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- PDB-1g03: NMR STRUCTURE OF N-TERMINAL DOMAIN OF HTLV-I CA1-134 -

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Basic information

Entry
Database: PDB / ID: 1g03
TitleNMR STRUCTURE OF N-TERMINAL DOMAIN OF HTLV-I CA1-134
ComponentsHTLV-I CAPSID PROTEIN
KeywordsVIRAL PROTEIN / Beta Hairpin loop / helix core
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 / Retroviral nucleocapsid Gag protein p24, N-terminal / Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / gag protein p24 N-terminal domain / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal ...: / Delta-retroviral matrix protein / Major core protein p19 / Retroviral nucleocapsid Gag protein p24, N-terminal / Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / gag protein p24 N-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-lymphotropic virus 1
MethodSOLUTION NMR / distance geometry simulated annealing
AuthorsCornilescu, C.C. / Bouamr, F. / Yao, X. / Carter, C. / Tjandra, N.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Structural analysis of the N-terminal domain of the human T-cell leukemia virus capsid protein.
Authors: Cornilescu, C.C. / Bouamr, F. / Yao, X. / Carter, C. / Tjandra, N.
History
DepositionOct 5, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 6, 2016Group: Structure summary

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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)14,9011
Polymers14,9011
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein HTLV-I CAPSID PROTEIN


Mass: 14900.793 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN OF MAJOR CORE PROTEIN P24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human T-lymphotropic virus 1 / Genus: Deltaretrovirus / Species: Primate T-lymphotropic virus 1 / Plasmid: PCYB1 / Production host: Escherichia coli (E. coli) / References: UniProt: P14077

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1114D 13C/15N-separated NOESY
2224D 13C-separated NOESY
3333D 15N-separated NOESY
NMR detailsText: This structure was determined using dipolar couplings

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Sample preparation

Details
Solution-IDContentsSolvent system
10.6 mM HTLV-I Capsid U-15N,13C95% H2O/5% D2O
20.6 mM HTLV-I Capsid U-15N,13C99.9% D2O
30.6 mM HTLV-I Capsid U-15N95% H2O/5% D2O
40.6 mM HTLV-I Capsid U-15N,13C 4% DMPC/DHPC 3:195% H2O/5% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
110mM 6.0 ambient 300 K
210mM 6.0 ambient 302 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX6001
Bruker DMXBrukerDMX8002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.84Brungerrefinement
XWINNMR2.5Brukercollection
NMRPipe1.7DeLagliodata analysis
PIPP/STAPP4.2.8Garrettdata analysis
RefinementMethod: distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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