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- PDB-6y6p: Structure of Hantaan virus envelope glycoprotein Gn -

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Basic information

Entry
Database: PDB / ID: 6y6p
TitleStructure of Hantaan virus envelope glycoprotein Gn
ComponentsEnvelope polyprotein
KeywordsVIRAL PROTEIN / class-II fusion protein hantavirus bunyavirus
Function / homology
Function and homology information


symbiont-mediated suppression of host autophagy / : / symbiont-mediated suppression of host TRAF-mediated signal transduction / host cell Golgi membrane / host cell mitochondrion / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / host cell surface / symbiont-mediated suppression of host innate immune response / host cell endoplasmic reticulum membrane / endocytosis involved in viral entry into host cell ...symbiont-mediated suppression of host autophagy / : / symbiont-mediated suppression of host TRAF-mediated signal transduction / host cell Golgi membrane / host cell mitochondrion / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / host cell surface / symbiont-mediated suppression of host innate immune response / host cell endoplasmic reticulum membrane / endocytosis involved in viral entry into host cell / symbiont-mediated activation of host autophagy / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / virion membrane / cell surface / signal transduction / zinc ion binding / metal 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 / Envelopment polyprotein
Similarity search - Component
Biological speciesHantaan orthohantavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.938 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 27, 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 1.3Nov 13, 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)43,6643
Polymers42,8151
Non-polymers8492
Water3,639202
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint12 kcal/mol
Surface area17450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.596, 92.224, 94.033
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Envelope polyprotein / M polyprotein


Mass: 42815.191 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hantaan orthohantavirus / Plasmid: pT350 / Cell (production host): Schneider S2 cells / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q89839, UniProt: P08668*PLUS
#2: 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 2.71 Å3/Da / Density % sol: 54.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 25%(w/v) PEG 6000, 0.1M Hepes 7.5, 0.1M LiCl, 20% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.938→35.344 Å / Num. obs: 35256 / % possible obs: 99.6 % / Redundancy: 8.2 % / Biso Wilson estimate: 33.24 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.03 / Rrim(I) all: 0.085 / Net I/σ(I): 14.6
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
1.94-1.988.11.1171818022480.6550.4111.1921.895.6
9.09-35.346.60.0426274010.9970.0160.04440.398.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.36 Å35.34 Å
Translation6.36 Å35.34 Å

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Processing

Software
NameVersionClassification
PHENIX1.13refinement
XDSdata reduction
Aimless0.5.31data scaling
PHASER2.8.1phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5opg

5opg


Resolution: 1.938→35.344 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.38
RfactorNum. reflection% reflection
Rfree0.2106 1673 4.75 %
Rwork0.1667 --
obs0.1687 35189 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 142.97 Å2 / Biso mean: 46.6711 Å2 / Biso min: 20.39 Å2
Refinement stepCycle: final / Resolution: 1.938→35.344 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2662 0 56 202 2920
Biso mean--80.23 47.61 -
Num. residues----343
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9385-1.99550.25191530.2299266196
1.9955-2.05990.28881320.212765100
2.0599-2.13350.29341240.20422767100
2.1335-2.21890.25371640.19312733100
2.2189-2.31990.26721180.18932785100
2.3199-2.44220.2571270.18642790100
2.4422-2.59510.2371640.19162748100
2.5951-2.79540.23161320.18312807100
2.7954-3.07660.22471450.18052797100
3.0766-3.52140.19121380.16252816100
3.5214-4.43530.17251520.14022863100
4.4353-35.3440.18371240.1468298499
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)
10.72950.05490.45362.1851.32850.8122-0.0033-0.0560.0828-0.3170.0919-0.1841-0.24560.120.00120.3122-0.01920.01990.29850.01960.28132.793717.2423-14.0946
20.34490.1628-0.26261.14390.48850.441-0.0250.1416-0.17231.27920.4144-0.64420.82530.68380.00920.57450.0411-0.11210.5708-0.08880.561914.03597.54-12.0777
32.7998-0.0459-1.43013.1676-0.83831.13590.0390.17180.0052-0.03380.2476-0.10060.12710.68940.00430.32470.01360.02310.3305-0.00670.37174.327-5.5839-24.4035
40.3581-0.03560.26942.84461.72161.1529-0.0450.0481-0.01480.16210.1017-0.10450.14930.15720.00010.27240.01090.01570.3041-0.00460.26024.88736.7743-13.9877
51.2423-0.4107-0.36380.60790.14030.2022-0.27960.11580.0323-0.14360.11650.0081-0.0085-0.11960.00050.3227-0.0340.00750.40690.03430.2739-10.561725.8897-10.4415
61.5307-1.2144-1.36740.42090.52470.6757-0.27190.1832-0.48850.03550.02470.50830.2329-0.3119-0.01010.3902-0.06520.07970.3838-0.09090.4395-17.29966.3149-7.6
70.09910.09460.03330.0730.04880.0594-0.06430.0439-0.62450.2192-0.67880.04371.1339-0.4239-0.00030.7909-0.11720.20960.9298-0.16591.222-19.4879-11.2875-12.264
80.63680.59020.20471.44170.05281.1944-0.16990.09180.05270.3373-0.43221.41530.2572-0.5038-0.13960.3427-0.06370.19890.3669-0.16710.6374-13.79745.1047-9.2227
92.2030.4098-0.14752.24832.2372.28960.02980.2195-0.14930.0787-0.32460.41490.0472-0.045-0.00080.24440.0330.00540.2732-0.07880.2817-4.0385-7.6644-25.8664
101.8505-1.8764-1.27320.78041.05591.2149-0.0580.2456-0.23290.3592-0.2710.44730.2098-0.2857-0.01830.2899-0.03210.0450.3181-0.10490.3725-10.21332.3191-17.2587
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:32)A1 - 32
2X-RAY DIFFRACTION2(chain A and resid 33:48)A33 - 48
3X-RAY DIFFRACTION3(chain A and resid 49:72)A49 - 72
4X-RAY DIFFRACTION4(chain A and resid 73:151)A73 - 151
5X-RAY DIFFRACTION5(chain A and resid 152:173)A152 - 173
6X-RAY DIFFRACTION6(chain A and resid 174:209)A174 - 209
7X-RAY DIFFRACTION7(chain A and resid 210:220)A210 - 220
8X-RAY DIFFRACTION8(chain A and resid 221:259)A221 - 259
9X-RAY DIFFRACTION9(chain A and resid 270:313)A270 - 313
10X-RAY DIFFRACTION10(chain A and resid 314:353)A314 - 353

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