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

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Basic information

Entry
Database: PDB / ID: 7lyd
TitleCrystal Structure of Ebola zaire Envelope glycoprotein GP in complex with compound ARN0075146
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


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-YOD / Envelope glycoprotein
Similarity search - Component
Biological speciesZaire ebolavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 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 ARN0075146
Authors: Abendroth, J. / Dranow, D.M. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionMar 6, 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
Revision 1.2Nov 13, 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)53,62410
Polymers51,2322
Non-polymers2,3928
Water3,243180
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)160,87230
Polymers153,6956
Non-polymers7,17724
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 area36450 Å2
ΔGint-81 kcal/mol
Surface area49250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.170, 114.170, 308.720
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: 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.) 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: 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: 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-(1-3)-[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
[][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: 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, 183 molecules

#5: Chemical ChemComp-YOD / (1R,3S,5S,7S)-N-[(1r,4R)-4-aminocyclohexyl]-3-[(methylsulfanyl)methyl]-5-phenyladamantane-1-carboxamide


Mass: 412.631 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H36N2OS
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY
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: 63.6 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Molecular Dimensions/Calibre Morpheus screen A11: 10% (w/V) PEG 4000, 20% (V/V) glycerol, 30mM of each magnesium chloride and calcium chloride, 100mM bicine/Trizma base pH 8.5: EbzaA.19907.a. ...Details: Molecular Dimensions/Calibre Morpheus screen A11: 10% (w/V) PEG 4000, 20% (V/V) glycerol, 30mM of each magnesium chloride and calcium chloride, 100mM bicine/Trizma base pH 8.5: EbzaA.19907.a.HE11.PD38351 at 10.61 mg/ml: over night soak with 1mM compound ARN0075146 (BSI110990): tray 313149a11, cryo: direct: puck hdp6-5

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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: Nov 14, 2019 / 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: 2.35→50 Å / Num. obs: 32679 / % possible obs: 99.9 % / Redundancy: 6.824 % / Biso Wilson estimate: 54.11 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 22.26
Reflection shellResolution: 2.35→2.41 Å / Redundancy: 6.91 % / Rmerge(I) obs: 0.565 / Mean I/σ(I) obs: 2.96 / Num. unique obs: 2366 / % possible all: 100

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Processing

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

6f5u


Resolution: 2.35→41.63 Å / SU ML: 0.267 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.961
Stereochemistry target values: GEOSTD + MONOMER LIBRARY + CDL V1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.205 2032 6.23 %0
Rwork0.177 ---
obs0.179 32635 99.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 65.07 Å2
Refinement stepCycle: LAST / Resolution: 2.35→41.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2768 0 158 180 3106
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063014
X-RAY DIFFRACTIONf_angle_d0.7364119
X-RAY DIFFRACTIONf_dihedral_angle_d12.31054
X-RAY DIFFRACTIONf_chiral_restr0.048487
X-RAY DIFFRACTIONf_plane_restr0.007518
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.40.29731320.26112003X-RAY DIFFRACTION100
2.4-2.460.29191170.23972012X-RAY DIFFRACTION99
2.46-2.530.27991360.22012026X-RAY DIFFRACTION100
2.53-2.610.24071340.20242014X-RAY DIFFRACTION100
2.61-2.690.21831380.19241999X-RAY DIFFRACTION100
2.69-2.790.24391480.19952038X-RAY DIFFRACTION100
2.79-2.90.28221260.19662009X-RAY DIFFRACTION100
2.9-3.030.19691570.1812005X-RAY DIFFRACTION100
3.03-3.190.21961310.17782027X-RAY DIFFRACTION100
3.19-3.390.21071220.18762063X-RAY DIFFRACTION100
3.39-3.650.19611490.17262012X-RAY DIFFRACTION100
3.65-4.020.18241420.15432054X-RAY DIFFRACTION100
4.02-4.60.15281230.13372082X-RAY DIFFRACTION100
4.6-5.790.19121510.16162080X-RAY DIFFRACTION100
5.79-41.630.211260.19882179X-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)
16.5394-2.26231.37567.3042-1.95046.6346-0.6342-2.0747-1.30671.49121.0730.48380.5944-1.3515-0.39310.77330.00530.13640.66920.09080.4025-57.152511.62760.6838
29.31613.7452-4.84578.98991.01997.2091-0.6924-0.3565-1.45971.29750.1526-0.12771.6102-0.94680.49661.10550.05770.1370.84670.10020.6782-57.931319.90046.3543
31.9228-0.620.00021.95870.64483.8394-0.01220.152-0.1599-0.1974-0.11510.01950.4215-0.07080.11920.3903-0.01980.040.25160.01590.3115-55.234612.6382-26.5834
41.1823-0.53-0.89755.24613.64038.1665-0.15890.1667-0.1047-0.4372-0.0962-0.0650.60930.46920.22860.47870.06860.08430.28410.07870.3926-51.28615.9604-29.8044
55.15940.8607-0.77967.51271.41898.7874-0.43170.1474-0.6965-0.182-0.0177-0.17381.38970.38860.47711.040.14090.17950.4339-0.030.5234-44.5141-5.5689-39.1015
60.80591.1431.17264.97433.72933.0735-0.18190.214-0.1861-0.19130.026-0.291.76370.6160.15171.05650.2570.12190.56640.00420.6471-46.1945-7.249-38.3563
76.53432.95790.40795.5354-0.93864.5541-0.0498-0.118-0.48050.6027-0.0371-0.06320.93940.0580.08660.72460.04190.07290.32660.04150.4049-50.53734.0045-10.3394
87.22345.79941.93374.66981.27682.33722.0761-2.4069-0.10461.9429-1.90140.20680.49741.033-0.11080.7282-0.18060.02430.88480.12131.1827-33.93826.4546-12.7556
91.65442.6508-1.13984.9702-1.29191.0162-0.130.008-0.2184-0.0378-0.0337-0.68520.18150.08340.18280.39220.1130.01490.54370.06830.525-36.416120.4039-17.7303
102.7775-1.02680.22953.8524-0.92863.2248-0.1448-0.1929-0.08780.24390.03590.11720.3167-0.29030.0850.3964-0.05540.04480.3491-0.01620.3719-59.573314.9485-12.095
117.5914-0.99150.0875.2804-0.43896.4319-0.0967-1.3902-0.3991.4772-0.12630.74120.4727-1.16490.15230.7436-0.05560.07410.63780.04610.4518-60.495827.22798.1739
120.05270.0635-0.07740.0648-0.07690.10080.0627-0.17360.40840.8355-0.7045-0.31241.67910.16690.57381.6633-0.2188-0.243.3846-0.34520.9844-50.128530.45635.7339
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 31 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 237 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 238 THROUGH 263 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 264 THROUGH 293 )
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 550 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 551 THROUGH 583 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 584 THROUGH 612 )
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESID 613 THROUGH 629 )

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