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- PDB-6y68: Structure of Maporal virus envelope glycoprotein Gc in postfusion... -

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Basic information

Entry
Database: PDB / ID: 6y68
TitleStructure of Maporal virus envelope glycoprotein Gc in postfusion conformation
ComponentsEnvelope polyprotein
KeywordsVIRAL PROTEIN / class-II fusion protein hantavirus bunyavirus / postfusion conformation
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 / symbiont-mediated suppression of host innate immune response / symbiont entry into host cell / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell ...symbiont-mediated suppression of host TRAF-mediated signal transduction / host cell Golgi membrane / host cell mitochondrion / host cell surface / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host innate immune response / symbiont entry into host cell / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / virion membrane / signal transduction / zinc ion binding / membrane
Similarity search - Function
Hantavirus glycoprotein Gn / ITAM motif, hantavirus type / Envelope glycoprotein precursor, Hantavirus / : / Hantavirus glycoprotein Gn, head / Hantavirus ITAM motif / Hantavirus glycoprotein Gn, base / ITAM motif hantavirus type profile. / Hantavirus glycoprotein Gc / : ...Hantavirus glycoprotein Gn / ITAM motif, hantavirus type / Envelope glycoprotein precursor, Hantavirus / : / Hantavirus glycoprotein Gn, head / Hantavirus ITAM motif / Hantavirus glycoprotein Gn, base / ITAM motif hantavirus type profile. / Hantavirus glycoprotein Gc / : / Hantavirus glycoprotein Gc, N-terminal / Hantavirus glycoprotein Gc, C-terminal
Similarity search - Domain/homology
: / Envelopment polyprotein
Similarity search - Component
Biological speciesMaporal virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsSerris, A. / Rey, F.A. / Guardado-Calvo, P.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-18-CE11-0011 France
CitationJournal: Cell / Year: 2020
Title: The Hantavirus Surface Glycoprotein Lattice and Its Fusion Control Mechanism.
Authors: Alexandra Serris / Robert Stass / Eduardo A Bignon / Nicolás A Muena / Jean-Claude Manuguerra / Rohit K Jangra / Sai Li / Kartik Chandran / Nicole D Tischler / Juha T Huiskonen / Felix A ...Authors: Alexandra Serris / Robert Stass / Eduardo A Bignon / Nicolás A Muena / Jean-Claude Manuguerra / Rohit K Jangra / Sai Li / Kartik Chandran / Nicole D Tischler / Juha T Huiskonen / Felix A Rey / Pablo Guardado-Calvo /
Abstract: Hantaviruses are rodent-borne viruses causing serious zoonotic outbreaks worldwide for which no treatment is available. Hantavirus particles are pleomorphic and display a characteristic square ...Hantaviruses are rodent-borne viruses causing serious zoonotic outbreaks worldwide for which no treatment is available. Hantavirus particles are pleomorphic and display a characteristic square surface lattice. The envelope glycoproteins Gn and Gc form heterodimers that further assemble into tetrameric spikes, the lattice building blocks. The glycoproteins, which are the sole targets of neutralizing antibodies, drive virus entry via receptor-mediated endocytosis and endosomal membrane fusion. Here we describe the high-resolution X-ray structures of the heterodimer of Gc and the Gn head and of the homotetrameric Gn base. Docking them into an 11.4-Å-resolution cryoelectron tomography map of the hantavirus surface accounted for the complete extramembrane portion of the viral glycoprotein shell and allowed a detailed description of the surface organization of these pleomorphic virions. Our results, which further revealed a built-in mechanism controlling Gc membrane insertion for fusion, pave the way for immunogen design to protect against pathogenic hantaviruses.
History
DepositionFeb 26, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Envelope polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1356
Polymers53,9361
Non-polymers1,1985
Water1,49583
1
A: Envelope polyprotein
hetero molecules

A: Envelope polyprotein
hetero molecules

A: Envelope polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,40418
Polymers161,8093
Non-polymers3,59515
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
Buried area18760 Å2
ΔGint-59 kcal/mol
Surface area51140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.348, 90.348, 506.380
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-1379-

