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- PDB-6h3v: Bunyamwera Virus Glycoprotein Gc Head Domain -

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Basic information

Entry
Database: PDB / ID: 6h3v
TitleBunyamwera Virus Glycoprotein Gc Head Domain
ComponentsEnvelopment polyprotein
KeywordsVIRAL PROTEIN / Envelope Glycoprotein
Function / homology
Function and homology information


: / 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
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 speciesBunyamwera virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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 / pdbx_seq_map_depositor_info
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / _atom_site.label_entity_id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.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
Revision 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)30,1333
Polymers29,5271
Non-polymers6062
Water00
1
A: Envelopment polyprotein
hetero molecules

A: Envelopment polyprotein
hetero molecules

A: Envelopment polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,3989
Polymers88,5803
Non-polymers1,8186
Water0
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
Unit cell
Length a, b, c (Å)125.440, 125.440, 46.550
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321

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Components

#1: Protein Envelopment polyprotein / M polyprotein


Mass: 29526.775 Da / Num. of mol.: 1 / Fragment: Glycoprotein Gc Head Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bunyamwera virus / Gene: GP / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P04505
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
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: 3.79 Å3/Da / Density % sol: 67.51 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 uL of 22.2 mg/mL BUNV Gc head domain in 20 mM Tris-Cl pH 8.0, 150 mM NaCl were added to 0.2 uL of reservoir solution containing 0.2 M sodium acetate, 0.1 M Tris-Cl pH 8.5, 30% w/v PEG 4K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 1.033199 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033199 Å / Relative weight: 1
ReflectionResolution: 2.9→46.55 Å / Num. obs: 9534 / % possible obs: 99.8 % / Redundancy: 9.6 % / Biso Wilson estimate: 82 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.03 / Rrim(I) all: 0.09 / Net I/σ(I): 16.1
Reflection shellResolution: 2.9→3.08 Å / Redundancy: 10 % / Rmerge(I) obs: 1.27 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1519 / CC1/2: 0.7 / Rpim(I) all: 0.42 / Rrim(I) all: 1.34 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6H3W

6h3w


Resolution: 2.9→46.55 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.74
RfactorNum. reflection% reflection
Rfree0.2164 945 9.91 %
Rwork0.1673 --
obs0.1723 9532 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 237.71 Å2 / Biso mean: 103.2644 Å2 / Biso min: 52.84 Å2
Refinement stepCycle: final / Resolution: 2.9→46.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1958 0 39 0 1997
Biso mean--137.17 --
Num. residues----240
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092048
X-RAY DIFFRACTIONf_angle_d1.1552766
X-RAY DIFFRACTIONf_chiral_restr0.056304
X-RAY DIFFRACTIONf_plane_restr0.006345
X-RAY DIFFRACTIONf_dihedral_angle_d16.4551244
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.9-3.05290.32881330.263612001333
3.0529-3.24410.2921280.215112091337
3.2441-3.49450.26251320.203412271359
3.4945-3.8460.26161320.168312171349
3.846-4.40220.21521400.148412101350
4.4022-5.54480.21741330.154812461379
5.5448-46.5560.17161470.159512781425
Refinement TLS params.Method: refined / Origin x: 62.4934 Å / Origin y: -16.19 Å / Origin z: 19.9856 Å
111213212223313233
T0.7918 Å2-0.0743 Å20.1297 Å2-0.4656 Å2-0.119 Å2--0.6329 Å2
L6.8065 °2-1.7542 °22.2592 °2-4.3356 °2-1.7673 °2--5.0509 °2
S-0.1361 Å °-0.0765 Å °0.0048 Å °-0.1167 Å °0.2617 Å °-0.0978 Å °-0.2207 Å °0.1228 Å °-0.1255 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 478 through 803)

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