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- PDB-7a59: Crimean-Congo Hemorrhagic Fever Virus Envelope Glycoprotein Gc W1... -

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Basic information

Entry
Database: PDB / ID: 7a59
TitleCrimean-Congo Hemorrhagic Fever Virus Envelope Glycoprotein Gc W1191H/W1197A/W1199A Mutant in Postfusion Conformation (Orthorhombic Crystal Form)
ComponentsEnvelopment polyprotein
KeywordsVIRAL PROTEIN / Virus Entry / Class II Membrane Fusion Protein
Function / homology
Function and homology information


host cell Golgi membrane / clathrin-dependent endocytosis of virus by host cell / host cell endoplasmic reticulum membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / virion membrane / membrane
Similarity search - Function
Nairovirus M polyprotein-like / : / : / : / : / Nairovirus GP38 / Nairovirus, structural glycoprotein Gn / Nairovirus, mucin-like domain / Nairovirus NSm / Hantavirus glycoprotein Gc ...Nairovirus M polyprotein-like / : / : / : / : / Nairovirus GP38 / Nairovirus, structural glycoprotein Gn / Nairovirus, mucin-like domain / Nairovirus NSm / Hantavirus glycoprotein Gc / : / Hantavirus glycoprotein Gc, N-terminal / Hantavirus glycoprotein Gc, C-terminal
Similarity search - Domain/homology
PHOSPHATE ION / Envelopment polyprotein
Similarity search - Component
Biological speciesCrimean-Congo hemorrhagic fever virus strain IbAr10200
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.197 Å
AuthorsHellert, J. / Guardado-Calvo, P. / Rey, F.A.
Funding support1items
OrganizationGrant numberCountry
Laboratories of Excellence (LabEx)ANR-10-LABX-62-IBEID
CitationJournal: Science / Year: 2022
Title: Structural basis of synergistic neutralization of Crimean-Congo hemorrhagic fever virus by human antibodies.
Authors: Mishra, A.K. / Hellert, J. / Freitas, N. / Guardado-Calvo, P. / Haouz, A. / Fels, J.M. / Maurer, D.P. / Abelson, D.M. / Bornholdt, Z.A. / Walker, L.M. / Chandran, K. / Cosset, F.L. / McLellan, J.S. / Rey, F.A.
History
DepositionAug 20, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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: Envelopment polyprotein
B: Envelopment polyprotein
C: Envelopment polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,25713
Polymers179,6123
Non-polymers1,64510
Water13,133729
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20920 Å2
ΔGint-109 kcal/mol
Surface area54930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.961, 216.083, 274.283
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1710-

HOH

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Envelopment polyprotein / M polyprotein


Mass: 59870.797 Da / Num. of mol.: 3 / Mutation: W1191H, W1197A, W1199A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Crimean-Congo hemorrhagic fever virus strain IbAr10200
Strain: Nigeria/IbAr10200/1970 / Gene: GP / Plasmid: pMT / Cell line (production host): Schneider 2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q8JSZ3

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Sugars , 2 types, 3 molecules

#2: 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)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 894.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-4/a4-b1_a6-e1_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]{}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: 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.: 2 / 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, 736 molecules

#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 729 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.89 Å3/Da / Density % sol: 57.38 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.75 uL of 12 mg/mL protein in 20 mM Tris-Cl pH 8.0 and 150 mM NaCl were added to 0.50 uL of reservoir solution containing 0.1 M MES pH 6.5, 0.1 M MgCl2 and 30% (v/v) PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.044 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 10, 2016 / Details: Silicon toroidal mirror coated with Rhodium
RadiationMonochromator: Silicon (1 1 1) channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.044 Å / Relative weight: 1
ReflectionResolution: 2.197→49.37 Å / Num. obs: 105875 / % possible obs: 99.8 % / Redundancy: 7.1 % / Biso Wilson estimate: 51.09 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.028 / Rrim(I) all: 0.076 / Net I/σ(I): 15.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.197-2.237.21.16749750.6740.4591.25695.8
12.03-49.376.70.0327320.9990.0130.03598.4

