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- PDB-7m2d: Crystal Structure of Ebola zaire Envelope glycoprotein GP in comp... -

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Basic information

Entry
Database: PDB / ID: 7m2d
TitleCrystal Structure of Ebola zaire Envelope glycoprotein GP in complex with compound ARN0074953
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-YPS / Envelope glycoprotein
Similarity search - Component
Biological speciesZaire ebolavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 ARN0074953
Authors: Abendroth, J. / Horanyi, P.S. / Lorimer, D.D. / Edwards, T.E.
History
DepositionMar 16, 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 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)53,1918
Polymers51,1472
Non-polymers2,0446
Water1,53185
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)159,57224
Polymers153,4406
Non-polymers6,13218
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 area34370 Å2
ΔGint-96 kcal/mol
Surface area47490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.110, 115.110, 309.020
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: 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: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q05320
#2: Protein GP2


Mass: 18922.320 Da / Num. of mol.: 1 / 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 , 2 types, 86 molecules

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


Mass: 410.592 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H38N2O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 3.44 Å3/Da / Density % sol: 64.2 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Molecular Dimensions / Calibre Proplex screen b3: 200mM sodium acetate trihydrate, 100mM sodium citrate pH 5.5, 10% (w/V) PEG 4000: EbzaA.19907.a.HE11.PD38351 at 10.61 mg/ml + 1mM compound ...Details: Molecular Dimensions / Calibre Proplex screen b3: 200mM sodium acetate trihydrate, 100mM sodium citrate pH 5.5, 10% (w/V) PEG 4000: EbzaA.19907.a.HE11.PD38351 at 10.61 mg/ml + 1mM compound AN0074953/BSI110987: tray 313163b3, cryo: 20% ethylene glycol + 5mM compound: puck auf7-9

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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 4, 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: 2.7→50 Å / Num. obs: 22091 / % possible obs: 99.9 % / Redundancy: 7.885 % / Biso Wilson estimate: 65.88 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 19.49
Reflection shellResolution: 2.7→2.77 Å / Redundancy: 8.12 % / Rmerge(I) obs: 0.655 / Mean I/σ(I) obs: 2.88 / Num. unique obs: 1625 / % possible all: 99.9

