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- PDB-5y10: SFTSV Gn head domain -

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Basic information

Entry
Database: PDB / ID: 5y10
TitleSFTSV Gn head domain
ComponentsMembrane glycoprotein polyprotein
KeywordsVIRAL PROTEIN / SFTSV / GN / Phlebovirus / bunyavirus
Function / homology
Function and homology information


host cell Golgi membrane / entry receptor-mediated virion attachment to host cell / 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
Phlebovirus glycoprotein G1 / Phlebovirus glycoprotein G1 / Phlebovirus glycoprotein G2, fusion domain / Phlebovirus glycoprotein G2, C-terminal domain / Phlebovirus glycoprotein G2 fusion domain / Phlebovirus glycoprotein G2 C-terminal domain
Similarity search - Domain/homology
Envelopment polyprotein / Envelopment polyprotein
Similarity search - Component
Biological speciesSevere fever with thrombocytopenia virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsWu, Y. / Gao, F. / Qi, J.X. / Chai, Y. / Gao, G.F.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Structures of phlebovirus glycoprotein Gn and identification of a neutralizing antibody epitope
Authors: Wu, Y. / Zhu, Y.H. / Gao, F. / Jiao, Y.J. / Oladejo, B.O. / Chai, Y. / Bi, Y.H. / Lu, S. / Dong, M.Q. / Zhang, C. / Huang, G.M. / Wong, G. / Li, N. / Zhang, Y.F. / Li, Y. / Feng, W.H. / Shi, ...Authors: Wu, Y. / Zhu, Y.H. / Gao, F. / Jiao, Y.J. / Oladejo, B.O. / Chai, Y. / Bi, Y.H. / Lu, S. / Dong, M.Q. / Zhang, C. / Huang, G.M. / Wong, G. / Li, N. / Zhang, Y.F. / Li, Y. / Feng, W.H. / Shi, Y. / Liang, M.F. / Zhang, R.G. / Qi, J.X. / Gao, G.F.
History
DepositionJul 19, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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.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 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Membrane glycoprotein polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9542
Polymers35,3671
Non-polymers5871
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area810 Å2
ΔGint8 kcal/mol
Surface area14620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.410, 87.410, 91.003
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Membrane glycoprotein polyprotein


Mass: 35367.039 Da / Num. of mol.: 1 / Fragment: UNP residues 20-340
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe fever with thrombocytopenia virus
Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: A0A1L2DAC8, UniProt: W8GRF8*PLUS
#2: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{}}}}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: 2.46 Å3/Da / Density % sol: 49.95 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 20% (w/v) PEG 4000, 20% (v/v) 2-propanol, 0.1M sodium citrate pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97853 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 10777 / % possible obs: 96.3 % / Redundancy: 4.2 % / Net I/σ(I): 15.5
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.848 / Num. unique obs: 1108 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→36.643 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 38.7
RfactorNum. reflection% reflection
Rfree0.2851 504 4.68 %
Rwork0.2206 --
obs0.2237 10773 92.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.6→36.643 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2450 0 39 0 2489
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122562
X-RAY DIFFRACTIONf_angle_d1.5283465
X-RAY DIFFRACTIONf_dihedral_angle_d8.2621524
X-RAY DIFFRACTIONf_chiral_restr0.064364
X-RAY DIFFRACTIONf_plane_restr0.009443
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5174-2.77060.39251130.30572305X-RAY DIFFRACTION83
2.7706-3.17130.38011160.27692785X-RAY DIFFRACTION100
3.1713-3.99480.24991550.22742731X-RAY DIFFRACTION99
3.9948-36.64680.28231200.19662448X-RAY DIFFRACTION87
Refinement TLS params.Method: refined / Origin x: -19.197 Å / Origin y: 31.4017 Å / Origin z: -7.4899 Å
111213212223313233
T0.4754 Å20.0078 Å20.0652 Å2-0.5819 Å20.115 Å2--0.5872 Å2
L2.8594 °21.471 °21.1299 °2-3.5588 °21.0354 °2--3.2754 °2
S0.3089 Å °-0.3227 Å °-0.4155 Å °0.1767 Å °-0.0457 Å °-0.2761 Å °0.22 Å °-0.0682 Å °-0.255 Å °
Refinement TLS groupSelection details: all

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