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- PDB-7a57: La Crosse Virus Envelope Glycoprotein Gc W1066H Mutant Fusion Dom... -

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Basic information

Entry
Database: PDB / ID: 7a57
TitleLa Crosse Virus Envelope Glycoprotein Gc W1066H Mutant Fusion Domains in Postfusion Conformation
ComponentsEnvelopment polyprotein
KeywordsVIRAL PROTEIN / Virus Entry / Class II Membrane Fusion Protein
Function / homology
Function and homology information


modulation by virus of host process / host cell Golgi membrane / host cell endoplasmic reticulum membrane / symbiont entry into host cell / virion attachment to host cell / virion membrane / membrane
Similarity search - Function
M polyprotein precursor, Orthobunyavirus type / Bunyavirus glycoprotein G2 / Bunyavirus nonstructural protein NSm / Bunyavirus glycoprotein G2 / Bunyavirus glycoprotein G1 / Bunyavirus glycoprotein G1
Similarity search - Domain/homology
Envelopment polyprotein
Similarity search - Component
Biological speciesLa Crosse virus L78
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.155 Å
AuthorsHellert, J. / Guardado-Calvo, P. / Rey, F.A.
Funding support2items
OrganizationGrant numberCountry
Innovative Medicines Initiative115760
Laboratories of Excellence (LabEx)ANR-10-LABX-62-IBEID
CitationJournal: Cell Rep / Year: 2023
Title: Structure, function, and evolution of the Orthobunyavirus membrane fusion glycoprotein.
Authors: Hellert, J. / Aebischer, A. / Haouz, A. / Guardado-Calvo, P. / Reiche, S. / Beer, M. / Rey, F.A.
History
DepositionAug 20, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 1, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Envelopment polyprotein
B: Envelopment polyprotein
C: Envelopment polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,5476
Polymers152,8353
Non-polymers1,7123
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19700 Å2
ΔGint-43 kcal/mol
Surface area53940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.873, 170.873, 379.220
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 929 or resseq 931:945 or (resid...
21(chain B and (resseq 929 or resseq 931:945 or (resid...
31(chain C and (resseq 929 or resseq 931:945 or (resid...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resseq 929 or resseq 931:945 or (resid...A929
121(chain A and (resseq 929 or resseq 931:945 or (resid...A931 - 945
131(chain A and (resseq 929 or resseq 931:945 or (resid...A946
141(chain A and (resseq 929 or resseq 931:945 or (resid...A928 - 2444
151(chain A and (resseq 929 or resseq 931:945 or (resid...A928 - 2444
161(chain A and (resseq 929 or resseq 931:945 or (resid...A928 - 2444
171(chain A and (resseq 929 or resseq 931:945 or (resid...A928 - 2444
181(chain A and (resseq 929 or resseq 931:945 or (resid...A928 - 2444
191(chain A and (resseq 929 or resseq 931:945 or (resid...A928 - 2444
211(chain B and (resseq 929 or resseq 931:945 or (resid...B929
221(chain B and (resseq 929 or resseq 931:945 or (resid...B931 - 945
231(chain B and (resseq 929 or resseq 931:945 or (resid...B946
241(chain B and (resseq 929 or resseq 931:945 or (resid...B916 - 2444
251(chain B and (resseq 929 or resseq 931:945 or (resid...B916 - 2444
261(chain B and (resseq 929 or resseq 931:945 or (resid...B916 - 2444
271(chain B and (resseq 929 or resseq 931:945 or (resid...B916 - 2444
281(chain B and (resseq 929 or resseq 931:945 or (resid...B916 - 2444
311(chain C and (resseq 929 or resseq 931:945 or (resid...C929
321(chain C and (resseq 929 or resseq 931:945 or (resid...C931 - 945
331(chain C and (resseq 929 or resseq 931:945 or (resid...C946
341(chain C and (resseq 929 or resseq 931:945 or (resid...C929 - 2444
351(chain C and (resseq 929 or resseq 931:945 or (resid...C929 - 2444
361(chain C and (resseq 929 or resseq 931:945 or (resid...C929 - 2444
371(chain C and (resseq 929 or resseq 931:945 or (resid...C929 - 2444
381(chain C and (resseq 929 or resseq 931:945 or (resid...C929 - 2444

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Components

#1: Protein Envelopment polyprotein / M polyprotein


Mass: 50944.988 Da / Num. of mol.: 3 / Mutation: W1066H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) La Crosse virus L78 / Gene: GP / Plasmid: pMT / Cell line (production host): Schneider 2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q8JPR1
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
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

