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- PDB-7a5a: Crimean-Congo Hemorrhagic Fever Virus Envelope Glycoprotein Gc W1... -

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Basic information

Entry
Database: PDB / ID: 7a5a
TitleCrimean-Congo Hemorrhagic Fever Virus Envelope Glycoprotein Gc W1191H/W1197A/W1199A Mutant in Postfusion Conformation (Monoclinic 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
Envelopment polyprotein
Similarity search - Component
Biological speciesCrimean-Congo hemorrhagic fever virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.989 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 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Oct 9, 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: Envelopment polyprotein
B: Envelopment polyprotein
C: Envelopment polyprotein
D: Envelopment polyprotein
E: Envelopment polyprotein
F: Envelopment polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)361,91020
Polymers359,7426
Non-polymers2,16814
Water00
1
A: Envelopment polyprotein
B: Envelopment polyprotein
C: Envelopment polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,30412
Polymers179,8713
Non-polymers1,4349
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19730 Å2
ΔGint-79 kcal/mol
Surface area55370 Å2
MethodPISA
2
D: Envelopment polyprotein
E: Envelopment polyprotein
F: Envelopment polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,6058
Polymers179,8713
Non-polymers7355
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18970 Å2
ΔGint-65 kcal/mol
Surface area54800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.971, 108.260, 223.535
Angle α, β, γ (deg.)90.000, 93.220, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 1066 and (name O or name...
21(chain B and ((resid 1066 and (name O or name...
31(chain C and ((resid 1066 and (name N or name...
41(chain D and ((resid 1066 and (name N or name...
51(chain E and ((resid 1066 and (name N or name...
61(chain F and ((resid 1066 and (name N or name...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAALAALA(chain A and ((resid 1066 and (name O or name...AA106634
12THRTHRSERSER(chain A and ((resid 1066 and (name O or name...AA1060 - 156428 - 532
13THRTHRSERSER(chain A and ((resid 1066 and (name O or name...AA1060 - 156428 - 532
14THRTHRSERSER(chain A and ((resid 1066 and (name O or name...AA1060 - 156428 - 532
21ALAALAALAALA(chain B and ((resid 1066 and (name O or name...BB106634
22THRTHRSERSER(chain B and ((resid 1066 and (name O or name...BB1060 - 156428 - 532
23THRTHRSERSER(chain B and ((resid 1066 and (name O or name...BB1060 - 156428 - 532
24THRTHRSERSER(chain B and ((resid 1066 and (name O or name...BB1060 - 156428 - 532
31ALAALAALAALA(chain C and ((resid 1066 and (name N or name...CC106634
32SERSERSERSER(chain C and ((resid 1066 and (name N or name...CC1061 - 156429 - 532
33SERSERSERSER(chain C and ((resid 1066 and (name N or name...CC1061 - 156429 - 532
34SERSERSERSER(chain C and ((resid 1066 and (name N or name...CC1061 - 156429 - 532
41ALAALAALAALA(chain D and ((resid 1066 and (name N or name...DD106634
42THRTHRSERSER(chain D and ((resid 1066 and (name N or name...DD1060 - 156428 - 532
43THRTHRSERSER(chain D and ((resid 1066 and (name N or name...DD1060 - 156428 - 532
44THRTHRSERSER(chain D and ((resid 1066 and (name N or name...DD1060 - 156428 - 532
51ALAALAALAALA(chain E and ((resid 1066 and (name N or name...EE106634
52THRTHRSERSER(chain E and ((resid 1066 and (name N or name...EE1060 - 156428 - 532
53THRTHRSERSER(chain E and ((resid 1066 and (name N or name...EE1060 - 156428 - 532
54THRTHRSERSER(chain E and ((resid 1066 and (name N or name...EE1060 - 156428 - 532
61ALAALAALAALA(chain F and ((resid 1066 and (name N or name...FF106634
62THRTHRSERSER(chain F and ((resid 1066 and (name N or name...FF1060 - 156428 - 532
63THRTHRSERSER(chain F and ((resid 1066 and (name N or name...FF1060 - 156428 - 532
64THRTHRSERSER(chain F and ((resid 1066 and (name N or name...FF1060 - 156428 - 532

