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- PDB-2w2r: Structure of the vesicular stomatitis virus matrix protein -

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Basic information

Entry
Database: PDB / ID: 2w2r
TitleStructure of the vesicular stomatitis virus matrix protein
ComponentsMATRIX PROTEIN
KeywordsVIRAL PROTEIN / VIRAL ASSEMBLY / VIRAL MORPHOGENESIS / VSV / POLYMER / MATRIX PROTEIN
Function / homology
Function and homology information


host cell nuclear membrane / viral budding via host ESCRT complex / symbiont-mediated suppression of host mRNA export from nucleus / symbiont-mediated suppression of host gene expression / structural constituent of virion / viral envelope / virion membrane / membrane
Similarity search - Function
VSV matrix protein / VSV matrix protein / Vesiculovirus matrix / VSV matrix superfamily / Vesiculovirus matrix protein / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesVESICULAR STOMATITIS VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.83 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.
CitationJournal: 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.
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 / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Oct 9, 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 ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification

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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)26,5251
Polymers26,5251
Non-polymers00
Water2,648147
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)86.260, 86.260, 70.320
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
DetailsTHE PROTEIN IS A NON-COVALENT LINEAR POLYMER WHERE GLOBULAR DOMAINS (RESIDUES ARE 58-229) ARE NON-COVALENTLY ASSOCIATED BY A FLEXIBLE LINKER, WITH RESIDUES 41-52 MEDIATING THE INTER-MOLECULAR INTERACTION. RESIDUES 41-52, WHICH INTERACT WITH THE GLOBULAR DOMAIN (RESIDUES 58-229) IN THE LOOPS BETWEEN BETA SHEET 1 TO ALPHA HELIX 1, ALPHA HELIX 2 TO ALPHA HELIX 2.5 AND THE LOOP PRECEDING ALPHA HELIX 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 [-X-1/2,-Y-1/2,Z-1/2]. 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 41-52 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 -43.1300 -0.0000 -1.0000 -0.0000 -43.1300 -0.0000 -0.0000 1.0000 -35.1600

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Components

#1: Protein MATRIX PROTEIN / VESICULAR STOMATITS VIRUS MATRIX PROTEIN


Mass: 26525.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) VESICULAR STOMATITIS VIRUS / Strain: NEW JERSEY / Plasmid: POPINS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA PLYSS / References: UniProt: P08325*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE SEQUENCE OF THE PROTEIN WAS DERIVED FROM GENBANK ENTRY EU917223 WHICH WAS UNRELEASED AT THE ...THE SEQUENCE OF THE PROTEIN WAS DERIVED FROM GENBANK ENTRY EU917223 WHICH WAS UNRELEASED AT THE TIME OF PROCESSING.

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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: 2.52 Å3/Da / Density % sol: 51.13 % / Description: NONE
Crystal growMethod: vapor diffusion, sitting drop / pH: 5.6
Details: SITTING DROPS CONTAINING 100 NL 1.2 MG/ML PROTEIN AND 100 NL OF RESERVOIR SOLUTION (20% V/V ISOPROPANOL, 20% W/V PEG 4000 AND 0.1 M SODIUM CITRATE (PH 5.6)) WERE EQUILIBRATED AGAINST 95 UL ...Details: SITTING DROPS CONTAINING 100 NL 1.2 MG/ML PROTEIN AND 100 NL OF RESERVOIR SOLUTION (20% V/V ISOPROPANOL, 20% W/V PEG 4000 AND 0.1 M SODIUM CITRATE (PH 5.6)) WERE EQUILIBRATED AGAINST 95 UL RESERVIOURS AT 20.5C. CRYSTALS WERE CRYOPROTECTED BY A QUICK SWEEP THROUGH RESERVOIR SUPPLEMENTED WITH 20% V/V GLYCEROL.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9802
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 17, 2008 / Details: MIRRORS
RadiationMonochromator: SI (111) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9802 Å / Relative weight: 1
ReflectionResolution: 1.83→35.16 Å / Num. obs: 22813 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 21.1 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.7
Reflection shellResolution: 1.83→1.88 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 2 / % possible all: 99.6

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Processing

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

Resolution: 1.83→33.83 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.44 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.179 1130 5 %RANDOM
Rwork0.157 ---
obs0.158 21673 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.26 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2---0.03 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.83→33.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1483 0 0 147 1630
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221551
X-RAY DIFFRACTIONr_bond_other_d0.0010.021077
X-RAY DIFFRACTIONr_angle_refined_deg1.2491.9582105
X-RAY DIFFRACTIONr_angle_other_deg1.59832618
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8255190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.56823.3871
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.08215265
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.645159
X-RAY DIFFRACTIONr_chiral_restr0.0830.2225
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211712
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02338
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_it2.0732931
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.57531511
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.4454620
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.696590
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: 1.83→1.88 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.244 85
Rwork0.266 1603
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)
112.95216.19321.08194.6745-0.82051.13520.1514-0.5557-0.5724-0.43530.0767-0.26650.0081-0.1484-0.22810.193-0.0552-0.08090.01850.04110.1538-16.7273-38.3869-14.2914
20.2548-0.19230.03130.58720.53670.7420.03190.0035-0.02460.01820.01950.03910.02760.0005-0.05140.1465-0.0134-0.0150.11410.00750.1384-15.2817-18.151-9.0322
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A41 - 52
2X-RAY DIFFRACTION2A58 - 229

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