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- PDB-2n1r: NMR Structure of the Myristylated Feline Immunodeficiency Virus M... -

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Basic information

Entry
Database: PDB / ID: 2n1r
TitleNMR Structure of the Myristylated Feline Immunodeficiency Virus Matrix Protein
ComponentsMatrix protein p15
KeywordsVIRAL PROTEIN / myristoylated / FIV / HIV / SIV / feline / matrix / p15
Function / homology
Function and homology information


viral budding via host ESCRT complex / viral nucleocapsid / structural constituent of virion / nucleic acid binding / zinc ion binding
Similarity search - Function
Immunodeficiency lentiviruses, gag gene matrix protein p17 / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / DNA polymerase; domain 1 / Retrovirus capsid, C-terminal / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily ...Immunodeficiency lentiviruses, gag gene matrix protein p17 / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / DNA polymerase; domain 1 / Retrovirus capsid, C-terminal / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesFeline immunodeficiency virus
MethodSOLUTION NMR / CYANA
Model detailsfewest violations, model2
AuthorsBrown, L.A. / Cox, C. / Button, R.J. / Baptiste, J. / Bahlow, K. / Spurrier, V. / Luttge, B.G. / Kuo, L. / Freed, E.O. / Summers, M.F. ...Brown, L.A. / Cox, C. / Button, R.J. / Baptiste, J. / Bahlow, K. / Spurrier, V. / Luttge, B.G. / Kuo, L. / Freed, E.O. / Summers, M.F. / Kyser, J. / Summers, H.R.
CitationJournal: Viruses / Year: 2015
Title: NMR structure of the myristylated feline immunodeficiency virus matrix protein.
Authors: Brown, L.A. / Cox, C. / Baptiste, J. / Summers, H. / Button, R. / Bahlow, K. / Spurrier, V. / Kyser, J. / Luttge, B.G. / Kuo, L. / Freed, E.O. / Summers, M.F.
History
DepositionApr 15, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 27, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2022Group: Data collection / Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / pdbx_nmr_software / struct_conn / struct_ref_seq_dif
Item: _citation.country / _citation.journal_id_ISSN ..._citation.country / _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Matrix protein p15


Theoretical massNumber of molelcules
Total (without water)14,7291
Polymers14,7291
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20020 structures for lowest energy
RepresentativeModel #1fewest violations

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Components

#1: Protein Matrix protein p15


Mass: 14728.980 Da / Num. of mol.: 1 / Mutation: Q5A, G6S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Feline immunodeficiency virus (isolate Petaluma)
Strain: Petaluma strain / Gene: gag / Variant: clone 34TF10 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: P16087
Sequence detailsMyristylated

