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- PDB-2kod: A high-resolution NMR structure of the dimeric C-terminal domain ... -

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Database: PDB / ID: 2kod
TitleA high-resolution NMR structure of the dimeric C-terminal domain of HIV-1 CA
DescriptorHIV-1 CA C-terminal domain
KeywordsVIRAL PROTEIN / HIV-1 capsid / C-terminal domain
Specimen sourceHiv-1 m:b_hxb2r / HIV-1
MethodSolution NMR (Simulated annealing)
AuthorsByeon, I.-J.L. / Jung, J. / Ahn, J. / concel, J. / Gronenborn, A.M.
CitationCell(Cambridge,Mass.), 2009, 139, 780-790

Cell(Cambridge,Mass.), 2009, 139, 780-790 Yorodumi Papers
Structural convergence between Cryo-EM and NMR reveals intersubunit interactions critical for HIV-1 capsid function.
Byeon, I.J. / Meng, X. / Jung, J. / Zhao, G. / Yang, R. / Ahn, J. / Shi, J. / Concel, J. / Aiken, C. / Zhang, P. / Gronenborn, A.M.

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Sep 18, 2009 / Release: Nov 24, 2009
RevisionDateData content typeGroupProviderType
1.0Nov 24, 2009Structure modelrepositoryInitial release
1.1Jul 13, 2011Structure modelVersion format compliance
1.2Mar 21, 2012Structure modelDatabase references

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Deposited unit
A: HIV-1 CA C-terminal domain
B: HIV-1 CA C-terminal domain

Theoretical massNumber of molelcules
Total (without water)19,6792

TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
Number of conformers (submitted / calculated)30 / 500structures with the lowest energy
RepresentativeModel #1lowest energy


#1: Polypeptide(L)HIV-1 CA C-terminal domain

Mass: 9839.316 Da / Num. of mol.: 2 / Source: (gene. exp.) Hiv-1 m:b_hxb2r / References: UniProt: P04585

Cellular component

Molecular function

Biological process

Experimental details


ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions IDExperiment IDSolution IDType
1122D 1H-15N HSQC
1222D 1H-13C HSQC
1523D HNCA
1623D HN(CO)CA
1923D simultaneous 13C,15N-edited NOESY
11013D 13C/15N-filtered, 13C-edited NOESY

Sample preparation

NMR sample details
Solution IDContentsSolvent system
11.4 mM [U-100% 13C; U-100% 15N] HIV-1 CA C-terminal domain, 1.4 mM NATURAL ABUNDANCE HIV-1 CA C-terminal domain, 25 mM sodium phosphate, 2 mM DTT, 0.02 % sodium azide, 93% H2O/7% D2O93% H2O/7% D2O
22 mM [U-100% 13C; U-100% 15N] HIV-1 CA C-terminal domain, 25 mM sodium phosphate, 2 mM DTT, 0.02 % sodium azide, 93% H2O/7% D2O93% H2O/7% D2O
NMR experiment sample
Conc.UnitsComponentIsotopic labelingSolution ID
1.4mMHIV-1 CA C-terminal domain[U-100% 13C; U-100% 15N]1
1.4mMNATURAL ABUNDANCE HIV-1 CA C-terminal domain1
25mMsodium phosphate1
0.02%sodium azide1
2mMHIV-1 CA C-terminal domain[U-100% 13C; U-100% 15N]2
25mMsodium phosphate2
0.02%sodium azide2
NMR experiment sample conditionsIonic strength: 25 / pH: 6.5 / Pressure: ambient / Temperature: 298 kelvins / Temperature units: K

NMR measurement

NMR spectrometer
TypeManufacturerModelField strengthSpectrometer ID
Bruker AvanceBrukerAvance9001
Bruker AvanceBrukerAvance8002
Bruker AvanceBrukerAvance7003
Bruker AvanceBrukerAvance6004


NMR software
NMRPipeDelaglio, F. et al.processing
SPARKYGoddard, T.D. et al.data analysis
SPARKYGoddard, T.D. et al.peak picking
CYANAGuntert, P. et al.noe peak assignments
CANDIDHerrmann, T. et al.noe peak assignments
X-PLOR_NIHSchwieters, C.D. et al.refinement
NMR refineMethod: simulated annealing / Software ordinal: 1
Details: The residues 223-231 exhibit unfolded/disordered structure and thus no meaning should be given to the coordinates for these residues.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 30

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