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- PDB-6yrq: Crystal structure of the tetramerization domain of the glycoprote... -

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Basic information

Entry
Database: PDB / ID: 6yrq
TitleCrystal structure of the tetramerization domain of the glycoprotein Gn (Andes virus) at pH 4.6
Components
  • Envelope polyprotein
  • RNA (5'-R(*AP*UP*UP*UP*A)-3')
KeywordsVIRAL PROTEIN / class-II fusion protein hantavirus bunyavirus
Function / homology
Function and homology information


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 / endocytosis involved in viral entry into host cell / host cell surface / host cell endoplasmic reticulum membrane / induction by virus of host autophagy / fusion of virus membrane with host endosome membrane / viral envelope ...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 / endocytosis involved in viral entry into host cell / host cell surface / host cell endoplasmic reticulum membrane / induction by virus of host autophagy / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / 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
RNA / Envelopment polyprotein
Similarity search - Component
Biological speciesAndes orthohantavirus
Drosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.902 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
DepositionApr 20, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Envelope polyprotein
B: Envelope polyprotein
C: Envelope polyprotein
D: Envelope polyprotein
E: RNA (5'-R(*AP*UP*UP*UP*A)-3')
F: RNA (5'-R(*AP*UP*UP*UP*A)-3')
G: RNA (5'-R(*AP*UP*UP*UP*A)-3')
H: RNA (5'-R(*AP*UP*UP*UP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,59315
Polymers69,8888
Non-polymers1,7057
Water2,468137
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.636, 123.056, 90.119
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Protein / RNA chain , 2 types, 8 molecules ABCDEFGH

#1: Protein
Envelope polyprotein / M polyprotein


Mass: 15939.975 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Andes orthohantavirus / Gene: M, ADT63_77597gpM, ADT63_77598gpM / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q9E006
#2: RNA chain
RNA (5'-R(*AP*UP*UP*UP*A)-3')


Mass: 1531.952 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly)

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Sugars , 3 types, 3 molecules

#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.: 1
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
#5: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
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

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Non-polymers , 2 types, 141 molecules

#6: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 298 K / Method: vapor diffusion, hanging drop / Details: 0.2M CaCl2, 0.1M Na-acetate 4.6, 30% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→45.32 Å / Num. obs: 39873 / % possible obs: 99.8 % / Redundancy: 13.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.033 / Rrim(I) all: 0.12 / Net I/σ(I): 11.1 / Num. measured all: 542782 / Scaling rejects: 2
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
1.9-1.9412.83.0123147324510.5370.8543.1340.997
9.12-45.3212.30.05850894140.9980.0180.06135.999.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PHENIX1.14rc3refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YRB