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11515N-1HN HSQC
12113C-1HN HNCA
13113C-1HN HN(CO)CA
141CBCANH
151CBCA(CO)NH
161CARBON-NITROGEN NOESY (CNNOE)
17515N EDITED 3D NOESY
1841H-13C HMQC
194CARBON CARBON NOSEY (CCNOE)
11021H-1H NOESY
111213C-1H HMQC NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
150 mM sodium phosphate, 150 mM sodium chloride, 10 mM DTT, 1 g/L [U-99% 15N] ammonium chloride, 4 g/L glucose, 0.5 mg/mL MYRISTIC ACID, 50 mM sodium phosphate, 150 mM sodium chloride, 10 mM DTT, 1 g/L ammonium chloride, 4 g/L glucose, 0.5 mg/mL [U-100% 13C] MYRISTIC ACID, 90% H2O, 10% D2O90% H2O/10% D2O
250 mM sodium phosphate, 150 mM sodium chloride, 10 mM DTT, 4 g/L [U-100% 13C] glucose, 1 g/L ammonium chloride, 0.5 mg/mL MYRISTIC ACID, 50 mM sodium phosphate, 150 mM sodium chloride, 10 mM DTT, 4 g/L [U-100% 13C] glucose, 1 g/L [U-99% 15N] ammonium chloride, 0.5 mg/mL MYRISTIC ACID, 50 mM sodium phosphate, 150 mM sodium chloride, 10 mM DTT, 4 g/L glucose, 1 g/L ammonium chloride, 0.5 mg/mL MYRISTIC ACID, 100% D2O100% D2O
350 mM sodium phosphate, 150 mM sodium chloride, 10 mM DTT, 4 g/L [U-100% 13C] glucose, 1 g/L ammonium chloride, 0.5 mg/mL MYRISTIC ACID, 50 mM sodium phosphate, 150 mM sodium chloride, 10 mM DTT, 4 g/L [U-100% 13C] glucose, 1 g/L [U-99% 15N] ammonium chloride, 0.5 mg/mL MYRISTIC ACID, 50 mM sodium phosphate, 150 mM sodium chloride, 10 mM DTT, 4 g/L glucose, 1 g/L ammonium chloride, 0.5 mg/mL MYRISTIC ACID, 100% D2O100% D2O
450 mM sodium phosphate, 150 mM sodium chloride, 10 mM DTT, 4 g/L [U-100% 13C] glucose, 1 g/L ammonium chloride, 0.5 mg/mL MYRISTIC ACID, 50 mM sodium phosphate, 150 mM sodium chloride, 10 mM DTT, 4 g/L [U-100% 13C] glucose, 1 g/L [U-99% 15N] ammonium chloride, 0.5 mg/mL MYRISTIC ACID, 50 mM sodium phosphate, 150 mM sodium chloride, 10 mM DTT, 4 g/L glucose, 1 g/L ammonium chloride, 0.5 mg/mL MYRISTIC ACID, 100% D2O100% D2O
550 mM sodium phosphate, 150 mM sodium chloride, 10 mM DTT, 1 g/L [U-99% 15N] ammonium chloride, 4 g/L glucose, 0.5 mg/mL MYRISTIC ACID, 50 mM sodium phosphate, 150 mM sodium chloride, 10 mM DTT, 1 g/L ammonium chloride, 4 g/L glucose, 0.5 mg/mL [U-100% 13C] MYRISTIC ACID, 90% H2O, 10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
50 mMsodium phosphate-11
150 mMsodium chloride-21
10 mMDTT-31
1 g/Lammonium chloride-4[U-99% 15N]1
4 g/Lglucose-51
0.5 mg/mLMYRISTIC ACID-61
50 mMsodium phosphate-71
150 mMsodium chloride-81
10 mMDTT-91
1 g/Lammonium chloride-101
4 g/Lglucose-111
0.5 mg/mLMYRISTIC ACID-12[U-100% 13C]1
50 mMsodium phosphate-132
150 mMsodium chloride-142
10 mMDTT-152
4 g/Lglucose-16[U-100% 13C]2
1 g/Lammonium chloride-172
0.5 mg/mLMYRISTIC ACID-182
50 mMsodium phosphate-192
150 mMsodium chloride-202
10 mMDTT-212
4 g/Lglucose-22[U-100% 13C]2
1 g/Lammonium chloride-23[U-99% 15N]2
0.5 mg/mLMYRISTIC ACID-242
50 mMsodium phosphate-252
150 mMsodium chloride-262
10 mMDTT-272
4 g/Lglucose-282
1 g/Lammonium chloride-292
0.5 mg/mLMYRISTIC ACID-302
50 mMsodium phosphate-313
150 mMsodium chloride-323
10 mMDTT-333
4 g/Lglucose-34[U-100% 13C]3
1 g/Lammonium chloride-353
0.5 mg/mLMYRISTIC ACID-363
50 mMsodium phosphate-373
150 mMsodium chloride-383
10 mMDTT-393
4 g/Lglucose-40[U-100% 13C]3
1 g/Lammonium chloride-41[U-99% 15N]3
0.5 mg/mLMYRISTIC ACID-423
50 mMsodium phosphate-433
150 mMsodium chloride-443
10 mMDTT-453
4 g/Lglucose-463
1 g/Lammonium chloride-473
0.5 mg/mLMYRISTIC ACID-483
50 mMsodium phosphate-494
150 mMsodium chloride-504
10 mMDTT-514
4 g/Lglucose-52[U-100% 13C]4
1 g/Lammonium chloride-534
0.5 mg/mLMYRISTIC ACID-544
50 mMsodium phosphate-554
150 mMsodium chloride-564
10 mMDTT-574
4 g/Lglucose-58[U-100% 13C]4
1 g/Lammonium chloride-59[U-99% 15N]4
0.5 mg/mLMYRISTIC ACID-604
50 mMsodium phosphate-614
150 mMsodium chloride-624
10 mMDTT-634
4 g/Lglucose-644
1 g/Lammonium chloride-654
0.5 mg/mLMYRISTIC ACID-664
50 mMsodium phosphate-675
150 mMsodium chloride-685
10 mMDTT-695
1 g/Lammonium chloride-70[U-99% 15N]5
4 g/Lglucose-715
0.5 mg/mLMYRISTIC ACID-725
50 mMsodium phosphate-735
150 mMsodium chloride-745
10 mMDTT-755
1 g/Lammonium chloride-765
4 g/Lglucose-775
0.5 mg/mLMYRISTIC ACID-78[U-100% 13C]5
Sample conditionsIonic strength: 150mM NaCl / pH: 7 / Pressure: ambient, 1atm atm / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX8001
Bruker DMXBrukerDMX6002

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Processing

NMR software
NameDeveloperClassification
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificdata analysis
NMRViewJohnson, One Moon Scientificpeak picking
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TopSpinBruker Biospincollection
CYANArefinement
RefinementMethod: CYANA / Software ordinal: 1
Details: Structures were calculated in torsion angle space with CYANA (http://www.las.jp/index_eg.html) starting from random initial angles. Upper interproton distance bounds of 2.7, 3.3 and 5.0 aE ...Details: Structures were calculated in torsion angle space with CYANA (http://www.las.jp/index_eg.html) starting from random initial angles. Upper interproton distance bounds of 2.7, 3.3 and 5.0 aE (with appropriate corrections for pseudoatoms) were employed for NOE cross peaks of strong, medium, and weak intensity respectively, which were qualitatively determined following intensity normalization of the different NOE data sets. Residual dipolar couplings were prohibited due to precipitation of the sample. No backbone hydrogen bond or chemical shift-based torsion angle restraints were employed.
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: 20 structures for lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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