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- PDB-6lgx: Structure of Rabies virus glycoprotein at basic pH -

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Basic information

Entry
Database: PDB / ID: 6lgx
TitleStructure of Rabies virus glycoprotein at basic pH
ComponentsGlycoprotein,Glycoprotein,Glycoprotein
KeywordsVIRAL PROTEIN / functional class
Function / homologyRhabdovirus glycoprotein / Rhabdovirus spike glycoprotein / viral envelope / virion membrane / membrane / Glycoprotein / Glycoprotein / Glycoprotein / Glycoprotein
Function and homology information
Biological speciesRabies lyssavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.097 Å
AuthorsYang, F.L. / Lin, S. / Ye, F. / Yang, J. / Qi, J.X. / Chen, Z.J. / Lin, X. / Wang, J.C. / Yue, D. / Cheng, Y.W. ...Yang, F.L. / Lin, S. / Ye, F. / Yang, J. / Qi, J.X. / Chen, Z.J. / Lin, X. / Wang, J.C. / Yue, D. / Cheng, Y.W. / Chen, Z.M. / Chen, H. / You, Y. / Zhang, Z.L. / Yang, Y. / Yang, M. / Sun, H.L. / Li, Y.H. / Cao, Y. / Yang, S.Y. / Wei, Y.Q. / Gao, G.F. / Lu, G.W.
CitationJournal: Cell Host Microbe / Year: 2020
Title: Structural Analysis of Rabies Virus Glycoprotein Reveals pH-Dependent Conformational Changes and Interactions with a Neutralizing Antibody.
Authors: Yang, F. / Lin, S. / Ye, F. / Yang, J. / Qi, J. / Chen, Z. / Lin, X. / Wang, J. / Yue, D. / Cheng, Y. / Chen, Z. / Chen, H. / You, Y. / Zhang, Z. / Yang, Y. / Yang, M. / Sun, H. / Li, Y. / ...Authors: Yang, F. / Lin, S. / Ye, F. / Yang, J. / Qi, J. / Chen, Z. / Lin, X. / Wang, J. / Yue, D. / Cheng, Y. / Chen, Z. / Chen, H. / You, Y. / Zhang, Z. / Yang, Y. / Yang, M. / Sun, H. / Li, Y. / Cao, Y. / Yang, S. / Wei, Y. / Gao, G.F. / Lu, G.
History
DepositionDec 6, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Nov 22, 2023Group: 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

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Assembly

Deposited unit
A: Glycoprotein,Glycoprotein,Glycoprotein
B: Glycoprotein,Glycoprotein,Glycoprotein


Theoretical massNumber of molelcules
Total (without water)99,2672
Polymers99,2672
Non-polymers00
Water0
1
A: Glycoprotein,Glycoprotein,Glycoprotein

B: Glycoprotein,Glycoprotein,Glycoprotein


Theoretical massNumber of molelcules
Total (without water)99,2672
Polymers99,2672
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area5380 Å2
ΔGint-45 kcal/mol
Surface area39280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)192.440, 138.447, 61.442
Angle α, β, γ (deg.)90.000, 100.020, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Glycoprotein,Glycoprotein,Glycoprotein


Mass: 49633.281 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rabies lyssavirus / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q5JZZ2, UniProt: Q2Z2I1, UniProt: D8VEC1, UniProt: O92284*PLUS

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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: 4.06 Å3/Da / Density % sol: 69.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1 M BICINE, 14% Polyethylene glycol 300

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 3.097→50 Å / Num. obs: 28680 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Biso Wilson estimate: 106.98 Å2 / CC1/2: 0.985 / Net I/σ(I): 14.45
Reflection shellResolution: 3.097→3.21 Å / Redundancy: 6.7 % / Num. unique obs: 2852 / CC1/2: 0.659 / % possible all: 99.7

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
Cootmodel building
PHENIX1.16-3549refinement
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LGW

6lgw


Resolution: 3.097→47.398 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 36.37
RfactorNum. reflection% reflection
Rfree0.2846 1344 4.69 %
Rwork0.2422 --
obs0.2442 28656 99.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 248.86 Å2 / Biso mean: 123.7361 Å2 / Biso min: 50.24 Å2
Refinement stepCycle: final / Resolution: 3.097→47.398 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5695 0 0 0 5695
Num. residues----725
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045851
X-RAY DIFFRACTIONf_angle_d0.7397934
X-RAY DIFFRACTIONf_chiral_restr0.048873
X-RAY DIFFRACTIONf_plane_restr0.0061008
X-RAY DIFFRACTIONf_dihedral_angle_d14.7843564
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.097-3.20720.43971260.3982260995
3.2072-3.33560.38361150.3412705100
3.3356-3.48730.37971370.30832746100
3.4873-3.67110.4081470.30042734100
3.6711-3.9010.30781420.2789270699
3.901-4.20210.30911340.22742741100
4.2021-4.62460.23291350.2042761100
4.6246-5.29310.24831310.20032752100
5.2931-6.66570.27091330.24832781100
6.6657-47.3980.25211440.2229277799
Refinement TLS params.Method: refined / Origin x: 42.622 Å / Origin y: 23.2452 Å / Origin z: 14.9364 Å
111213212223313233
T0.5812 Å20.0271 Å20.0523 Å2-0.5983 Å2-0.0712 Å2--0.6259 Å2
L0.0862 °20.0934 °20.3157 °2-0.2929 °20.2595 °2--1.2198 °2
S0.0434 Å °0.0059 Å °0.0082 Å °0.1656 Å °-0.0617 Å °0.0118 Å °-0.0949 Å °-0.0262 Å °0.0247 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 419
2X-RAY DIFFRACTION1allB2 - 408

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