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Components

#1: Protein
Envelopment polyprotein / M polyprotein


Mass: 59956.949 Da / Num. of mol.: 6 / Mutation: W1191H, W1199A, W1197A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Crimean-Congo hemorrhagic fever virus (strain Nigeria/IbAr10200/1970)
Strain: Nigeria/IbAr10200/1970 / Gene: GP / Plasmid: pMT / Cell line (production host): Schneider 2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q8JSZ3
#2: 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.: 9 / 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
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
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: 2.58 Å3/Da / Density % sol: 52.41 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.5 uL of 13.4 mg/mL protein in 20 mM Tris-Cl pH 8.0, 150 mM NaCl were added to 0.5 uL of reservoir solution containing 0.1 M HEPES pH 7.5, 10% (w/v) PEG 8K, 8% (v/v) ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 8, 2017
Details: Cryogenically cooled channel cut crystal monochromator, a convex prefocussing mirror and a Kirkpatrick-Baez pair of focussing mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.989→49.6 Å / Num. obs: 73919 / % possible obs: 99.3 % / Redundancy: 7 % / Biso Wilson estimate: 79.08 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.184 / Rpim(I) all: 0.075 / Rrim(I) all: 0.198 / Net I/σ(I): 7.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.99-3.0561.4112443140430.5550.6161.5441.289.2
14.64-49.65.70.05137396610.9970.0230.05626.196.8

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.32data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.25data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7A59