HOH

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Components

#1: Protein Envelope polyprotein / M polyprotein


Mass: 53936.430 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Maporal virus / Plasmid: pT350 / Cell (production host): Schneider S2 cells / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q5MYC0
#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: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cd / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 3.69 Å3/Da / Density % sol: 66.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 30% (w/v) PEG 400, 0.1M CdCl2, 0.1M Na-acetate 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.4→39.83 Å / Num. obs: 31958 / % possible obs: 100 % / Redundancy: 15.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.174 / Rpim(I) all: 0.046 / Rrim(I) all: 0.18 / Net I/σ(I): 11.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.4-2.49162.7525280333100.5060.7092.8431100
8.98-39.83130.05290356970.9990.0150.05535.599

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.13 Å39.83 Å
Translation3.13 Å39.83 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.21data scaling
PHASER2.8.1phasing
PHENIX1.14rc3refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ljz

5ljz


Resolution: 2.4→39.828 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 23.75
RfactorNum. reflection% reflection
Rfree0.236 2914 4.83 %
Rwork0.1963 --
obs0.1981 31948 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 288.52 Å2 / Biso mean: 69.9704 Å2 / Biso min: 31.16 Å2
Refinement stepCycle: final / Resolution: 2.4→39.828 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3154 0 53 83 3290
Biso mean--86.43 57.03 -
Num. residues----414
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.4001-2.43940.33631280.32162798
2.4394-2.48150.3721060.32552742
2.4815-2.52660.32941600.30452718
2.5266-2.57520.31671150.29082736
2.5752-2.62780.33581550.27172723
2.6278-2.68490.29271830.26932680
2.6849-2.74730.27351510.25652723
2.7473-2.8160.28791550.25922695
2.816-2.89210.28091160.24842767
2.8921-2.97720.28951260.22862726
2.9772-3.07330.25221280.23492745
3.0733-3.18310.23371730.21572687
3.1831-3.31050.25891460.20772729
3.3105-3.4610.23661620.19612735
3.461-3.64340.20171280.17912724
3.6434-3.87150.22781330.17322724
3.8715-4.17010.21581470.15512707
4.1701-4.58920.19341140.14572788
4.5892-5.2520.14691490.13482716
5.252-6.61210.22251290.18042754
6.6121-39.8280.27391100.21582775
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)
10.57091.012-0.37962.0631-0.47871.71940.02470.19340.0496-0.2732-0.1064-0.1209-0.02460.018800.4703-0.0342-0.01280.437-0.01220.466739.027471.575161.768
20.02710.0185-0.03150.0156-0.01240.0534-0.00070.9003-0.4112-0.9536-0.0924-1.3913-0.55981.49530.00120.99150.08370.09451.09420.12120.845727.37172.9072144.5184
30.77810.3475-0.30431.07680.90991.31980.174-0.5964-0.13070.8479-0.10930.05160.5993-0.258-0.00031.0505-0.06390.05820.90810.08070.577331.004869.8084220.7687
40.9127-0.1307-0.07940.549-0.17552.5387-0.0563-0.2021-0.03510.1028-0.01670.08350.2152-0.1065-0.00010.4667-0.02040.0150.45130.00660.568632.056171.9776185.0734
50.98260.19830.04160.80310.22031.65320.0545-0.43490.04260.3695-0.0730.10510.09540.1374-0.00070.61190.00730.02470.58710.00160.580533.277875.8243200.1278
60.9812-0.3323-0.97091.49421.21341.8359-0.0039-0.034-0.18530.0875-0.03950.10910.1503-0.33970.00010.4632-0.0160.00890.4940.05020.637141.07751.587182.2541
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 657:691)A657 - 691
2X-RAY DIFFRACTION2(chain A and resid 692:704)A692 - 704
3X-RAY DIFFRACTION3(chain A and resid 705:785)A705 - 785
4X-RAY DIFFRACTION4(chain A and resid 786:868)A786 - 868
5X-RAY DIFFRACTION5(chain A and resid 869:967)A869 - 967
6X-RAY DIFFRACTION6(chain A and resid 968:1069)A968 - 1069

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