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- PDB-6y62: Crystal structure of the envelope glycoprotein complex of Maporal... -

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Basic information

Entry
Database: PDB / ID: 6y62
TitleCrystal structure of the envelope glycoprotein complex of Maporal virus in a prefusion conformation
ComponentsEnvelope polyprotein,Envelope polyprotein
KeywordsVIRAL PROTEIN / class-II fusion protein hantavirus bunyavirus / prefusion complex
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 / symbiont-mediated suppression of host innate immune response / host cell endoplasmic reticulum membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / virion attachment to host cell ...symbiont-mediated suppression of host TRAF-mediated signal transduction / host cell Golgi membrane / host cell mitochondrion / host cell surface / symbiont-mediated suppression of host innate immune response / host cell endoplasmic reticulum membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / 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 / Resolution: 2.2 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 1.3Nov 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,Envelope polyprotein
B: Envelope polyprotein,Envelope polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,8635
Polymers193,1442
Non-polymers1,7193
Water4,702261
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5770 Å2
ΔGint8 kcal/mol
Surface area34690 Å2
Unit cell
Length a, b, c (Å)120.330, 65.013, 144.757
Angle α, β, γ (deg.)90.000, 99.720, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Envelope polyprotein,Envelope polyprotein / M polyprotein


Mass: 96572.000 Da / Num. of mol.: 2
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.: 2
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: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / 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

Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1M MgCl2, 0.1M TrisHCl 8.5, 17% (w/v) PEG 20K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.2→38.07 Å / Num. obs: 55909 / % possible obs: 99.5 % / Redundancy: 4.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.047 / Rrim(I) all: 0.102 / Net I/σ(I): 11 / Num. measured all: 258945 / Scaling rejects: 63
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
2.2-2.2631.2541372345050.3380.861.5260.998.9
9.33-38.074.50.03533127430.9980.0170.03933.895.2

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.21data scaling
PHENIX1.14rc3_3199refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Y5F