7a59


Resolution: 2.989→49.05 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / Phase error: 24.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2395 2001 2.7085 %
Rwork0.2042 140640 -
obs-73878 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 273.9 Å2 / Biso mean: 93.9536 Å2 / Biso min: 38.9 Å2
Refinement stepCycle: final / Resolution: 2.989→49.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23321 0 131 0 23452
Biso mean--152.28 --
Num. residues----3005
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00424046
X-RAY DIFFRACTIONf_angle_d0.59832664
X-RAY DIFFRACTIONf_chiral_restr0.0453709
X-RAY DIFFRACTIONf_plane_restr0.0044133
X-RAY DIFFRACTIONf_dihedral_angle_d15.92714568
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A13051X-RAY DIFFRACTION8.505TORSIONAL
12B13051X-RAY DIFFRACTION8.505TORSIONAL
13C13051X-RAY DIFFRACTION8.505TORSIONAL
14D13051X-RAY DIFFRACTION8.505TORSIONAL
15E13051X-RAY DIFFRACTION8.505TORSIONAL
16F13051X-RAY DIFFRACTION8.505TORSIONAL
LS refinement shellResolution: 2.989→3.096 Å
RfactorNum. reflection% reflection
Rfree0.3686 193 -
Rwork0.3458 6719 -
obs--93.49 %
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)
11.5297-0.07-2.03181.18020.01015.972-0.05610.3268-0.1262-0.01170.10090.420.2886-1.1771-0.00870.9549-0.08960.07311.17260.07881.045550.255830.4871-15.4275
21.6604-0.5142-0.3482.06221.046.05380.14140.67250.1764-0.6201-0.07290.2499-0.7443-0.464-0.03841.4460.2090.05411.53290.20041.219653.462753.5897-35.8202
31.22240.8368-0.92514.14634.09327.01710.1415-0.4438-0.4548-0.04960.0209-0.60220.28940.4771-0.02891.5562-0.28250.31772.4449-0.06851.653950.831419.8018-38.2645
41.24340.2796-1.17551.2268-0.70984.9036-0.1553-0.1196-0.10650.0643-0.00160.01790.58420.24030.18671.03610.00680.13920.80690.02850.833172.780624.0436-5.7426
53.5543-0.1878-2.5761.90470.15154.3204-0.43160.4532-0.4068-0.47170.16860.0871.1495-0.32620.2991.881-0.27020.12631.1773-0.12941.200264.79887.9929-30.9565
64.0523-5.06350.32066.3306-0.34560.5653-0.62841.0015-0.8394-0.4451-0.4308-2.59630.1121.95020.93691.62350.460.50612.51210.57932.333493.630822.2412-20.0723
71.3462-0.0395-1.45411.471-0.1094.91610.1836-0.01160.19780.08170.04460.1447-0.5923-0.1139-0.24070.86920.02150.13990.8090.00760.865166.740548.3628-8.4309
82.5760.0572-1.36662.3035-1.27917.6579-0.0035-0.01740.2843-0.1838-0.0063-0.6052-0.47661.45080.10331.1049-0.06690.13021.3684-0.03321.126895.346841.4533-17.9905
91.51660.6105-1.55426.30770.69221.89320.16780.80630.6021-1.279-0.671-0.2638-0.19990.17610.48032.2660.0422-0.07661.71060.44741.79470.657560.9883-30.1258
101.4689-0.0404-1.45061.23950.43713.7999-0.08730.1596-0.1556-0.1718-0.08080.03090.3254-0.15730.20730.47260.0286-0.03680.4459-0.01890.711919.494819.8085100.3025
112.44270.7846-2.82382.2118-1.89414.8919-0.157-0.5299-0.10110.2893-0.1695-0.35520.4570.69620.31170.61960.1477-0.09020.78460.03790.86335.053920.3377127.0269
127.5052-6.34626.64078.5986-6.4176.041.2458-1.8715-1.6996-0.48160.34390.84642.0677-1.4013-1.54661.1079-0.27990.08110.95510.26331.48537.23716.4774121.575
131.387-0.0552-1.52741.2733-0.2134.77690.122-0.06860.0694-0.1983-0.0631-0.2799-0.23460.4666-0.05220.4134-0.02950.00670.46190.00290.739832.069741.3702104.772
141.06260.54570.03491.19570.38727.87980.0471-0.15650.13220.1743-0.12650.2289-0.4766-0.06670.10180.62540.06320.04990.5454-0.00520.933914.200561.378119.4229
152.40044.14253.06349.04136.23994.3738-0.2816-1.05630.50211.55381.0488-1.2943-0.12061.0168-0.81371.1840.0622-0.20721.0228-0.03351.542237.432444.6687132.0039
161.1602-0.1116-1.42521.23480.35285.15140.11490.30910.1569-0.3246-0.10420.1042-0.4065-0.4388-0.0570.4820.0714-0.10250.53160.01980.72118.22142.091996.2067
173.542-1.0834-1.58121.73420.39513.61090.0594-0.0402-0.0961-0.0432-0.02690.48910.0611-0.3332-0.02070.5512-0.1467-0.05540.7337-0.03820.9332-9.13621.9127111.2745
189.92170.6763.14693.0904-3.50045.51010.46380.31770.04550.5831-0.20830.6722-1.1652-0.2234-0.20281.26910.42590.2371.1896-0.04361.4816-3.05554.276114.1067
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'E' and ((resseq 1077:1438) or (resseq 1547:1564))E0
2X-RAY DIFFRACTION2chain 'E' and ((resseq 1439:1546))E0
3X-RAY DIFFRACTION3chain 'E' and ((resseq 1060:1070))E0
4X-RAY DIFFRACTION4chain 'D' and ((resseq 1077:1438) or (resseq 1547:1564))D0
5X-RAY DIFFRACTION5chain 'D' and ((resseq 1439:1546))D0
6X-RAY DIFFRACTION6chain 'D' and ((resseq 1060:1070))D0
7X-RAY DIFFRACTION7chain 'F' and ((resseq 1077:1438) or (resseq 1547:1564))F0
8X-RAY DIFFRACTION8chain 'F' and ((resseq 1439:1546))F0
9X-RAY DIFFRACTION9chain 'F' and ((resseq 1060:1070))F0
10X-RAY DIFFRACTION10chain 'A' and ((resseq 1076:1438) or (resseq 1547:1564))A0
11X-RAY DIFFRACTION11chain 'A' and ((resseq 1439:1546))A0
12X-RAY DIFFRACTION12chain 'A' and ((resseq 1060:1075))A0
13X-RAY DIFFRACTION13chain 'B' and ((resseq 1076:1438) or (resseq 1547:1564))B0
14X-RAY DIFFRACTION14chain 'B' and ((resseq 1439:1546))B0
15X-RAY DIFFRACTION15chain 'B' and ((resseq 1060:1075))B0
16X-RAY DIFFRACTION16chain 'C' and ((resseq 1077:1438) or (resseq 1547:1564))C0
17X-RAY DIFFRACTION17chain 'C' and ((resseq 1439:1546))C0
18X-RAY DIFFRACTION18chain 'C' and ((resseq 1061:1070))C0

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