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- PDB-4d4t: RSV Matrix protein -

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Basic information

Entry
Database: PDB / ID: 4d4t
TitleRSV Matrix protein
ComponentsMATRIX PROTEINViral matrix protein
KeywordsVIRAL PROTEIN
Function / homology
Function and homology information


virion assembly / host cell cytoplasm / structural constituent of virion / viral envelope / host cell nucleus / host cell plasma membrane / membrane
Similarity search - Function
HRSV-S2 matrix protein, N-terminal domain / Pneumovirus matrix protein / Pneumovirus matrix, N-terminal / Pneumovirus matrix protein / Topoisomerase I; domain 3 / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Matrix protein / Matrix protein
Similarity search - Component
Biological speciesRESPIRATORY SYNCYTIAL VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsForster, A. / Maertens, G. / Bajorek, M.
CitationJournal: J.Virol. / Year: 2015
Title: Dimerization of Matrix Protein is Required for Budding of Respiratory Syncytial Virus.
Authors: Forster, A. / Maertens, G.N. / Farrell, P.J. / Bajorek, M.
History
DepositionOct 31, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
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_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MATRIX PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2504
Polymers29,0231
Non-polymers2273
Water2,144119
1
A: MATRIX PROTEIN
hetero molecules

A: MATRIX PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5008
Polymers58,0452
Non-polymers4556
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area3830 Å2
ΔGint-29.2 kcal/mol
Surface area22040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.127, 87.127, 144.721
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein MATRIX PROTEIN / Viral matrix protein


Mass: 29022.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RESPIRATORY SYNCYTIAL VIRUS / Strain: A2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA 2 / References: UniProt: P03419, UniProt: P0DOE7*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 9

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Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.4 % / Description: NONE
Crystal growpH: 6.5 / Details: 30% GLYCEROL 0.1 M MES (6.5) 1.8 M AM2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 27, 2014 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.9→33.45 Å / Num. obs: 25922 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Biso Wilson estimate: 23.16 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.5
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 3.2 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VQP

2vqp


Resolution: 1.9→33.453 Å / SU ML: 0.19 / σ(F): 1.34 / Phase error: 19.8 / Stereochemistry target values: ML / Details: RESIDUES 170-178 ARE DISORDERED.
RfactorNum. reflection% reflection
Rfree0.2056 1283 4.9 %
Rwork0.1825 --
obs0.1836 25922 98.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.8 Å2
Refinement stepCycle: LAST / Resolution: 1.9→33.453 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1936 0 12 119 2067
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0162086
X-RAY DIFFRACTIONf_angle_d1.0382838
X-RAY DIFFRACTIONf_dihedral_angle_d11.883778
X-RAY DIFFRACTIONf_chiral_restr0.041344
X-RAY DIFFRACTIONf_plane_restr0.005353
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.97610.2711330.21852685X-RAY DIFFRACTION99
1.9761-2.0660.23951340.20252702X-RAY DIFFRACTION99
2.066-2.17490.1831400.18352703X-RAY DIFFRACTION99
2.1749-2.31110.21561430.18482708X-RAY DIFFRACTION99
2.3111-2.48950.25241380.18642714X-RAY DIFFRACTION99
2.4895-2.740.21891430.18632711X-RAY DIFFRACTION99
2.74-3.13620.21321460.18172727X-RAY DIFFRACTION98
3.1362-3.95030.18921650.16552755X-RAY DIFFRACTION98
3.9503-33.45840.18281410.18212934X-RAY DIFFRACTION97
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)
14.0306-0.61170.85345.5715-1.75174.3157-0.04510.3322-0.7428-0.2168-0.09860.20050.2334-0.18550.04390.25080.014-0.02490.2333-0.11480.201624.400822.2393-13.3444
21.951.16971.04362.42771.85112.577-0.03040.10340.0014-0.23960.0621-0.0942-0.23310.08090.00460.13320.00980.00460.18220.01960.150929.315935.0462-6.3864
32.6519-0.71020.36941.44880.00342.5604-0.1134-0.1909-0.16280.13250.05690.20440.065-0.25440.05360.1537-0.0007-0.00060.1426-0.00710.179513.891922.40295.7022
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID -1 THROUGH 13 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 14 THROUGH 120 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 121 THROUGH 254 )

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