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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: 2.7→47.44 Å / SU ML: 0.389 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.666
Stereochemistry target values: GEOSTD + MONOMER LIBRARY + CDL V1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.225 2123 9.62 %0
Rwork0.189 ---
obs0.192 22058 99.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 74.29 Å2
Refinement stepCycle: LAST / Resolution: 2.7→47.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2721 0 136 85 2942
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052927
X-RAY DIFFRACTIONf_angle_d0.6553997
X-RAY DIFFRACTIONf_dihedral_angle_d12.8291019
X-RAY DIFFRACTIONf_chiral_restr0.048470
X-RAY DIFFRACTIONf_plane_restr0.006502
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.760.38691440.3591317X-RAY DIFFRACTION100
2.76-2.830.33481560.29731280X-RAY DIFFRACTION100
2.83-2.910.30761470.25561308X-RAY DIFFRACTION100
2.91-2.990.29391320.21361312X-RAY DIFFRACTION100
2.99-3.090.27291160.2241329X-RAY DIFFRACTION100
3.09-3.20.26421410.22841316X-RAY DIFFRACTION100
3.2-3.330.27011090.23631344X-RAY DIFFRACTION100
3.33-3.480.30031340.24491328X-RAY DIFFRACTION100
3.48-3.660.21451420.18521326X-RAY DIFFRACTION100
3.66-3.890.2211640.16661293X-RAY DIFFRACTION100
3.89-4.190.16191500.15591319X-RAY DIFFRACTION100
4.19-4.620.17231590.13481331X-RAY DIFFRACTION100
4.62-5.280.20441300.14851356X-RAY DIFFRACTION100
5.28-6.650.19851140.18121382X-RAY DIFFRACTION100
6.65-47.440.231850.19821394X-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)
13.5105-3.1727-3.88912.88863.54044.32710.8883-1.5980.41440.8706-0.6811-0.28571.423-5.5092-0.10291.75950.02760.1332.4521-0.36521.0113-50.807329.828230.8945
24.5618-4.98832.93095.401-3.13571.832-0.7203-2.1695-0.83981.75091.16870.38110.4111-1.4605-0.20660.8725-0.0020.00920.79560.04760.5442-58.090411.9020.5839
33.23994.9069-1.84837.9962-0.68577.3857-0.964-0.3412-1.77770.7110.4617-0.78531.1494-1.34780.32691.01250.03480.14090.9920.03880.8351-58.485820.04876.3355
42.6671-0.05930.21232.68250.78823.9389-0.05340.166-0.1482-0.2439-0.08920.00440.38110.00350.13580.4749-0.02830.05850.30130.01010.4376-56.02912.7362-26.8869
51.1415-0.7461-1.55575.60734.44045.9847-0.22110.0977-0.0546-0.22110.3175-0.40590.56931.2722-0.06810.47010.08820.00650.41260.00610.536-49.12919.4759-22.7828
66.2093-5.6882-4.66115.12434.2263.5543-0.25540.8646-1.1467-0.1719-0.16450.46961.0826-0.13830.53741.22370.01870.02910.6744-0.04290.716-56.850.785-40.6603
76.2182-0.1429-0.87146.79742.67226.2364-0.28390.1898-0.69010.1923-0.27270.77270.7065-1.02920.7330.9517-0.03440.06870.494-0.12910.7074-50.5358-4.778-40.2435
82.84082.01250.83618.1618-0.7793.3154-0.01560.1618-1.66420.65570.2919-1.27521.72212.2854-0.40781.0730.29690.12470.7614-0.16780.9341-40.5365-5.9121-38.3041
91.32981.39312.47383.92114.06415.663-0.31950.1522-0.380.19550.1284-0.15611.68440.59090.25141.36450.28540.25240.6618-0.03720.9562-46.8641-6.8961-39.5681
109.28234.0429-0.12393.5115-2.81364.29950.1662-0.0068-0.42340.7686-0.12560.18470.9736-0.29870.02120.77270.01110.15180.3516-0.03730.6326-51.47094.1453-10.3842
114.7004-4.4735-1.41586.5563-1.31735.19650.3916-1.57811.50681.1658-0.6703-4.25120.3261.26350.05420.9343-0.1201-0.1450.94840.11561.3335-39.490924.2938-11.1317
120.8329-0.08810.25793.51753.42375.1067-0.5795-0.43391.47571.18221.23661.87840.1984-2.0267-0.64140.66790.1530.15471.06080.17541.4256-28.371829.0537-14.4964
133.88224.9525-2.2467.0915-2.04662.1821-0.0756-0.0852-0.411-0.1059-0.2352-1.00970.4580.52330.34750.4850.1443-0.01890.65940.04970.5889-37.029320.4179-17.686
145.3425-3.38663.525.9806-3.75535.5322-0.1028-0.3103-0.09170.10910.0671-0.02220.5378-0.50870.01870.5085-0.0590.08540.4012-0.06610.4996-60.287615.1902-12.0663
157.6805-3.0321-2.75484.56155.43376.6160.0874-0.4747-0.52430.5551-0.01870.55280.8904-0.5331-0.06990.4691-0.0393-0.0320.37880.05450.4596-60.015427.08910.6794
163.9359-1.5797-1.54943.6474-4.01467.7757-1.1129-1.7406-0.76961.78620.72430.7781.3223-0.05410.41371.38210.13690.14721.12870.11830.8121-62.133327.843117.3583
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'B' AND (RESID 613 THROUGH 622 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 31 THROUGH 45 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 46 THROUGH 59 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 60 THROUGH 176 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 177 THROUGH 223 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 224 THROUGH 237 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 238 THROUGH 249 )
8X-RAY DIFFRACTION8CHAIN 'A' AND (RESID 250 THROUGH 263 )
9X-RAY DIFFRACTION9CHAIN 'A' AND (RESID 264 THROUGH 292 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 502 THROUGH 519 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 520 THROUGH 524 )
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESID 525 THROUGH 529 )
13X-RAY DIFFRACTION13CHAIN 'B' AND (RESID 530 THROUGH 550 )
14X-RAY DIFFRACTION14CHAIN 'B' AND (RESID 551 THROUGH 583 )
15X-RAY DIFFRACTION15CHAIN 'B' AND (RESID 584 THROUGH 597 )
16X-RAY DIFFRACTION16CHAIN 'B' AND (RESID 598 THROUGH 612 )

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