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- PDB-6h3x: Oropouche Virus Glycoprotein Gc Head Domain -

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Basic information

Entry
Database: PDB / ID: 6h3x
TitleOropouche Virus Glycoprotein Gc Head Domain
ComponentsPolyprotein
KeywordsVIRAL PROTEIN / Envelope Glycoprotein
Function / homology
Function and homology information


modulation by virus of host process / host cell Golgi membrane / membrane => GO:0016020 / host cell endoplasmic reticulum membrane / virion membrane
Similarity search - Function
M polyprotein precursor, Orthobunyavirus type / Bunyavirus glycoprotein G2 / Bunyavirus nonstructural protein NSm / Bunyavirus glycoprotein G2 / Bunyavirus glycoprotein G1 / Bunyavirus glycoprotein G1
Similarity search - Domain/homology
Envelopment polyprotein
Similarity search - Component
Biological speciesOropouche virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.092 Å
AuthorsHellert, J. / Aebischer, A. / Wernike, K. / Haouz, A. / Brocchi, E. / Reiche, S. / Guardado-Calvo, P. / Beer, M. / Rey, F.A.
Funding support1items
OrganizationGrant numberCountry
Innovative Medicines Initiative115760
CitationJournal: Nat Commun / Year: 2019
Title: Orthobunyavirus spike architecture and recognition by neutralizing antibodies.
Authors: Hellert, J. / Aebischer, A. / Wernike, K. / Haouz, A. / Brocchi, E. / Reiche, S. / Guardado-Calvo, P. / Beer, M. / Rey, F.A.
History
DepositionJul 19, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7347
Polymers26,9511
Non-polymers7836
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-46 kcal/mol
Surface area11470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.638, 104.638, 133.504
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Polyprotein


Mass: 26950.680 Da / Num. of mol.: 1 / Fragment: Glycoprotein Gc Head Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oropouche virus / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: A0A0D4BSW3
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O

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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: 2.73 Å3/Da / Density % sol: 54.89 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 1.0 uL of 20.0 mg/mL OROV Gc head domain in 20 mM Tris-Cl pH 8.0, 150 mM NaCl was added to 1.0 uL of reservoir solution containing 0.5 M lithium sulfate, 15% w/v PEG 8K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.09→44.5 Å / Num. obs: 16679 / % possible obs: 99.1 % / Redundancy: 11.1 % / Biso Wilson estimate: 47.8 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.03 / Rrim(I) all: 0.09 / Net I/σ(I): 13.4
Reflection shellResolution: 2.09→2.15 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1159 / CC1/2: 0.8 / Rpim(I) all: 0.23 / Rrim(I) all: 0.75 / % possible all: 89.2

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.092→33.898 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 26.09
RfactorNum. reflection% reflection
Rfree0.2333 1696 10.17 %
Rwork0.2027 --
obs0.2058 16678 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 166.57 Å2 / Biso mean: 75.4951 Å2 / Biso min: 39.11 Å2
Refinement stepCycle: final / Resolution: 2.092→33.898 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1802 0 45 40 1887
Biso mean--118.65 66.25 -
Num. residues----221
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031878
X-RAY DIFFRACTIONf_angle_d0.6132539
X-RAY DIFFRACTIONf_chiral_restr0.043287
X-RAY DIFFRACTIONf_plane_restr0.003317
X-RAY DIFFRACTIONf_dihedral_angle_d11.239718
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0918-2.15330.31591230.26551118124190
2.1533-2.22280.3471440.260412341378100
2.2228-2.30220.30251360.257212441380100
2.3022-2.39440.29171420.249612411383100
2.3944-2.50330.28811440.23912581402100
2.5033-2.63530.28321360.246112461382100
2.6353-2.80030.27091410.235112531394100
2.8003-3.01640.2951370.241312631400100
3.0164-3.31970.2611400.240712591399100
3.3197-3.79950.25281460.207712641410100
3.7995-4.78490.18391460.163412801426100
4.7849-33.90210.19831610.178913221483100
Refinement TLS params.Method: refined / Origin x: 21.5188 Å / Origin y: 11.2909 Å / Origin z: 53.6557 Å
111213212223313233
T0.476 Å20.1403 Å2-0.0812 Å2-0.3603 Å20.0242 Å2--0.4566 Å2
L2.8615 °22.4032 °23.4013 °2-3.6913 °24.4905 °2--9.1682 °2
S-0.2636 Å °0.2604 Å °0.2973 Å °-0.6071 Å °-0.2356 Å °0.4549 Å °-1.0274 Å °-0.092 Å °0.3676 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 482 through 702)

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