6yrb


Resolution: 1.902→45.318 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 28.38
RfactorNum. reflection% reflection
Rfree0.2304 1957 4.92 %
Rwork0.1874 --
obs0.1896 39739 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 137.16 Å2 / Biso mean: 53.6698 Å2 / Biso min: 29.76 Å2
Refinement stepCycle: final / Resolution: 1.902→45.318 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2999 256 113 137 3505
Biso mean--91.83 52.49 -
Num. residues----415
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.902-1.94920.42421230.382256096
1.9492-2.00190.34821510.3082692100
2.0019-2.06080.32271420.26692665100
2.0608-2.12730.24971350.24132669100
2.1273-2.20340.30851240.21632686100
2.2034-2.29160.2611570.20452647100
2.2916-2.39590.2781370.20062701100
2.3959-2.52220.21711280.18722712100
2.5222-2.68020.24551170.1872717100
2.6802-2.88710.2551420.18062703100
2.8871-3.17750.22251570.18252696100
3.1775-3.63720.19931560.16882721100
3.6372-4.58180.15071380.16312754100
4.5818-45.3180.26791500.18272859100
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)
12.041-0.57340.53371.17210.87261.34760.07410.30330.3185-0.2052-0.2524-0.2593-0.17790.30450.00020.39370.00840.02230.4630.08510.436136.514716.3104-10.0399
20.92310.29960.71451.27760.30630.6701-0.12680.1391-0.08220.0664-0.3169-0.13490.50320.64560.00030.50480.0602-0.00180.55190.07280.462242.71697.16660.7861
30.3641-0.28410.11770.3034-0.25490.43840.0809-0.4330.2678-0.178-0.23590.1736-0.545-0.2359-0.00020.5189-0.0469-0.01930.4965-0.00720.487933.53623.45475.0412
40.90810.18960.46170.4508-0.30840.62010.2427-0.24341.05570.32960.0654-0.0089-0.4178-0.003-0.00030.7919-0.11320.05080.5292-0.01680.831336.582435.73848.6265
51.06330.55460.03470.484-0.66092.37160.27160.05080.4590.157-0.3135-0.1803-0.6209-0.1641-0.00020.5584-0.0634-0.01640.48680.05860.598737.351130.35731.6378
61.4833-0.2768-0.00741.043-0.51891.84640.0145-0.02290.15560.232-0.0248-0.3553-0.28230.3046-00.4425-0.0533-0.04120.50640.00360.502938.319721.613410.0034
71.03770.1807-0.46091.3087-0.2570.57410.2274-0.703-0.0870.351-0.1759-0.0212-0.0141-0.0771-0.00010.4057-0.02590.00370.4598-0.00010.410822.77217.700314.0007
80.0640.13670.1610.26750.23940.3144-0.01180.41370.30830.0798-0.12980.1426-0.3488-0.2717-0.00010.52280.0592-0.01780.47070.00360.42816.868722.2341-9.0175
90.7249-0.08940.47770.5970.58120.9990.30620.29510.6667-0.6717-0.1550.2342-0.6219-0.04680.00050.61030.12810.01380.60710.00080.679513.133133.0874-12.8878
101.3531-0.7808-0.16650.4445-0.12321.71210.0843-0.12420.4759-0.1462-0.09820.297-0.73960.14850.00010.65430.0566-0.04720.5385-0.06530.572913.528931.1828-7.7278
110.8765-0.37390.36660.68040.35220.634-0.15270.38750.1817-0.0790.0518-0.5071-0.0749-0.2840.00080.57630.23160.02920.5807-0.02120.66747.203627.0492-14.5669
123.6828-0.2451-0.37411.80980.04941.11210.1830.4316-0.3597-0.3098-0.28630.0450.0778-0.1305-00.39270.0654-0.00020.4867-0.05230.394222.82488.4746-14.6175
130.60340.3737-0.13820.3355-0.23270.30460.1804-0.07060.65960.1985-0.2171-0.4612-0.4851-0.31650.00040.45770.0079-0.00560.4609-0.05050.402118.216922.81176.6434
141.10040.8055-0.7860.6979-0.29421.1631-0.08540.16040.4436-0.1470.05450.4026-0.9343-0.1147-0.00010.74930.0386-0.06940.5386-0.11820.636116.204234.68478.8674
152.54710.3796-0.45390.92040.70850.7841-0.00210.13370.26380.2281-0.16480.1651-0.60690.0017-0.00010.61940.0080.01540.5142-0.06840.511819.796429.31919.3675
161.07190.27590.69720.2974-0.46732.2090.0499-0.22540.1165-0.0162-0.04760.056-0.3082-0.04850.00010.37380.02120.01320.4849-0.09270.434913.380219.71698.6773
170.5748-0.38750.36550.8509-0.37870.60640.21770.09970.0043-0.1444-0.01040.4370.1115-0.6799-0.00020.4558-0.00830.00250.5334-0.06720.49629.38526.1041-3.196
180.2774-0.02940.170.08230.03280.1110.10580.09570.641-0.0996-0.31560.2262-0.28850.26230.00060.5230.0129-0.00090.54110.08650.586232.215122.1484-10.1779
190.7024-0.2803-0.80280.41-0.02351.31420.02470.21750.78940.1068-0.2178-0.5598-0.93910.44960.00030.7737-0.0366-0.04720.60790.23060.823734.813232.9501-14.8711
202.82860.2280.43370.7426-0.77850.91570.0581-0.03350.5739-0.1183-0.2555-0.2985-0.538-0.00630.00020.73330.07670.02840.50340.08380.578229.820428.0474-14.1634
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain B and resid 433:465)B433 - 465
2X-RAY DIFFRACTION2(chain B and resid 466:482)B466 - 482
3X-RAY DIFFRACTION3(chain C and resid 379:393)C379 - 393
4X-RAY DIFFRACTION4(chain C and resid 394:407)C394 - 407
5X-RAY DIFFRACTION5(chain C and resid 408:431)C408 - 431
6X-RAY DIFFRACTION6(chain C and resid 432:457)C432 - 457
7X-RAY DIFFRACTION7(chain C and resid 458:482)C458 - 482
8X-RAY DIFFRACTION8(chain D and resid 379:393)D379 - 393
9X-RAY DIFFRACTION9(chain D and resid 394:410)D394 - 410
10X-RAY DIFFRACTION10(chain D and resid 411:431)D411 - 431
11X-RAY DIFFRACTION11(chain D and resid 432:442)D432 - 442
12X-RAY DIFFRACTION12(chain D and resid 443:483)D443 - 483
13X-RAY DIFFRACTION13(chain A and resid 379:391)A379 - 391
14X-RAY DIFFRACTION14(chain A and resid 392:412)A392 - 412
15X-RAY DIFFRACTION15(chain A and resid 413:434)A413 - 434
16X-RAY DIFFRACTION16(chain A and resid 435:461)A435 - 461
17X-RAY DIFFRACTION17(chain A and resid 462:482)A462 - 482
18X-RAY DIFFRACTION18(chain B and resid 379:393)B379 - 393
19X-RAY DIFFRACTION19(chain B and resid 394:411)B394 - 411
20X-RAY DIFFRACTION20(chain B and resid 412:432)B412 - 432

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