6y5f


Resolution: 2.2→35.144 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.15
RfactorNum. reflection% reflection
Rfree0.2262 2814 5.04 %
Rwork0.1942 --
obs0.1958 55841 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 136.75 Å2 / Biso mean: 58.1255 Å2 / Biso min: 26.94 Å2
Refinement stepCycle: final / Resolution: 2.2→35.144 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5895 0 114 261 6270
Biso mean--83.57 49.38 -
Num. residues----771
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2001-2.2380.35771320.3142260698
2.238-2.27870.36341450.30362621100
2.2787-2.32260.29631480.28452645100
2.3226-2.370.30771380.26662630100
2.37-2.42150.28361350.2619264999
2.4215-2.47780.27991370.25482631100
2.4778-2.53970.26861440.2442265299
2.5397-2.60840.28191560.24432645100
2.6084-2.68510.27461210.24022624100
2.6851-2.77170.27281520.22982632100
2.7717-2.87080.29961410.232690100
2.8708-2.98570.23141510.20792621100
2.9857-3.12150.25421410.212677100
3.1215-3.28590.21811410.20562664100
3.2859-3.49160.251340.19712651100
3.4916-3.76090.18651430.1912268499
3.7609-4.13890.20111330.1691264399
4.1389-4.73650.1761360.1427267699
4.7365-5.96280.18491420.1483267299
5.9628-35.1440.19351440.1671271497
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)
10.8970.5247-0.19510.63660.78262.3877-0.2152-0.4792-0.16340.30960.07110.07690.3053-0.39390.00170.45680.16340.05560.57470.03970.444-46.771115.023135.3137
21.8427-0.9161-0.04780.83910.11021.0761-0.1946-0.05720.0163-0.0075-0.09330.4395-0.3565-0.8622-0.05180.40190.0994-0.00140.5237-0.03080.4294-51.603817.529119.5325
30.3547-0.057-0.22830.66730.61680.65970.17030.4555-0.477-0.5982-0.54940.6215-0.0916-1.2131-0.06660.5463-0.038-0.10280.6521-0.14110.5716-48.70290.776-1.5047
41.1239-1.2137-0.57011.30230.44092.6195-0.1304-0.10130.07580.071-0.08050.0502-0.1979-0.26030.00010.34120.13360.02240.40360.0010.371-46.590220.812525.8938
51.582-0.13380.94322.19440.14451.9417-0.0036-0.9014-0.23460.6071-0.09670.02840.1607-0.8420.06660.51650.1880.12230.7069-0.0080.3995-47.394516.479842.5266
61.9983-0.6940.31851.19940.67841.7338-0.2312-0.30020.09790.15360.1729-0.1715-0.21620.2166-0.00060.35360.1239-0.00730.3031-0.02620.3958-27.751622.532329.2308
71.2792-0.87470.5520.733-0.49921.4049-0.093-0.06990.06950.04510.1380.0553-0.51680.20160.00030.44570.06410.00890.3567-0.07170.4728-25.670519.62123.3544
80.23830.08690.07430.1547-0.04840.06830.70040.0589-1.48240.98970.72651.31480.9928-1.05060.01070.8675-0.01120.01310.96620.0711.1164-37.08741.637923.3692
92.21520.2190.01522.60721.25211.2298-0.21180.1095-0.0418-0.19750.24950.03640.0748-0.66870.00670.35840.01050.05140.4407-0.03310.3633-43.62418.98257.9411
101.179-0.108-0.39180.66110.99851.8325-0.06270.08660.031-0.17620.0456-0.0498-0.1139-0.11910.00140.34670.08480.0130.2532-0.00390.3671-36.399517.57618.027
110.0126-0.0262-0.0190.2080.18950.16710.81160.41690.63120.1712-0.75530.17440.0946-0.2559-0.00161.11960.0265-0.03791.1965-0.15171.168417.81416.99469.2432
120.33790.06930.01430.4993-0.26870.57560.111-0.5399-0.5216-0.4145-0.30810.18790.1995-0.16410.00320.55370.1525-0.02810.6050.01240.510416.02942.467458.579
130.665-0.6584-0.46511.927-0.01710.77080.177-0.78060.5420.171-0.2167-0.2803-0.3422-0.06970.00420.61850.1118-0.06590.8031-0.11940.552424.619911.390463.7422
141.5865-0.14610.56650.25070.30081.7446-0.063-0.0677-0.20290.08110.05440.04540.4421-0.0842-0.01260.47750.05310.00960.2699-0.02350.4337-26.5996-1.173316.0918
151.5388-0.28760.19930.03030.05691.06470.20080.0107-0.1941-0.1642-0.1207-0.0502-0.19510.06280.00540.54010.1786-0.01060.6007-0.01460.448614.76855.780346.3098
162.47860.69730.70880.63070.86932.71990.0653-0.037-0.44760.24210.1886-0.02310.71940.35150.00870.5960.2186-0.03710.35140.02280.5186-17.702-4.397428.452
171.49730.39360.62880.2452-0.05840.5690.4342-0.1294-0.027-0.1832-0.20630.25110.2017-0.1567-0.00750.54330.2974-0.06240.6533-0.06760.49695.74616.134747.0908
180.47610.50360.1780.9297-0.40290.93140.244-0.20530.6799-0.62810.0465-0.9208-0.48780.5490.02490.699-0.05220.02080.9968-0.07130.762729.653519.805163.4739
192.4953-0.84460.21673.83832.54962.61490.1659-0.3581-0.3408-0.1133-0.35550.15980.1119-0.00740.0010.5378-0.0285-0.0250.6554-0.07710.453211.809323.986270.452
200.1228-0.0357-0.03790.37770.25140.1651-0.1399-0.04020.3650.331-0.24380.2770.54880.7221-0.00360.94790.00250.07651.5032-0.22210.88487.646313.100468.2636
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 22:63)A22 - 63
2X-RAY DIFFRACTION2(chain A and resid 64:89)A64 - 89
3X-RAY DIFFRACTION3(chain A and resid 90:103)A90 - 103
4X-RAY DIFFRACTION4(chain A and resid 104:147)A104 - 147
5X-RAY DIFFRACTION5(chain A and resid 148:177)A148 - 177
6X-RAY DIFFRACTION6(chain A and resid 178:262)A178 - 262
7X-RAY DIFFRACTION7(chain A and resid 263:283)A263 - 283
8X-RAY DIFFRACTION8(chain A and resid 284:289)A284 - 289
9X-RAY DIFFRACTION9(chain A and resid 290:322)A290 - 322
10X-RAY DIFFRACTION10(chain A and resid 323:374)A323 - 374
11X-RAY DIFFRACTION11(chain B and resid 654:674)B654 - 674
12X-RAY DIFFRACTION12(chain B and resid 675:688)B675 - 688
13X-RAY DIFFRACTION13(chain B and resid 689:714)B689 - 714
14X-RAY DIFFRACTION14(chain B and resid 715:798)B715 - 798
15X-RAY DIFFRACTION15(chain B and resid 799:851)B799 - 851
16X-RAY DIFFRACTION16(chain B and resid 852:932)B852 - 932
17X-RAY DIFFRACTION17(chain B and resid 933:957)B933 - 957
18X-RAY DIFFRACTION18(chain B and resid 958:979)B958 - 979
19X-RAY DIFFRACTION19(chain B and resid 980:1060)B980 - 1060
20X-RAY DIFFRACTION20(chain B and resid 1061:1083)B1061 - 1083

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