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- PDB-2mv4: Solution structure of myristoylated Y28F/Y67F mutant of the Mason... -

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Basic information

Entry
Database: PDB / ID: 2mv4
TitleSolution structure of myristoylated Y28F/Y67F mutant of the Mason-Pfizer monkey virus matrix protein
ComponentsMatrix protein p10
KeywordsVIRAL PROTEIN / Gag / matrix protein / M-PMV / myristoyl switch / myristoylation / retrovirus
Function / homology
Function and homology information


viral budding via host ESCRT complex / viral nucleocapsid / host cell cytoplasm / nucleic acid binding / structural constituent of virion / zinc ion binding / metal ion binding
Similarity search - Function
GAG-polyprotein viral zinc-finger / Beta-retroviral matrix protein / Beta-retroviral matrix superfamily / Retroviral GAG p10 protein / gag protein p24 N-terminal domain / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal ...GAG-polyprotein viral zinc-finger / Beta-retroviral matrix protein / Beta-retroviral matrix superfamily / Retroviral GAG p10 protein / gag protein p24 N-terminal domain / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile.
Similarity search - Domain/homology
Biological speciesMason-Pfizer monkey virus
MethodSOLUTION NMR / torsion angle dynamics (Cyana 2.1), distance geometry dynamics, explicit water (YASARA 13.3.26)
Model detailslowest energy, model1
AuthorsDolezal, M. / Hrabal, R.
CitationJournal: Biomol.Nmr Assign. / Year: 2015
Title: Resonance assignments of the myristoylated Y28F/Y67F mutant of the Mason-Pfizer monkey virus matrix protein.
Authors: Dolezal, M. / Hrabal, R. / Ruml, T. / Rumlova, M.
History
DepositionSep 23, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 1, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2015Group: Database references
Revision 1.2Dec 21, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Matrix protein p10


Theoretical massNumber of molelcules
Total (without water)14,8921
Polymers14,8921
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)40 / 100structures with favorable non-bond energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Matrix protein p10 / MPMV_MA_Y28F_Y67F


Mass: 14891.988 Da / Num. of mol.: 1 / Fragment: UNP residues 2-118 / Mutation: Y28F, Y67F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mason-Pfizer monkey virus / Gene: gag / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P07567

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1332D 1H-13C HSQC
1442D 1H-13C HSQC
1512D CON
1612D CaCO
1713D HNCO
1833D HNCO
1913D HNCA
11033D HNCA
11113D CBCA(CO)NH
11233D CBCA(CO)NH
11313D HN(CA)CB
11413D HBHA(CBCACO)NH
11513D H(CCCO)NH-TOCSY
11643D (H)CCH-COSY
11713D (H)CCH-TOCSY
11843D (H)CCH-TOCSY
11943D (H)CCH-COSY
12013D (H)CCH-TOCSY
12143D (H)CCH-TOCSY
12222D 1H-13C HSQC aro
12322D (HB)CB(CGCD)HD
12422D (HB)CB(CGCDCE)HE
12522D (H)CB(CGCC-TOCSY)Har-phe
12622D (H)CB(CGCC-TOCSY)Har-trp
12722D (H)CB(CGCC-TOCSY)Har-tyr

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0 mM [U-99% 13C; U-99% 15N; NA-MYR] MPMV_MA_Y28F_Y67F, 300.0 mM NaCl, 2.5 mM TCEP, 50.0 mM sodium phosphate, 95% H2O/5% D2O95% H2O/5% D2O
21.0 mM [U-99% 13C; U-99% 15N; NA-MYR,H] MPMV_MA_Y28F_Y67F, 300.0 mM NaCl, 2.5 mM TCEP, 50.0 mM sodium phosphate, 95% H2O/5% D2O95% H2O/5% D2O
31.0 mM [U-99% 13C; U-99% 15N] MPMV_MA_Y28F_Y67F, 300.0 mM NaCl, 2.5 mM TCEP, 50.0 mM sodium phosphate, 95% H2O/5% D2O95% H2O/5% D2O
41.0 mM [U-99% 13C]-MYR MPMV_MA_Y28F_Y67F, 300.0 mM NaCl, 2.5 mM TCEP, 50.0 mM sodium phosphate, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMMPMV_MA_Y28F_Y67F-1[U-99% 13C; U-99% 15N; NA-MYR]1
300.0 mMNaCl-21
2.5 mMTCEP-31
50.0 mMsodium phosphate-41
95 %H2O-51
5 %D2O-61
1.0 mMMPMV_MA_Y28F_Y67F-7[U-99% 13C; U-99% 15N; NA-MYR,H]2
300.0 mMNaCl-82
2.5 mMTCEP-92
50.0 mMsodium phosphate-102
95 %H2O-112
5 %D2O-122
1.0 mMMPMV_MA_Y28F_Y67F-13[U-99% 13C; U-99% 15N]3
300.0 mMNaCl-143
2.5 mMTCEP-153
50.0 mMsodium phosphate-163
95 %H2O-173
5 %D2O-183
1.0 mMMPMV_MA_Y28F_Y67F-19[U-99% 13C]-MYR4
300.0 mMNaCl-204
2.5 mMTCEP-214
50.0 mMsodium phosphate-224
95 %H2O-234
5 %D2O-244
Sample conditionsIonic strength: 0.600 / pH: 6.000 / Pressure: ambient / Temperature: 298.000 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.2Bruker Biospinspectra acquisition
TopSpin3.2Bruker Biospinspectra procession
CcpNmr Analysis2.3CCPNresonance assignment
CYANA2.1Guntert, Mumenthaler and Wuthrichnoesy spectra assignment
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure calculation
YASARA13.3.26Elmar Kriegerrefinement
PSVS1.5Bhattacharya and Montelionestructure quality assessment
PdbStat5.9Roberto Tejerostructure quality assessment
AVSMoseley and Montelioneresonance assignment validation
RefinementMethod: torsion angle dynamics (Cyana 2.1), distance geometry dynamics, explicit water (YASARA 13.3.26)
Software ordinal: 1 / Details: structure refinement in water
NMR constraintsNOE constraints total: 2105 / NOE intraresidue total count: 573 / NOE long range total count: 433 / NOE medium range total count: 515 / NOE sequential total count: 584
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with favorable non-bond energy
Conformers calculated total number: 100 / Conformers submitted total number: 40 / Maximum torsion angle constraint violation: 5 ° / Maximum upper distance constraint violation: 0.21 Å

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