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- PDB-4v23: RSV Matrix protein -

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Basic information

Entry
Database: PDB / ID: 4v23
TitleRSV Matrix protein
ComponentsMATRIX PROTEINViral matrix protein
KeywordsVIRAL PROTEIN / VIRAL BUDDING RESPIRATORY SYNCYTIAL VIRUS MATRIX 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 / SAD / Resolution: 1.7 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 5, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 25, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2015Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_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_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.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)28,7862
Polymers28,7461
Non-polymers391
Water3,297183
1
A: MATRIX PROTEIN
hetero molecules

A: MATRIX PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5714
Polymers57,4932
Non-polymers782
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area2660 Å2
ΔGint-222 kcal/mol
Surface area23300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.294, 79.156, 65.945
Angle α, β, γ (deg.)90.00, 96.24, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein MATRIX PROTEIN / Viral matrix protein


Mass: 28746.410 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) RESPIRATORY SYNCYTIAL VIRUS / Strain: A2 / References: UniProt: P03419, UniProt: P0DOE7*PLUS
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 48 % / Description: NONE
Crystal growDetails: 10% W/V PEG 8000, 20% V/V ETHYLENE GLYCOL, 0.02 M EACH OF SODIUM FORMATE, AMMONIUM ACETATE, TRISODIUM CITRATE, SODIUM POTASSIUM TARTRATE, 0.1 M MOPS/HEPES-NA (7.5)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Aug 29, 2014 / Details: OSMIC VARIMAX VHF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→23.5 Å / Num. obs: 29385 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Biso Wilson estimate: 15.99 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.1
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2.9 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-3000data reduction
HKL-3000data scaling
SHELXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.7→65.554 Å / SU ML: 0.19 / σ(F): 2.8 / Phase error: 20.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2111 2827 5.1 %
Rwork0.1749 --
obs0.1767 29385 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.76 Å2
Refinement stepCycle: LAST / Resolution: 1.7→65.554 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2003 0 1 183 2187
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0172129
X-RAY DIFFRACTIONf_angle_d1.3162896
X-RAY DIFFRACTIONf_dihedral_angle_d12.244803
X-RAY DIFFRACTIONf_chiral_restr0.064352
X-RAY DIFFRACTIONf_plane_restr0.006362
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.72930.23841130.23332350X-RAY DIFFRACTION86
1.7293-1.76080.29681350.21652396X-RAY DIFFRACTION87
1.7608-1.79460.29951400.19852446X-RAY DIFFRACTION90
1.7946-1.83130.26561350.21312432X-RAY DIFFRACTION88
1.8313-1.87110.24671570.22447X-RAY DIFFRACTION90
1.8711-1.91460.24031610.19422447X-RAY DIFFRACTION92
1.9146-1.96250.23911430.18232575X-RAY DIFFRACTION94
1.9625-2.01560.20011390.18122684X-RAY DIFFRACTION96
2.0156-2.07490.24111430.1732657X-RAY DIFFRACTION97
2.0749-2.14190.21971490.16922703X-RAY DIFFRACTION98
2.1419-2.21840.18811190.16452673X-RAY DIFFRACTION98
2.2184-2.30720.20971660.15852662X-RAY DIFFRACTION98
2.3072-2.41230.17951460.17252669X-RAY DIFFRACTION98
2.4123-2.53940.20751520.16792700X-RAY DIFFRACTION98
2.5394-2.69860.20131280.17912721X-RAY DIFFRACTION98
2.6986-2.90690.2351360.19552716X-RAY DIFFRACTION98
2.9069-3.19940.19391310.19012713X-RAY DIFFRACTION98
3.1994-3.66240.20541290.16982751X-RAY DIFFRACTION100
3.6624-4.6140.19531420.15072723X-RAY DIFFRACTION100
4.614-65.60320.18761630.16322735X-RAY DIFFRACTION100
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)
12.18970.32481.16721.56590.78353.41020.0231-0.04990.083-0.02910.02240.0886-0.0651-0.212-0.05110.09420.01940.01730.14060.02540.0996-19.925236.769920.8796
23.0936-0.8622-0.80540.6621-0.31332.2075-0.0457-0.1823-0.03590.16370.0217-0.0047-0.0508-0.0742-0.01510.1276-0.0462-0.01260.12190.01750.115-13.032635.286622.8515
32.9454-0.6067-0.87030.83560.26381.11270.09450.23560.1540.0051-0.0951-0.15070.0068-0.0340.02320.13550.0259-0.00210.11040.03460.13073.999433.620913.8647
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 1 THROUGH 95 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 96 THROUGH 134 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 135 THROUGH 255 )

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