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.32data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.25data extraction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.197→48.91 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / Phase error: 20.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1942 1997 1.8874 %
Rwork0.1609 200086 -
obs-105807 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 222.39 Å2 / Biso mean: 72.77 Å2 / Biso min: 29.85 Å2
Refinement stepCycle: final / Resolution: 2.197→48.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11761 0 99 729 12589
Biso mean--126.36 62.37 -
Num. residues----1513
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00612161
X-RAY DIFFRACTIONf_angle_d0.82716524
X-RAY DIFFRACTIONf_chiral_restr0.0521879
X-RAY DIFFRACTIONf_plane_restr0.0052081
X-RAY DIFFRACTIONf_dihedral_angle_d17.8617364
LS refinement shellResolution: 2.197→2.276 Å
RfactorNum. reflection% reflection
Rfree0.3247 194 -
Rwork0.2926 10059 -
obs--97.83 %
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)
16.1166-2.1112-6.58410.79482.43277.4772-0.8251-0.0005-0.3411.0805-0.15791.69460.1861-1.25470.32130.86580.00650.16071.8554-0.92131.6346-34.5988-19.465235.8224
22.2277-0.88570.52640.4643-0.18952.5577-0.0985-0.52850.05230.9245-0.16840.2655-0.0659-0.28280.31830.9993-0.02280.15720.7827-0.12440.4128-18.6245-22.925251.4851
31.32560.0350.05052.13750.37191.2736-0.0355-0.05270.0601-0.0497-0.05440.45820.0361-0.27580.08530.289-0.00470.03430.4373-0.05810.5375-29.9491-31.81910.2799
42.5790.8720.75492.4711.24485.3757-0.22510.4576-0.0406-0.69830.20060.4095-0.1382-0.13440.01710.6063-0.069-0.17270.53020.0040.545-33.2548-38.7337-21.8241
51.82360.0692-0.68293.17140.77583.99930.0564-0.3718-0.20590.846-0.14430.22670.4429-0.2780.14680.6888-0.05130.17110.57860.07470.4682-19.4412-49.420836.8464
63.7581-0.7809-1.57010.40950.36360.80550.5802-0.0702-1.87940.3496-1.344-0.13710.69420.64440.71891.43740.08820.08141.15670.21431.13970.5405-49.225934.1054
73.00010.43550.75781.87830.36396.0770.0068-0.4115-0.10640.81560.0577-0.25320.40130.2309-0.05810.86210.0285-0.16650.61040.04230.40242.7618-32.946348.6742
81.21310.0832-0.01241.9645-0.26340.8025-0.06720.0354-0.195-0.12340.012-0.07030.20350.12530.04270.35170.03340.03860.4144-0.02130.4403-3.8228-42.90977.1987
92.4130.11361.33791.6280.17764.5156-0.0290.8869-0.3682-0.94010.04250.15050.35840.2435-0.03140.9393-0.0162-0.02460.7363-0.13470.5299-13.0519-46.0135-24.6198
103.46690.27610.97962.1256-0.48734.68840.0749-0.4079-0.04240.35620.0108-0.6479-0.09380.6554-0.080.4639-0.0145-0.15910.7004-0.01850.772916.9187-22.61524.1619
114.6408-3.7845-0.53484.0367-0.54641.2131.491-0.43430.74310.8016-0.2954-1.44390.9050.0329-1.04921.0287-0.2962-0.30081.0734-0.05781.327.1564-5.058824.5956
122.36740.47830.21040.41121.25564.7889-0.0429-0.50970.32130.6941-0.1323-0.1104-0.52530.07590.10980.8608-0.0556-0.18430.5805-0.10520.4131-0.5382-9.495144.8402
131.25070.0530.30392.19140.36171.1467-0.06210.15770.1319-0.2850.0288-0.1219-0.1340.08760.03270.3193-0.0124-0.0030.33230.00590.3804-8.2102-15.10532.6337
142.7031-0.28290.36921.52411.68566.20930.00960.8561-0.0937-1.271-0.06850.103-0.0619-0.11950.07051.1222-0.0434-0.09360.8036-0.00780.5298-15.9005-25.5178-27.9162
152.15821.08043.15983.41711.83715.6305-0.529-0.69580.75960.48-0.01280.2677-0.8372-0.35030.34640.72560.1933-0.02850.6622-0.27110.844-25.4604-3.743228.9988
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and ((resseq 1060:1070))B0
2X-RAY DIFFRACTION2chain 'B' and ((resseq 1077:1140) or (resseq 1232:1268) or (resseq 1422:1440))B0
3X-RAY DIFFRACTION3chain 'B' and ((resseq 1141:1154) or (resseq 1216:1231) or (resseq 1269:1350) or (resseq 1377:1421) or (resseq 1547:1553))B0
4X-RAY DIFFRACTION4chain 'B' and ((resseq 1155:1215) or (resseq 1351:1376) or (resseq 1554:1578))B0
5X-RAY DIFFRACTION5chain 'B' and ((resseq 1441:1546))B0
6X-RAY DIFFRACTION6chain 'C' and ((resseq 1061:1071))C0
7X-RAY DIFFRACTION7chain 'C' and ((resseq 1075:1140) or (resseq 1232:1268) or (resseq 1422:1440))C0
8X-RAY DIFFRACTION8chain 'C' and ((resseq 1141:1154) or (resseq 1216:1231) or (resseq 1269:1350) or (resseq 1377:1421) or (resseq 1547:1553))C0
9X-RAY DIFFRACTION9chain 'C' and ((resseq 1155:1215) or (resseq 1351:1376) or (resseq 1554:1564))C0
10X-RAY DIFFRACTION10chain 'C' and ((resseq 1441:1546))C0
11X-RAY DIFFRACTION11chain 'A' and ((resseq 1060:1071))A0
12X-RAY DIFFRACTION12chain 'A' and ((resseq 1076:1140) or (resseq 1232:1268) or (resseq 1422:1440))A0
13X-RAY DIFFRACTION13chain 'A' and ((resseq 1141:1154) or (resseq 1216:1231) or (resseq 1269:1350) or (resseq 1377:1421) or (resseq 1547:1553))A0
14X-RAY DIFFRACTION14chain 'A' and ((resseq 1155:1215) or (resseq 1351:1376) or (resseq 1554:1562))A0
15X-RAY DIFFRACTION15chain 'A' and ((resseq 1441:1546))A0

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