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- PDB-6h3u: Schmallenberg Virus Glycoprotein Gc Head Domain in Complex with s... -

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Basic information

Entry
Database: PDB / ID: 6h3u
TitleSchmallenberg Virus Glycoprotein Gc Head Domain in Complex with scFv 4B6
Components
  • Envelopment polyprotein
  • scFv 4B6 VH
  • scFv 4B6 VL
KeywordsVIRAL PROTEIN / Envelope Glycoprotein / scFv Antibody
Function / homology
Function and homology information


symbiont-mediated perturbation of host process / host cell Golgi membrane / host cell endoplasmic reticulum membrane / fusion of virus membrane with host endosome membrane / symbiont entry into host cell / 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: 3.168 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 / 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.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 / _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
Revision 2.2Nov 20, 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
H: scFv 4B6 VH
L: scFv 4B6 VL
A: Envelopment polyprotein
B: Envelopment polyprotein
M: scFv 4B6 VL
I: scFv 4B6 VH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,31510
Polymers112,7046
Non-polymers3,6114
Water00
1
H: scFv 4B6 VH
L: scFv 4B6 VL
B: Envelopment polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1585
Polymers56,3523
Non-polymers1,8062
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint11 kcal/mol
Surface area22580 Å2
MethodPISA
2
A: Envelopment polyprotein
M: scFv 4B6 VL
I: scFv 4B6 VH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1585
Polymers56,3523
Non-polymers1,8062
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5150 Å2
ΔGint14 kcal/mol
Surface area21730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.842, 175.842, 153.684
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Antibody scFv 4B6 VH


Mass: 15066.347 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 4B6 VL


Mass: 12906.227 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
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: 6.31 Å3/Da / Density % sol: 80.51 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 0.75 uL of a 22.8 mg/mL solution of the GPC-purified complex in 20 mM Tris-Cl pH 8.0, 150 mM NaCl were added to 0.75 uL of reservoir solution containing 0.1 M sodium acetate pH 4.6, 3.5 M sodium formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980097 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: 0.980097 Å / Relative weight: 1
ReflectionResolution: 3.168→48.554 Å / Num. obs: 27774 / % possible obs: 59.1 % / Observed criterion σ(I): 1.2 / Redundancy: 20.9 % / CC1/2: 1 / Rmerge(I) obs: 0.22 / Rpim(I) all: 0.05 / Rrim(I) all: 0.23 / Net I/σ(I): 11.4
Reflection shellResolution: 3.17→3.61 Å / Redundancy: 18.7 % / Rmerge(I) obs: 1.78 / Mean I/σ(I) obs: 2 / Num. unique obs: 1391 / CC1/2: 0.72 / Rpim(I) all: 0.41 / Rrim(I) all: 1.82 / % possible all: 9.3

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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: 6H3T along with a Phyre2-generated model of the scFv 4B6 antibody fragment

6h3t


Resolution: 3.168→48.554 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 27.72
RfactorNum. reflection% reflection
Rfree0.2284 1984 7.15 %
Rwork0.1998 --
obs0.2019 27751 59.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 240.86 Å2 / Biso mean: 113.1078 Å2 / Biso min: 47.16 Å2
Refinement stepCycle: final / Resolution: 3.168→48.554 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7571 0 242 0 7813
Biso mean--164.4 --
Num. residues----954
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048019
X-RAY DIFFRACTIONf_angle_d0.75910929
X-RAY DIFFRACTIONf_chiral_restr0.0461280
X-RAY DIFFRACTIONf_plane_restr0.0041332
X-RAY DIFFRACTIONf_dihedral_angle_d12.3614788
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1676-3.24680.452360.520456622
3.2468-3.33460.4259100.37911351454
3.3346-3.43270.3206200.38552622829
3.4327-3.54350.4402350.325448051516
3.5435-3.67010.3414620.308874580724
3.6701-3.8170.2936850.27431137122237
3.817-3.99060.27441200.241609172952
3.9906-4.20090.25951890.21752433262278
4.2009-4.46390.22752360.204130893325100
4.4639-4.80830.20462380.169931293367100
4.8083-5.29160.20972440.159431243368100
5.2916-6.05610.21962470.183331253372100
6.0561-7.62530.23232450.22331773422100
7.6253-48.560.21722470.197832663513100
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)
11.70670.47570.10033.8942-0.66891.8797-0.3678-0.2735-0.6934-0.35650.0369-0.76280.75540.19840.29170.72870.21670.32830.81570.27630.9353-81.246536.1461-0.5644
22.13150.93670.20842.5629-0.39023.2603-0.2925-0.22210.06560.01560.0179-0.5388-0.1393-0.01770.1680.45810.11110.05930.80590.22470.7205-77.64556.28237.6595
34.48131.5036-0.47732.45790.03263.0330.20760.0791-0.32920.2854-0.1131-0.04570.3209-0.1397-0.06280.6505-0.18690.03180.5387-0.03160.6019-43.204252.2607-35.4273
43.24670.9349-0.42062.67010.7152.4749-0.54270.28920.2365-0.86140.3515-0.0704-0.52340.16460.15240.9813-0.14550.11520.52850.15760.6588-71.02468.8169-27.1168
50.96440.4784-0.29881.50490.4691.56430.5777-0.8447-0.1341.1325-0.76550.48950.9635-0.72630.06771.38-0.77810.08151.8338-0.13150.8706-35.280261.5066-1.2984
60.942-0.53560.02412.02950.46682.7178-0.0145-0.47250.69460.2517-0.13350.29990.4258-0.83040.06810.6623-0.24740.02821.3528-0.38250.9503-28.642980.9975-7.3597
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'H' and resid 1 through 112)H1 - 112
2X-RAY DIFFRACTION2(chain 'L' and resid 1 through 113)L1 - 113
3X-RAY DIFFRACTION3(chain 'A' and resid 467 through 810)A467 - 810
4X-RAY DIFFRACTION4(chain 'B' and resid 467 through 810)B467 - 810
5X-RAY DIFFRACTION5(chain 'M' and resid 1 through 107)M1 - 107
6X-RAY DIFFRACTION6(chain 'I' and resid 1 through 112)I1 - 112

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