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- PDB-7a56: Schmallenberg Virus Envelope Glycoprotein Gc Fusion Domains in Po... -

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Basic information

Entry
Database: PDB / ID: 7a56
TitleSchmallenberg Virus Envelope Glycoprotein Gc Fusion Domains in Postfusion Conformation
ComponentsEnvelopment polyprotein
KeywordsVIRAL PROTEIN / Virus Entry / Class II Membrane Fusion Protein
Function / homology
Function and homology information


modulation by virus of host process / host cell Golgi membrane / host cell endoplasmic reticulum membrane / symbiont entry into host cell / fusion of virus membrane with host endosome membrane / virion attachment to host cell / virion membrane / membrane
Similarity search - Function
Bunyavirus glycoprotein G2 / Bunyavirus nonstructural protein NSm / Bunyavirus glycoprotein G2 / Bunyavirus glycoprotein G1 / Bunyavirus glycoprotein G1
Similarity search - Domain/homology
: / PHOSPHATE ION / Envelopment polyprotein
Similarity search - Component
Biological speciesBovine Schmallenberg virus BH80/Germany/2011
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsHellert, J. / Guardado-Calvo, P. / Rey, F.A.
Funding support2items
OrganizationGrant numberCountry
Innovative Medicines Initiative115760
Laboratories of Excellence (LabEx)ANR-10-LABX-62-IBEID
CitationJournal: Cell Rep / Year: 2023
Title: Structure, function, and evolution of the Orthobunyavirus membrane fusion glycoprotein.
Authors: Hellert, J. / Aebischer, A. / Haouz, A. / Guardado-Calvo, P. / Reiche, S. / Beer, M. / Rey, F.A.
History
DepositionAug 20, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 1, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Envelopment polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,92915
Polymers48,3001
Non-polymers62914
Water7,548419
1
A: Envelopment polyprotein
hetero molecules

A: Envelopment polyprotein
hetero molecules

A: Envelopment polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,78645
Polymers144,9003
Non-polymers1,88642
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area17730 Å2
ΔGint-281 kcal/mol
Surface area52330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.790, 86.790, 358.090
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-1406-

CL

21A-1407-

PO4

31A-1407-

PO4

41A-1408-

PO4

51A-1408-

PO4

61A-1790-

HOH

71A-1821-

HOH

81A-1912-

HOH

91A-1919-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Envelopment polyprotein / M polyprotein


Mass: 48299.977 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bovine Schmallenberg virus BH80/Germany/2011
Gene: GP / Plasmid: pMT / Cell line (production host): Schneider 2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: H2AM12

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Non-polymers , 5 types, 433 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 419 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.69 Å3/Da / Density % sol: 54.22 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 0.5 uL of 4.5 mg/mL trimeric SBV Gc fusion domain fragment in 20 mM Tris-Cl pH 8.0, 150 mM NaCl were added to 0.5 uL of reservoir solution containing 20% w/v PEG 1K, 0.1 M Na/K phosphate pH 6.2 and 0.2 M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729 Å
DetectorType: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Aug 29, 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: 0.8729 Å / Relative weight: 1
ReflectionResolution: 1.85→43.4069 Å / Num. obs: 44636 / % possible obs: 99.2 % / Redundancy: 6.232 % / Biso Wilson estimate: 26.6 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.105 / Rrim(I) all: 0.115 / Χ2: 0.97 / Net I/σ(I): 9.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.85-1.96.5031.0941.832250.8261.18898.8
1.9-1.956.5150.8682.2331560.8810.94399
1.95-2.016.4950.6772.7830800.9370.73598.9
2.01-2.076.4420.5083.5730150.9480.55299.1
2.07-2.146.3660.4034.228860.9730.43999.1
2.14-2.216.2680.3474.8128410.970.37999.2
2.21-2.296.1580.2765.7427290.980.30199.3
2.29-2.395.7220.2316.3626370.9790.25499.4
2.39-2.496.1670.27.5225120.9880.21999.5
2.49-2.626.120.178.7624310.9890.18699.5
2.62-2.765.9540.13110.4422990.9940.14499.4
2.76-2.936.5180.11312.9722180.9950.12399.6
2.93-3.136.4020.09215.6820620.9960.199.6
3.13-3.386.3550.07718.9919260.9960.08499.2
3.38-3.76.2550.06821.4317890.9960.07499.8
3.7-4.145.9340.06222.9516290.9960.06999.7
4.14-4.785.6010.05724.1514400.9960.06399.4
4.78-5.855.5860.05924.4112300.9960.06599.2
5.85-8.276.3810.06225.819710.9950.06898.9
8.27-43.40695.7140.06226.655600.9960.06794.4

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.25data extraction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.85→43.4069 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2085 1998 4.48 %
Rwork0.1699 42581 -
obs0.1717 44579 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 127.55 Å2 / Biso mean: 40.6672 Å2 / Biso min: 17.04 Å2
Refinement stepCycle: final / Resolution: 1.85→43.4069 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3228 0 26 419 3673
Biso mean--62.72 45.94 -
Num. residues----419
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0163310
X-RAY DIFFRACTIONf_angle_d1.3624494
X-RAY DIFFRACTIONf_chiral_restr0.086511
X-RAY DIFFRACTIONf_plane_restr0.008570
X-RAY DIFFRACTIONf_dihedral_angle_d16.1942032
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.85-1.89620.32221380.2782295699
1.8962-1.94750.24851400.2518297799
1.9475-2.00480.2381410.2183300399
2.0048-2.06950.26781410.1965299799
2.0695-2.14350.25021410.1937299499
2.1435-2.22930.22841430.1832303099
2.2293-2.33070.2091410.1783300599
2.3307-2.45360.23261410.1845303499
2.4536-2.60730.24071430.1844303599
2.6073-2.80860.21271420.1795305899
2.8086-3.09120.22421450.17353065100
3.0912-3.53830.21691440.1573306999
3.5383-4.45720.15641470.14033132100
4.4572-43.40690.18581510.1527322698
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)
10.2187-0.0007-0.28160.12530.23583.45260.04820.0150.0258-0.01780.01720.0171-0.4028-0.359-0.07140.18820.06880.00590.22430.01310.191932.2094-16.542126.6613
22.53270.3371.49023.33410.43152.3994-0.04860.723-0.4274-0.4759-0.09320.45190.2965-0.76360.1170.31-0.1184-0.06020.5854-0.06920.353818.8524-34.562132.333
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and ((resseq 885:1220))A0
2X-RAY DIFFRACTION2chain 'A' and ((resseq 1221:1306))A0

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