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- PDB-1qrj: Solution structure of htlv-i capsid protein -

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Basic information

Entry
Database: PDB / ID: 1qrj
TitleSolution structure of htlv-i capsid protein
ComponentsHTLV-I CAPSID PROTEIN
KeywordsVIRAL PROTEIN / HTLV-I / CAPSID PROTEIN / RETROVIRUS / TWO-DOMAIN PROTEIN / ALPHA HELICAL PROTEIN / HETERONUCLEAR NMR SPECTROSCOPY / VIRUS/VIRAL PROTEIN
Function / homology
Function and homology information


viral process / viral nucleocapsid / nucleic acid binding / structural molecule activity / zinc ion binding
Similarity search - Function
Delta-retroviral matrix protein / Major core protein p19 / Retrovirus capsid C-terminal domain / Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / gag protein p24 N-terminal domain / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retrovirus capsid, C-terminal ...Delta-retroviral matrix protein / Major core protein p19 / Retrovirus capsid C-terminal domain / Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / 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 knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHuman T-cell lymphotrophic virus type 1
MethodSOLUTION NMR / TORSION ANGLE DYNAMICS, SIMULATED ANNEALING
AuthorsKhorasanizadeh, S. / Campos-Olivas, R. / Clark, C.A. / Summers, M.F.
CitationJournal: J.Biomol.NMR / Year: 1999
Title: Sequence-specific 1H, 13C and 15N chemical shift assignment and secondary structure of the HTLV-I capsid protein.
Authors: Khorasanizadeh, S. / Campos-Olivas, R. / Clark, C.A. / Summers, M.F.
History
DepositionJun 14, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / 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_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HTLV-I CAPSID PROTEIN


Theoretical massNumber of molelcules
Total (without water)23,8511
Polymers23,8511
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)20 / 20STRUCTURES WITH LOWEST DYANA TARGET FUNCTION: RANGE 0.37-0.74 ANGSTROM SQUARED
RepresentativeModel #1

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Components

#1: Protein HTLV-I CAPSID PROTEIN


Mass: 23850.949 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human T-cell lymphotrophic virus type 1
Genus: Deltaretrovirus / Species: Primate T-lymphotropic virus 1 / Strain: ATK / Description: T7-RNA POLYMERASE-BASED EXPRESSION SYSTEM / Gene: GAG / Plasmid: PET16B / Cell line (production host): HMS174(DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: P03345

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: SEE THE PUBLICATION FOR THE SPECIFIC EXPERIMENTS

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Sample preparation

DetailsContents: 1 MM HTLV-I CAPSID U- 15N, U-13C/15N, U-13C/ 15N/2H; 50 MM PHOSPHATE BUFFER PH 6.0, 300 MM NACL
Sample conditionspH: 6.00 / Pressure: 1 atm / Temperature: 303.00 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
DYANA1.4GUNTERT, P. ET AL.refinement
XwinNMR2.1structure solution
NMRPipe1.7structure solution
NMRView2.1structure solution
RefinementMethod: TORSION ANGLE DYNAMICS, SIMULATED ANNEALING / Software ordinal: 1
NMR ensembleConformer selection criteria: STRUCTURES WITH LOWEST DYANA TARGET FUNCTION: RANGE 0.37-0.74 ANGSTROM SQUARED
Conformers calculated total number: 20 / Conformers submitted total number: 20

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