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- PDB-6h3w: La Crosse Virus Glycoprotein Gc Head Domain -

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Basic information

Entry
Database: PDB / ID: 6h3w
TitleLa Crosse Virus Glycoprotein Gc Head Domain
ComponentsEnvelopment polyprotein
KeywordsVIRAL PROTEIN / Envelope Glycoprotein
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 / 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 speciesBunyavirus La Crosse
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.098 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: Advisory / Atomic model ...Advisory / 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 / pdbx_struct_special_symmetry / pdbx_validate_close_contact / 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 / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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

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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)29,4872
Polymers28,5761
Non-polymers9111
Water4,017223
1
A: Envelopment polyprotein
hetero molecules

A: Envelopment polyprotein
hetero molecules

A: Envelopment polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,4626
Polymers85,7293
Non-polymers2,7323
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Unit cell
Length a, b, c (Å)73.227, 73.227, 280.713
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-918-

HOH

21A-1123-

HOH

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Components

#1: Protein Envelopment polyprotein / M polyprotein


Mass: 28576.375 Da / Num. of mol.: 1 / Fragment: Glycoprotein Gc Head Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bunyavirus La Crosse / Gene: GP / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q8JPR1
#2: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 2.57 Å3/Da / Density % sol: 52.16 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 0.75 uL of a 11.1 mg/mL protein sample in 20 mM Tris-Cl pH 8.0, 150 mM NaCl were added to 0.75 uL of reservoir solution containing 0.1 M HEPES pH7.5, 10% v/v 2-propanol, 20% w/v PEG 4K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97717 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97717 Å / Relative weight: 1
ReflectionResolution: 2.098→47.052 Å / Num. obs: 17376 / % possible obs: 99.3 % / Redundancy: 7.9 % / Biso Wilson estimate: 44.1 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.03 / Rrim(I) all: 0.09 / Net I/σ(I): 11.4
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 7.6 % / Rmerge(I) obs: 1.02 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1378 / CC1/2: 0.65 / Rpim(I) all: 0.39 / Rrim(I) all: 1.09 / % possible all: 98

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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: 6H3X

6h3x


Resolution: 2.098→47.052 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0.02 / Phase error: 19.45
RfactorNum. reflection% reflection
Rfree0.2129 1677 10 %
Rwork0.1649 --
obs0.1698 16768 95.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 107.62 Å2 / Biso mean: 31.7246 Å2 / Biso min: 7.12 Å2
Refinement stepCycle: final / Resolution: 2.098→47.052 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1979 0 61 223 2263
Biso mean--48.63 36.52 -
Num. residues----246
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072098
X-RAY DIFFRACTIONf_angle_d0.9462849
X-RAY DIFFRACTIONf_chiral_restr0.05317
X-RAY DIFFRACTIONf_plane_restr0.005352
X-RAY DIFFRACTIONf_dihedral_angle_d16.3121257
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 (%)
2.098-2.15970.28451260.23691128125488
2.1597-2.22940.25291290.20561170129990
2.2294-2.30910.24761320.19151183131593
2.3091-2.40150.19551360.17191228136495
2.4015-2.51080.23471400.16241257139796
2.5108-2.64320.241390.16871246138597
2.6432-2.80880.20491420.15721286142899
2.8088-3.02560.21251450.16621297144299
3.0256-3.330.20931440.15731297144199
3.33-3.81170.18411440.14631301144599
3.8117-4.80160.16681460.13991314146098
4.8016-47.06340.23771540.17181384153897
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)
11.8823-0.4324-0.10792.8644-0.93044.1791-0.0890.50490.0258-0.731-0.0168-0.5177-0.27970.29260.08540.468-0.00920.06970.379-0.05280.305517.979128.607104.2117
21.92460.0819-0.3961.8179-0.16091.4891-0.0159-0.0122-0.272-0.02280.0176-0.00060.13530.0258-0.01840.10880.0119-0.0230.0876-0.00460.11555.42225.9531124.81
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 474 through 550 )A474 - 550
2X-RAY DIFFRACTION2chain 'A' and (resid 551 through 719 )A551 - 719

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