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- PDB-5fyn: Sub-tomogram averaging of Tula virus glycoprotein spike -

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Basic information

Entry
Database: PDB / ID: 5fyn
TitleSub-tomogram averaging of Tula virus glycoprotein spike
ComponentsPUUMALA VIRUS GN GLYCOPROTEIN
KeywordsVIRAL PROTEIN / TULA VIRUS / MEMBRANE PROTEIN / GLYCOPROTEIN / HANTAVIRUS / BUNYAVIRUS / RECEPTOR BINDING
Function / homology
Function and homology information


: / symbiont-mediated suppression of host TRAF-mediated signal transduction / host cell Golgi membrane / host cell mitochondrion / host cell surface / host cell endoplasmic reticulum membrane / virion membrane / signal transduction / membrane / metal ion binding
Similarity search - Function
: / Hantavirus glycoprotein Gn, base / Hantavirus glycoprotein Gn / ITAM motif, hantavirus type / Envelope glycoprotein precursor, Hantavirus / Hantavirus glycoprotein Gn, head / Hantavirus ITAM motif / ITAM motif hantavirus type profile. / : / Hantavirus glycoprotein Gc, C-terminal ...: / Hantavirus glycoprotein Gn, base / Hantavirus glycoprotein Gn / ITAM motif, hantavirus type / Envelope glycoprotein precursor, Hantavirus / Hantavirus glycoprotein Gn, head / Hantavirus ITAM motif / ITAM motif hantavirus type profile. / : / Hantavirus glycoprotein Gc, C-terminal / Hantavirus glycoprotein Gc / Hantavirus glycoprotein Gc, N-terminal
Similarity search - Domain/homology
Envelopment polyprotein
Similarity search - Component
Biological speciesPUUMALA VIRUS
MethodELECTRON MICROSCOPY / electron tomography / cryo EM / Resolution: 15.6 Å
AuthorsLi, S. / Rissanen, I. / Zeltina, A. / Hepojoki, J. / Raghwani, J. / Harlos, K. / Pybus, O.G. / Huiskonen, J.T. / Bowden, T.A.
CitationJournal: Cell Rep / Year: 2016
Title: A Molecular-Level Account of the Antigenic Hantaviral Surface.
Authors: Sai Li / Ilona Rissanen / Antra Zeltina / Jussi Hepojoki / Jayna Raghwani / Karl Harlos / Oliver G Pybus / Juha T Huiskonen / Thomas A Bowden /
Abstract: Hantaviruses, a geographically diverse group of zoonotic pathogens, initiate cell infection through the concerted action of Gn and Gc viral surface glycoproteins. Here, we describe the high- ...Hantaviruses, a geographically diverse group of zoonotic pathogens, initiate cell infection through the concerted action of Gn and Gc viral surface glycoproteins. Here, we describe the high-resolution crystal structure of the antigenic ectodomain of Gn from Puumala hantavirus (PUUV), a causative agent of hemorrhagic fever with renal syndrome. Fitting of PUUV Gn into an electron cryomicroscopy reconstruction of intact Gn-Gc spike complexes from the closely related but non-pathogenic Tula hantavirus localized Gn tetramers to the membrane-distal surface of the virion. The accuracy of the fitting was corroborated by epitope mapping and genetic analysis of available PUUV sequences. Interestingly, Gn exhibits greater non-synonymous sequence diversity than the less accessible Gc, supporting a role of the host humoral immune response in exerting selective pressure on the virus surface. The fold of PUUV Gn is likely to be widely conserved across hantaviruses.
History
DepositionMar 8, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 8, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Data collection / Derived calculations / Refinement description
Category: em_3d_fitting / em_software / pdbx_struct_assembly
Item: _em_3d_fitting.target_criteria / _em_software.details ..._em_3d_fitting.target_criteria / _em_software.details / _em_software.fitting_id / _em_software.image_processing_id / _em_software.name / _pdbx_struct_assembly.details
Revision 1.2Apr 3, 2019Group: Data collection / Derived calculations / Source and taxonomy
Category: entity_src_gen / struct_conn
Item: _entity_src_gen.pdbx_host_org_cell_line / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Oct 23, 2019Group: Data collection / Other / Category: cell / Item: _cell.Z_PDB
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...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 / 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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

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Assembly

Deposited unit
A: PUUMALA VIRUS GN GLYCOPROTEIN
B: PUUMALA VIRUS GN GLYCOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,0756
Polymers77,8912
Non-polymers2,1844
Water0
1
A: PUUMALA VIRUS GN GLYCOPROTEIN
B: PUUMALA VIRUS GN GLYCOPROTEIN
hetero molecules

A: PUUMALA VIRUS GN GLYCOPROTEIN
B: PUUMALA VIRUS GN GLYCOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,15012
Polymers155,7814
Non-polymers4,3688
Water0
TypeNameSymmetry operationNumber
identity operation1_5551
point symmetry operation1

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Components

#1: Protein PUUMALA VIRUS GN GLYCOPROTEIN


Mass: 38945.363 Da / Num. of mol.: 2 / Fragment: ECTODOMAIN, UNP RESIDUES 29-383
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PUUMALA VIRUS / Plasmid: PHLSEC / Cell line (production host): HEK293 / Production host: HOMO SAPIENS (human) / References: UniProt: Q9WJ31
#2: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...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: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-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
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: electron tomography

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Sample preparation

ComponentName: GLYCOPROTEIN SPIKE OF TULA HANTAVIRUS / Type: VIRUS
Buffer solutionName: 25 MM TRIS, 75 MM NACL / pH: 8 / Details: 25 MM TRIS, 75 MM NACL
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE-PROPANE / Details: LIQUID ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300 / Date: Aug 14, 2014
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 160000 X / Calibrated magnification: 37037 X / Nominal defocus max: 3800 nm / Nominal defocus min: 2000 nm / Cs: 2 mm
Specimen holderTemperature: 100 K / Tilt angle max: 45 ° / Tilt angle min: -45 °
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansNum. digital images: 30

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Processing

EM software
IDNameCategoryDetails
1UCSF Chimeramodel fitting
2Dynamo3D reconstruction
3IMOD3D reconstruction
4UCSF Chimeramodel fittingSegger
CTF correctionDetails: EACH TILTED IMAGE
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionMethod: SUBTOMOGRAM AVERAGING / Resolution: 15.6 Å / Num. of particles: 5449 / Actual pixel size: 2.7 Å / Magnification calibration: KNOWN ATOMIC MODEL
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-3364. (DEPOSITION ID: 14310).
Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL / Target criteria: Cross-correlation coefficient
Details: METHOD--LOCAL CORRELATION REFINEMENT PROTOCOL--X-RAY
Atomic model buildingPDB-ID: 5FXU

5fxu

RefinementHighest resolution: 15.6 Å
Refinement stepCycle: LAST / Highest resolution: 15.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5046 0 145 0 5191

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