CrystalDensity Matthews: 5.23 Å3/Da / Density % sol: 76.47 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2 uL of 8.5 mg/mL trimeric LACV Gc(918-1364) W1066H in 20 mM Tris-Cl pH 8.0, 150 mM NaCl were added to 0.2 uL of reservoir solution containing 0.1 M Bis-Tris propane pH 7 and 1.2 M K/Na ...Details: 0.2 uL of 8.5 mg/mL trimeric LACV Gc(918-1364) W1066H in 20 mM Tris-Cl pH 8.0, 150 mM NaCl were added to 0.2 uL of reservoir solution containing 0.1 M Bis-Tris propane pH 7 and 1.2 M K/Na tartrate (final pH: 8.0)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 2, 2016
Details: Be-lenses transfocator, channel cut cryogenically cooled monochromator, Kirkpatrick-Baez pair of bi-morph mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 3.155→48.173 Å / Num. obs: 38252 / % possible obs: 67.1 % / Redundancy: 6.3 % / Biso Wilson estimate: 99.63 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.057 / Rrim(I) all: 0.144 / Net I/σ(I): 9.2
Reflection shellResolution: 3.155→3.485 Å / Redundancy: 6 % / Rmerge(I) obs: 1.076 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1913 / CC1/2: 0.717 / Rpim(I) all: 0.47 / Rrim(I) all: 1.177 / % possible all: 13.3

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.25data extraction
STARANISOdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7A56

7a56


Resolution: 3.155→48.057 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2263 2298 6.01 %
Rwork0.1993 35940 -
obs0.2009 38238 67.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 239.9 Å2 / Biso mean: 109.5936 Å2 / Biso min: 46.05 Å2
Refinement stepCycle: final / Resolution: 3.155→48.057 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10271 0 114 0 10385
Biso mean--147.5 --
Num. residues----1322
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00510614
X-RAY DIFFRACTIONf_angle_d0.92414422
X-RAY DIFFRACTIONf_chiral_restr0.0571711
X-RAY DIFFRACTIONf_plane_restr0.0061802
X-RAY DIFFRACTIONf_dihedral_angle_d10.0238846
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6066X-RAY DIFFRACTION6.269TORSIONAL
12B6066X-RAY DIFFRACTION6.269TORSIONAL
13C6066X-RAY DIFFRACTION6.269TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.1551-3.22370.619620.5231291
3.2237-3.29870.3728150.39812688
3.2987-3.38120.3821370.351455517
3.3812-3.47260.3087520.34381825
3.4726-3.57470.3313700.2858110334
3.5747-3.69010.3497940.2791145944
3.6901-3.82190.29691310.2608205862
3.8219-3.97480.24921730.2418269581
3.9748-4.15570.25541990.21310294
4.1557-4.37460.21032130.18893336100
4.3746-4.64850.22762130.16983319100
4.6485-5.0070.18062150.14963362100
5.007-5.51030.18392160.15783376100
5.5103-6.30610.21552180.19013397100
6.3061-7.93920.23462190.22463434100
7.9392-48.0570.22472310.201362999
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)
13.28952.02341.6292.2491.31181.9199-0.12-0.56440.52040.1142-0.2010.4251-0.4977-0.3080.26830.93360.161200.5141-0.0580.535942.3232-62.47077.1966
27.0188-1.26540.66326.44735.26577.70120.0119-0.6234-0.32680.17020.0212-0.0119-0.02120.6748-0.05950.7672-0.1083-0.08470.5930.05070.422765.6399-70.265115.471
34.3533.92962.56175.57472.83062.4088-0.29070.6033-0.2254-0.32860.4399-0.2584-0.44390.4617-0.15430.8878-0.00920.03850.607-0.07230.3862.0073-65.4746-6.4915
44.6871.4211.75171.12060.73261.9451-0.45171.98910.4021-0.73040.4435-0.068-1.09020.99460.06022.0124-0.657-0.0851.41430.15870.765363.8063-48.7527-25.6384
52.63441.25291.2362.62281.04431.9787-0.51120.37180.7884-0.61140.2170.4133-1.1091-0.02170.20071.22560.0372-0.22420.54080.1240.756443.1398-52.4251-14.5706
61.65371.016-0.02536.33050.09720.6022-0.2084-0.89131.62470.4363-0.08511.1516-1.3841-1.21390.10181.69010.5429-0.10760.9589-0.39861.721728.8428-43.12965.2481
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and ((resseq 928:1259) or (resseq 1350:1364))A0
2X-RAY DIFFRACTION2chain 'A' and ((resseq 1260:1349))A0
3X-RAY DIFFRACTION3chain 'B' and ((resseq 916:1259) or (resseq 1350:1364))B0
4X-RAY DIFFRACTION4chain 'B' and ((resseq 1260:1349))B0
5X-RAY DIFFRACTION5chain 'C' and ((resseq 929:1259) or (resseq 1350:1364))C0
6X-RAY DIFFRACTION6chain 'C' and ((resseq 1260:1349))C0

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