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

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Basic information

Entry
Database: PDB / ID: 6yrb
TitleCrystal structure of the tetramerization domain of the glycoprotein Gn (Andes virus) at pH 7.5
Components
  • Envelope polyprotein
  • RNA (5'-D(*())-R(P*UP*UP*UP*())-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
IODIDE ION / RNA / Envelopment polyprotein
Similarity search - Component
Biological speciesAndes orthohantavirus
Drosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.351 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

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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: RNA (5'-D(*())-R(P*UP*UP*UP*())-3')
D: RNA (5'-D(*())-R(P*UP*UP*UP*())-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,43811
Polymers34,9444
Non-polymers1,4947
Water99155
1
A: Envelope polyprotein
C: RNA (5'-D(*())-R(P*UP*UP*UP*())-3')
D: RNA (5'-D(*())-R(P*UP*UP*UP*())-3')
hetero molecules

A: Envelope polyprotein
C: RNA (5'-D(*())-R(P*UP*UP*UP*())-3')
D: RNA (5'-D(*())-R(P*UP*UP*UP*())-3')
hetero molecules

A: Envelope polyprotein
C: RNA (5'-D(*())-R(P*UP*UP*UP*())-3')
D: RNA (5'-D(*())-R(P*UP*UP*UP*())-3')
hetero molecules

A: Envelope polyprotein
C: RNA (5'-D(*())-R(P*UP*UP*UP*())-3')
D: RNA (5'-D(*())-R(P*UP*UP*UP*())-3')
hetero molecules

B: Envelope polyprotein
C: RNA (5'-D(*())-R(P*UP*UP*UP*())-3')
D: RNA (5'-D(*())-R(P*UP*UP*UP*())-3')
hetero molecules

B: Envelope polyprotein
C: RNA (5'-D(*())-R(P*UP*UP*UP*())-3')
D: RNA (5'-D(*())-R(P*UP*UP*UP*())-3')
hetero molecules

B: Envelope polyprotein
C: RNA (5'-D(*())-R(P*UP*UP*UP*())-3')
D: RNA (5'-D(*())-R(P*UP*UP*UP*())-3')
hetero molecules

B: Envelope polyprotein
C: RNA (5'-D(*())-R(P*UP*UP*UP*())-3')
D: RNA (5'-D(*())-R(P*UP*UP*UP*())-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,00752
Polymers152,03124
Non-polymers5,97628
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation5_545x+1/2,y-1/2,z+1/21
crystal symmetry operation6_455-x-1/2,-y+1/2,z+1/21
crystal symmetry operation7_555-y+1/2,x+1/2,z+1/21
crystal symmetry operation8_445y-1/2,-x-1/2,z+1/21
Buried area25990 Å2
ΔGint-132 kcal/mol
Surface area35540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.854, 67.854, 121.891
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Envelope polyprotein / M polyprotein


Mass: 15939.975 Da / Num. of mol.: 2
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'-D(*())-R(P*UP*UP*UP*())-3')


Mass: 1531.952 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly)
#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: Chemical
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: I / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.01 Å3/Da / Density % sol: 38.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.2M NaCl, 0.1M Hepes 7.5, 35% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.8 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.8 Å / Relative weight: 1
ReflectionResolution: 2.35→37.7 Å / Num. obs: 11445 / % possible obs: 99.6 % / Redundancy: 10 % / CC1/2: 0.988 / Rmerge(I) obs: 0.199 / Rpim(I) all: 0.066 / Rrim(I) all: 0.209 / Net I/σ(I): 8.1 / Num. measured all: 114803 / Scaling rejects: 3
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
2.35-2.439.71.2941050110800.4550.4351.3661.796.4
9.1-37.79.80.14120552100.9860.0480.14915.799

