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- PDB-6h3t: Schmallenberg Virus Glycoprotein Gc Head Domain in Complex with s... -

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Basic information

Entry
Database: PDB / ID: 6h3t
TitleSchmallenberg Virus Glycoprotein Gc Head Domain in Complex with scFv 1C11
Components
  • Envelopment polyprotein
  • scFv 1C11 VH
  • scFv 1C11 VL
KeywordsVIRAL PROTEIN / Envelope Glycoprotein / scFv Antibody
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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Envelopment polyprotein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Bovine Schmallenberg virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.836 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 / 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 / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _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 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_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
H: scFv 1C11 VH
L: scFv 1C11 VL
A: Envelopment polyprotein
I: scFv 1C11 VH
M: scFv 1C11 VL
B: Envelopment polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,54210
Polymers112,9316
Non-polymers3,6114
Water00
1
H: scFv 1C11 VH
L: scFv 1C11 VL
A: Envelopment polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2715
Polymers56,4663
Non-polymers1,8062
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5850 Å2
ΔGint14 kcal/mol
Surface area21460 Å2
MethodPISA
2
I: scFv 1C11 VH
M: scFv 1C11 VL
B: Envelopment polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2715
Polymers56,4663
Non-polymers1,8062
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5810 Å2
ΔGint17 kcal/mol
Surface area21620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)262.789, 44.397, 93.593
Angle α, β, γ (deg.)90.000, 91.810, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody scFv 1C11 VH


Mass: 14546.911 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Drosophila melanogaster (fruit fly)
#2: Antibody scFv 1C11 VL


Mass: 13539.126 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Drosophila melanogaster (fruit fly)
#3: Protein Envelopment polyprotein / M polyprotein


Mass: 28379.520 Da / Num. of mol.: 2 / Fragment: Glycoprotein Gc Head Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bovine Schmallenberg virus / Gene: GP / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: H2AM12
#4: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1235.105 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1_e6-g1WURCSPDB2Glycan 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]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#5: 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.: 2
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

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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: 2.62 Å3/Da / Density % sol: 53.06 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 1.0 uL of a 21.7 mg/mL solution of the GPC-purified complex in 20 mM Tris-Cl pH 8.0, 150 mM NaCl was added to 0.75 uL of reservoir solution containing 0.1 M sodium acetate, 8% v/v 2-propanol, 25% w/v PEG 4K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980089 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980089 Å / Relative weight: 1
ReflectionResolution: 2.836→46.773 Å / Num. obs: 16839 / % possible obs: 64.2 % / Observed criterion σ(I): 2 / Redundancy: 6.8 % / CC1/2: 1 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.03 / Rrim(I) all: 0.08 / Net I/σ(I): 15.3
Reflection shellResolution: 2.836→3.17 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 842 / CC1/2: 0.84 / Rpim(I) all: 0.33 / Rrim(I) all: 0.87 / % possible all: 11.4

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
STARANISOdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6H3X along with a Phyre2-generated model of the scFv 1C11 antibody fragment

6h3x

1c11


Resolution: 2.836→46.773 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.12
RfactorNum. reflection% reflection
Rfree0.2621 1684 10.03 %
Rwork0.2127 --
obs0.2177 16782 63.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 245.28 Å2 / Biso mean: 88.2755 Å2 / Biso min: 22.42 Å2
Refinement stepCycle: final / Resolution: 2.836→46.773 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7282 0 242 0 7524
Biso mean--120.99 --
Num. residues----924
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047710
X-RAY DIFFRACTIONf_angle_d0.81910480
X-RAY DIFFRACTIONf_chiral_restr0.0521228
X-RAY DIFFRACTIONf_plane_restr0.0041282
X-RAY DIFFRACTIONf_dihedral_angle_d13.434670
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 (%)
2.8362-2.91960.514660.424862683
2.9196-3.01380.4996210.407418921010
3.0138-3.12150.4649360.37230734316
3.1215-3.24650.2976550.311348453925
3.2465-3.39420.3612840.293886594944
3.3942-3.57310.32621640.27311445160974
3.5731-3.79690.32811960.2581781197791
3.7969-4.08990.29382160.22061964218099
4.0899-4.50110.24362190.189419652184100
4.5011-5.15180.23612270.171819652192100
5.1518-6.48790.26632230.21319992222100
6.4879-46.77940.22332370.199520722309100
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)
15.04660.46811.46791.76770.18852.2358-0.50581.13440.7229-0.49460.22660.3943-0.27260.13990.16290.5904-0.207-0.09340.45230.14640.468137.451918.837710.0271
25.2243-0.49930.93131.86980.25551.3421-0.0862-1.37710.30690.331-0.16780.0979-0.3618-1.03160.10820.45060.15660.00430.9323-0.22240.359223.3814.544236.2274
32.0713-1.34541.48131.33770.09133.43460.23581.3558-0.6354-0.16770.0619-0.51210.51871.3665-0.590.61070.25670.13120.9244-0.60710.740577.28517.16820.2455
41.48330.2435-0.13211.0216-0.41230.6854-0.1822-0.5068-0.24660.2974-0.02110.9793-0.4684-1.1018-0.11030.65440.6011-0.12381.9163-0.67131.5091-17.221522.691325.1571
53.76740.06962.00671.50110.24333.7497-0.2146-0.14090.29380.54930.3497-0.66770.05410.3803-0.07490.53580.0464-0.10520.2429-0.17260.497671.619517.481938.2938
61.52430.3735-0.35840.92960.87971.2127-0.3227-0.16081.0937-0.4392-0.08090.2264-1.1052-0.7001-0.00171.18190.6057-0.47650.9353-0.48211.6152-6.796937.595613.0977
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A'A467 - 696
2X-RAY DIFFRACTION2chain 'B'B467 - 698
3X-RAY DIFFRACTION3chain 'H'H1 - 111
4X-RAY DIFFRACTION4chain 'I'I1 - 111
5X-RAY DIFFRACTION5chain 'L'L1 - 107
6X-RAY DIFFRACTION6chain 'M'M1 - 107

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