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- PDB-7m1w: NMR structure of the Human T-cell leukemia virus 1 matrix protein -

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Basic information

Entry
Database: PDB / ID: 7m1w
TitleNMR structure of the Human T-cell leukemia virus 1 matrix protein
ComponentsMatrix protein p19
KeywordsVIRAL PROTEIN / Matrix / membrane-binding protein / Gag / HTLV-1 / Human T-cell leukemia virus 1
Function / homology
Function and homology information


viral process / viral nucleocapsid / nucleic acid binding / aspartic-type endopeptidase activity / structural molecule activity / zinc ion binding
Similarity search - Function
: / Delta-retroviral matrix protein / Major core protein p19 / Retroviral nucleocapsid Gag protein p24, N-terminal / gag protein p24 N-terminal domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal ...: / Delta-retroviral matrix protein / Major core protein p19 / Retroviral nucleocapsid Gag protein p24, N-terminal / gag protein p24 N-terminal domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily
Similarity search - Domain/homology
Biological speciesHuman T-cell leukemia virus type I
MethodSOLUTION NMR / simulated annealing
AuthorsHerrmann, D. / Saad, J.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)9 R01 AI150901-10 United States
CitationJournal: J.Mol.Biol. / Year: 2021
Title: Structural Insights into the Mechanism of Human T-cell Leukemia Virus Type 1 Gag Targeting to the Plasma Membrane for Assembly.
Authors: Herrmann, D. / Zhou, L.W. / Hanson, H.M. / Willkomm, N.A. / Mansky, L.M. / Saad, J.S.
History
DepositionMar 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Matrix protein p19


Theoretical massNumber of molelcules
Total (without water)12,0271
Polymers12,0271
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200target function
RepresentativeModel #1target function

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Components

#1: Protein Matrix protein p19


Mass: 12026.986 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human T-cell leukemia virus type I / Gene: gag-pro / Production host: Escherichia coli (E. coli) / References: UniProt: Q9QR99

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D HNCA
121isotropic13D HNCO
131isotropic13D HN(CA)CB
141isotropic1HN(CO)CACB
151isotropic13D HN(CO)CA
1101isotropic12D 1H-15N HSQC
192isotropic13D (H)CCH-TOCSY ali.
182isotropic13D (H)CCH-TOCSY arom.
172isotropic13D 13C-separated NOESY
163isotropic13D 15N-separated NOESY
1113isotropic13D 15N-separated TOCSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution1100 mM sodium chloride, 50 mM sodium phosphate, 2 mM TCEP, 400 uM [U-99% 13C; U-99% 15N] HTLV-1 Matrix, 95% H2O/5% D2Osample 195% H2O/5% D2O
solution2100 mM sodium chloride, 50 mM sodium phosphate, 2 mM TCEP, 320 uM [U-99% 13C; U-99% 15N] HTLV-1 Matrix, 100% D2Osample 2100% D2O
solution3100 mM sodium chloride, 50 mM sodium phosphate, 2 mM TCEP, 500 uM [U-99% 15N] HTLV-1 Matrix, 95% H2O/5% D2Osample 395% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
100 mMsodium chloridenatural abundance1
50 mMsodium phosphatenatural abundance1
2 mMTCEPnatural abundance1
400 uMHTLV-1 Matrix[U-99% 13C; U-99% 15N]1
100 mMsodium chloridenatural abundance2
50 mMsodium phosphatenatural abundance2
2 mMTCEPnatural abundance2
320 uMHTLV-1 Matrix[U-99% 13C; U-99% 15N]2
100 mMsodium chloridenatural abundance3
50 mMsodium phosphatenatural abundance3
2 mMTCEPnatural abundance3
500 uMHTLV-1 Matrix[U-99% 15N]3
Sample conditionsIonic strength: 100 mM / Label: conditions_1 / pH: 6.0 / Pressure: 1 atm / Temperature: 308 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE II / Manufacturer: Bruker / Model: AVANCE II / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANAGuntert P.refinement
CcpNmr Analysis2.4CCPNchemical shift assignment
CARA1.9.1.2Keller and Wuthrichprocessing
UNIO10Torsten Herrmannchemical shift assignment
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 1005 distance restraints. 286 intraresidue, 256 sequential, 263 medium-range, and 200 long-range NOEs
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20

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