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- PDB-2w2s: Structure of the Lagos bat virus matrix protein -

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Basic information

Entry
Database: PDB / ID: 2w2s
TitleStructure of the Lagos bat virus matrix protein
ComponentsMATRIX PROTEIN
KeywordsVIRAL PROTEIN / VIRAL ASSEMBLY / VIRAL MORPHOGENESIS / LAGOS BAT VIRUS / POLYMER / MATRIX PROTEIN / VSV
Function / homology
Function and homology information


host cell endomembrane system / viral budding via host ESCRT complex / structural constituent of virion / viral envelope / virion membrane / membrane
Similarity search - Function
Rhabdovirus matrix protein M2 / Rhabdovirus matrix protein M / Rhabdovirus matrix protein superfamily / Rhabdovirus matrix protein M2 / VSV matrix protein / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesLAGOS BAT VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.75 Å
AuthorsGraham, S.C. / Assenberg, R. / Delmas, O. / Verma, A. / Gholami, A. / Talbi, C. / Owens, R.J. / Stuart, D.I. / Grimes, J.M. / Bourhy, H.
Citation
Journal: Plos Pathog. / Year: 2008
Title: Rhabdovirus Matrix Protein Structures Reveal a Novel Mode of Self-Association.
Authors: Graham, S.C. / Assenberg, R. / Delmas, O. / Verma, A. / Gholami, A. / Talbi, C. / Owens, R.J. / Stuart, D.I. / Grimes, J.M. / Bourhy, H.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2008
Title: Expression, Purification and Crystallization of a Lyssavirus Matrix (M) Protein.
Authors: Assenberg, R. / Delmas, O. / Graham, S.C. / Verma, A. / Berrow, N. / Stuart, D.I. / Owens, R.J. / Bourhy, H. / Grimes, J.M.
History
DepositionNov 3, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MATRIX PROTEIN


Theoretical massNumber of molelcules
Total (without water)23,1781
Polymers23,1781
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)56.870, 56.870, 187.910
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
DetailsTHE PROTEIN IS A NON-COVALENT LINEAR POLYMER WHERE GLOBULAR DOMAINS (RESIDUES ARE 48-202) ARE NON-COVALENTLY ASSOCIATED BY A FLEXIBLE LINKER, WITH RESIDUES 30-37 MEDIATING THE INTER-MOLECULAR INTERACTION. RESIDUES 30-37, WHICH INTERACT WITH THE GLOBULAR DOMAIN (RESIDUES 48-202) IN THE LOOPS BETWEEN BETA SHEET 1 TO ALPHA HELIX 1 AND BETA SHEET 2 TO BETA SHEET 3, ARE NOT COVALENTLY LINKED TO THIS GLOBULAR DOMAIN. RATHER, THEY ARE COVALENTLY LINKED TO AN ADJACENT GLOBULAR DOMAIN IN THE CRYSTAL RELATED BY THE SYMMETRY OPERATOR [1+X-Y,1-Y,1-Z]. REPEATED, THIS INTER-MOLECULAR INTERACTION GIVES RISE TO LINEAR POLYMERS OF THE M PROTEIN WHERE MOLECULES ARE NON-COVALENTLY LINKED VIA THE INTERACTION BETWEEN RESIDUES 30-37 AND THE GLOBULAR DOMAIN. IN ORDER TO GENERATE THE LINEAR POLYMER THE FOLLOWING TRANSFORMATION MATRIX SHOULD BE APPLIED: RX RY RZ T 1.0000 0.0000 0.0000 28.4350 0.0000 -1.0000 0.0000 49.2510 0.0000 0.0000 -1.0000 187.9100

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Components

#1: Protein MATRIX PROTEIN / LAGOS BAT VIRUS MATRIX PROTEIN


Mass: 23177.535 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LAGOS BAT VIRUS
Description: ISOLATE 8619NGA, GENOTYPE 2, ISOLATED FROM A FRUGIVOROUS BAT IN NIGERIA (BOULGER, L. R., AND J. S. PORTEFIELD. 1958. ISOLATION OF A VIRUS FROM NIGERIAN FRUIT BATS. TRANS.R.SOC.TROP.MED.HYG. 52\:421-424.)
Plasmid: POPINS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA PLYSS / References: UniProt: Q6JAM6
Has protein modificationY

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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: 1.91 Å3/Da / Density % sol: 35.61 % / Description: NONE
Crystal growMethod: vapor diffusion, sitting drop / pH: 4
Details: SITTING DROPS CONTAINING 100 NL OF 1.1 MG/ML PROTEIN AND 100 NL OF RESERVOIR SOLUTION (100 MM CITRATE PH 4.0 AND 10%(W/V) POLYETHYLENE GLYCOL (PEG) 6000) WERE EQUILIBRATED AGAINST 95 UL ...Details: SITTING DROPS CONTAINING 100 NL OF 1.1 MG/ML PROTEIN AND 100 NL OF RESERVOIR SOLUTION (100 MM CITRATE PH 4.0 AND 10%(W/V) POLYETHYLENE GLYCOL (PEG) 6000) WERE EQUILIBRATED AGAINST 95 UL RESERVOIRS AT 20.5C. CRYSTALS WERE CRYOPROTECTED BY BRIEF IMMERSION IN RESERVOIR SOLUTION SUPPLEMENTED WITH 25% V/V GLYCEROL.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 4, 2006 / Details: KB PAIR PT COATED SI MIRRORS
RadiationMonochromator: SI (111) CRYSTAL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.75→38.72 Å / Num. obs: 5164 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Biso Wilson estimate: 59.7 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 10.2
Reflection shellResolution: 2.75→2.82 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 2.2 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.4.0077refinement
XDSdata reduction
SCALAdata scaling
autoSHARPphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.75→38.72 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.893 / SU B: 29.934 / SU ML: 0.269 / Cross valid method: THROUGHOUT / ESU R Free: 0.374 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.255 291 5.6 %RANDOM
Rwork0.207 ---
obs0.21 4862 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 95.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.9 Å20.45 Å20 Å2
2--0.9 Å20 Å2
3----1.35 Å2
Refinement stepCycle: LAST / Resolution: 2.75→38.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1320 0 0 0 1320
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221350
X-RAY DIFFRACTIONr_bond_other_d0.0010.02927
X-RAY DIFFRACTIONr_angle_refined_deg1.0931.9471829
X-RAY DIFFRACTIONr_angle_other_deg1.1113.0022254
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9265161
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.2124.62767
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.51915240
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.019159
X-RAY DIFFRACTIONr_chiral_restr0.0540.2197
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211488
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02267
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5352811
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.07431312
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.6544539
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.7046517
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.75→2.82 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.376 19
Rwork0.277 343
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)
13.236-1.22571.10865.1932-3.32936.5411-0.07820.0147-0.0612-0.26020.12020.04180.09450.0702-0.0420.1291-0.0416-0.0330.14450.01680.10646.17927.69496.343
22.9183-3.7775-1.57217.64517.549533.02940.2501-0.22290.25470.1318-0.6307-0.3429-0.1246-0.36330.38050.2482-0.0780.00690.0980.10380.1539.45146.12983.537
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A48 - 202
2X-RAY DIFFRACTION2A30 - 37

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