3611.3272-50.443129.630430.8679
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 32 THROUGH 45 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 46 THROUGH 59 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 60 THROUGH 176 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 177 THROUGH 223 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 224 THROUGH 263 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 264 THROUGH 292 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 502 THROUGH 519 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 520 THROUGH 529 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 530 THROUGH 583 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 584 THROUGH 597 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 598 THROUGH 612 )
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESID 613 THROUGH 622 )

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