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- PDB-6tmr: Mokola virus glycoprotein, monomeric post-fusion conformation -

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Basic information

Entry
Database: PDB / ID: 6tmr
TitleMokola virus glycoprotein, monomeric post-fusion conformation
ComponentsGlycoprotein
KeywordsVIRAL PROTEIN / rhabdovirus / mokola virus / envelope protein / glycoprotein / membrane fusion / receptor binding / class III fusion protein
Function / homologyRhabdovirus glycoprotein / Rhabdovirus spike glycoprotein / membrane => GO:0016020 / viral envelope / virion membrane / TERBIUM(III) ION / Glycoprotein
Function and homology information
Biological speciesMokola virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.893 Å
AuthorsBelot, L. / Roche, S. / Legrand, P. / Gaudin, Y. / Albertini, A.
Funding support1items
OrganizationGrant numberCountry
French National Research AgencyANR CE11 MOBARHE
CitationJournal: Plos Pathog. / Year: 2020
Title: Crystal structure of Mokola virus glycoprotein in its post-fusion conformation.
Authors: Belot, L. / Ouldali, M. / Roche, S. / Legrand, P. / Gaudin, Y. / Albertini, A.A.
History
DepositionDec 5, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2020Group: 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 / _citation_author.name
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9248
Polymers52,7501
Non-polymers1,1757
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-29 kcal/mol
Surface area21380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.279, 81.951, 231.337
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Glycoprotein /


Mass: 52749.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mokola virus / Cell line (production host): S2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P0C572
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / 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 / 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
#3: Chemical
ChemComp-TB / TERBIUM(III) ION


Mass: 158.925 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Tb / Feature type: SUBJECT OF INVESTIGATION
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: 3.43 Å3/Da / Density % sol: 64.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEG 4000, sodium acetate, hepes

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.648727 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.648727 Å / Relative weight: 1
ReflectionResolution: 2.893→45.225 Å / Num. obs: 31149 / % possible obs: 99.6 % / Redundancy: 6.92 % / CC1/2: 0.998 / Rrim(I) all: 0.135 / Net I/σ(I): 10.16
Reflection scaleGroup code: 1
Reflection shellResolution: 2.893→3.07 Å / Mean I/σ(I) obs: 0.95 / Num. unique obs: 4917 / CC1/2: 0.798

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
SHELXDEphasing
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.893→45.225 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.92 / Phase error: 29.18 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2783 1465 5.11 %
Rwork0.2264 27188 -
obs0.229 28653 91.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 208.5 Å2 / Biso mean: 76.9419 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.893→45.225 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3108 0 20 0 3128
Biso mean--119.04 --
Num. residues----393
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8933-2.99670.3817880.3476160654
2.9967-3.11660.38091430.3404221475
3.1166-3.25840.42371420.3032262789
3.2584-3.43020.29711420.2817291698
3.4302-3.6450.26681810.24922935100
3.645-3.92630.30341730.22112979100
3.9263-4.32110.24621480.20043001100
4.3211-4.94570.23421600.18132934100
4.9457-6.22850.27921400.21133007100
6.2285-45.2250.24111480.2072969100
Refinement TLS params.Method: refined / Origin x: 28.6215 Å / Origin y: 11.4009 Å / Origin z: 62.4929 Å
111213212223313233
T0.375 Å20.0078 Å2-0.0624 Å2-0.4592 Å20.025 Å2--0.3667 Å2
L0.6437 °2-0.3619 °2-0.0158 °2-1.1888 °20.7782 °2--3.4956 °2
S-0.4049 Å °-0.1014 Å °0.0831 Å °0.1659 Å °0.3652 Å °0.1502 Å °-0.027 Å °-0.1282 Å °0.0286 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 501
2X-RAY DIFFRACTION1allB1 - 3
3X-RAY DIFFRACTION1allB4 - 6

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