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
SHELXDEphasing
PHENIX1.14rc3refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.351→37.699 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 30.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2655 570 4.98 %
Rwork0.226 10874 -
obs0.228 11444 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 159.69 Å2 / Biso mean: 47.7928 Å2 / Biso min: 22.73 Å2
Refinement stepCycle: final / Resolution: 2.351→37.699 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1498 130 55 55 1738
Biso mean--76.18 43.13 -
Num. residues----209
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.351-2.5870.34231260.2982269199
2.587-2.96120.32231280.26422723100
2.9612-3.73030.25991790.21192695100
3.7303-37.6990.24121370.20892765100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.0394-0.75910.31997.115-2.85071.14040.0815-0.38530.0914-1.25890.33080.74221.5888-0.1120.05720.43780.02640.0230.38960.0140.34433.539510.4266-21.6013
22.5718-2.1524-1.32231.91581.05921.0690.83330.22410.642-0.1544-0.8435-0.0425-0.2914-0.35120.42170.3912-0.12860.0040.45090.01880.26832.689815.3152-33.6715
31.4391-1.0444-0.0380.62820.0584-0.02860.03270.0397-0.1417-0.0556-0.0745-0.0441-0.1077-0.1566-0.00020.3508-0.01210.05580.37540.00540.34918.499310.7081-28.2786
40.61560.6558-1.30620.0391-0.60311.5538-0.1222-0.1015-0.116-0.2042-0.0738-0.4367-0.1080.3453-0.06870.3043-0.01450.03990.30890.0290.322-0.857413.3721-15.3295
50.4181.17880.12294.29011.7591.7306-0.05090.4281.04380.93920.07291.37910.71660.39360.02070.4530.0785-0.03140.45660.00660.4332-8.959417.0994-6.4804
61.977-0.76-0.64520.8110.50820.284-0.2069-0.712-0.45140.66860.3531-0.1809-0.0292-0.31980.00050.5162-0.0340.02140.4716-0.01590.4485-21.045132.7714-31.9908
72.71750.6196-0.06263.2455-0.17655.09350.3696-0.90350.62171.60860.95830.23130.16230.44552.23420.4902-0.00440.03550.4542-0.1770.4007-18.773842.6948-28.1853
80.2047-0.39420.03560.8013-0.15980.0240.0855-0.1666-0.3523-0.2529-0.25-0.45970.02070.3695-0.07890.36230.0082-0.05830.3599-0.00950.4305-22.032139.1454-33.6743
90.6538-0.51330.08231.47460.7590.548-0.29080.22920.3664-0.35510.0108-0.0536-0.37510.52160.00010.4261-0.0013-0.0420.39670.02080.406-18.138433.3924-42.0303
100.28380.30910.20710.28890.41580.7458-0.22570.27670.2380.17230.1357-0.11830.4306-0.138800.61090.0454-0.04330.5042-0.08270.4268-24.253621.1607-54.373
110.41080.1197-0.1060.33020.20970.2342-0.3025-0.2289-0.34830.72530.53-1.15150.33541.8501-0.05160.52540.0831-0.15990.6134-0.05120.5266-14.785827.5844-41.109
120.8313-0.00460.45170.1586-0.06550.2740.2146-0.54341.41730.90920.17830.602-1.3932-0.73460.01170.65780.06290.17050.44480.00470.5839-2.424120.1774-19.0684
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 379:392)A379 - 392
2X-RAY DIFFRACTION2(chain A and resid 393:407)A393 - 407
3X-RAY DIFFRACTION3(chain A and resid 408:433)A408 - 433
4X-RAY DIFFRACTION4(chain A and resid 434:468)A434 - 468
5X-RAY DIFFRACTION5(chain A and resid 469:483)A469 - 483
6X-RAY DIFFRACTION6(chain B and resid 379:402)B379 - 402
7X-RAY DIFFRACTION7(chain B and resid 403:413)B403 - 413
8X-RAY DIFFRACTION8(chain B and resid 419:433)B419 - 433
9X-RAY DIFFRACTION9(chain B and resid 434:461)B434 - 461
10X-RAY DIFFRACTION10(chain B and resid 462:482)B462 - 482
11X-RAY DIFFRACTION11(chain C and resid 0:4)C0 - 4
12X-RAY DIFFRACTION12(chain D and resid 0:4)D0 - 4

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