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

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Basic information

Entry
Database: PDB / ID: 2kod
TitleA high-resolution NMR structure of the dimeric C-terminal domain of HIV-1 CA
ComponentsHIV-1 CA C-terminal domain
KeywordsVIRAL PROTEIN / HIV-1 capsid / C-terminal domain
Function / homology
Function and homology information


integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / 2-LTR circle formation / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus ...integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / 2-LTR circle formation / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / Binding and entry of HIV virion / viral life cycle / Assembly Of The HIV Virion / HIV-1 retropepsin / : / Budding and maturation of HIV virion / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / protein processing / host multivesicular body / RNA-directed DNA polymerase / viral genome integration into host DNA / establishment of integrated proviral latency / viral penetration into host nucleus / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / peptidase activity / viral nucleocapsid / DNA recombination / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / symbiont-mediated suppression of host gene expression / lipid binding / host cell nucleus / structural molecule activity / host cell plasma membrane / virion membrane / DNA binding / RNA binding / zinc ion binding / membrane / identical protein binding
Similarity search - Function
Retrovirus capsid C-terminal domain / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain ...Retrovirus capsid C-terminal domain / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / 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. / Ribonuclease H superfamily / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHIV-1 M:B_HXB2R (virus)
MethodSOLUTION NMR / simulated annealing
AuthorsByeon, I.-J.L. / Jung, J. / Ahn, J. / concel, J. / Gronenborn, A.M.
CitationJournal: Cell / Year: 2009
Title: Structural convergence between Cryo-EM and NMR reveals intersubunit interactions critical for HIV-1 capsid function.
Authors: In-Ja L Byeon / Xin Meng / Jinwon Jung / Gongpu Zhao / Ruifeng Yang / Jinwoo Ahn / Jiong Shi / Jason Concel / Christopher Aiken / Peijun Zhang / Angela M Gronenborn /
Abstract: Mature HIV-1 particles contain conical-shaped capsids that enclose the viral RNA genome and perform essential functions in the virus life cycle. Previous structural analysis of two- and three- ...Mature HIV-1 particles contain conical-shaped capsids that enclose the viral RNA genome and perform essential functions in the virus life cycle. Previous structural analysis of two- and three-dimensional arrays of the capsid protein (CA) hexamer revealed three interfaces. Here, we present a cryoEM study of a tubular assembly of CA and a high-resolution NMR structure of the CA C-terminal domain (CTD) dimer. In the solution dimer structure, the monomers exhibit different relative orientations compared to previous X-ray structures. The solution structure fits well into the EM density map, suggesting that the dimer interface is retained in the assembled CA. We also identified a CTD-CTD interface at the local three-fold axis in the cryoEM map and confirmed its functional importance by mutagenesis. In the tubular assembly, CA intermolecular interfaces vary slightly, accommodating the asymmetry present in tubes. This provides the necessary plasticity to allow for controlled virus capsid dis/assembly.
History
DepositionSep 18, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 21, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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
Polymers19,6792
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)30 / 500structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein HIV-1 CA C-terminal domain


Mass: 9839.316 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HIV-1 M:B_HXB2R (virus) / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / References: UniProt: P04585

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1222D 1H-13C HSQC
1323D HN(CA)CB
1423D HN(COCA)CB
1523D HNCA
1623D HN(CO)CA
1723D HBHA(CO)NH
1823D (H)CCH-TOCSY
1923D simultaneous 13C,15N-edited NOESY
11013D 13C/15N-filtered, 13C-edited NOESY

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Sample preparation

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
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.4 mMHIV-1 CA C-terminal domain[U-100% 13C; U-100% 15N]1
1.4 mMNATURAL ABUNDANCE HIV-1 CA C-terminal domain1
25 mMsodium phosphate1
2 mMDTT1
0.02 %sodium azide1
2 mMHIV-1 CA C-terminal domain[U-100% 13C; U-100% 15N]2
25 mMsodium phosphate2
2 mMDTT2
0.02 %sodium azide2
Sample conditionsIonic strength: 25 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAvance9001
Bruker AvanceBrukerAvance8002
Bruker AvanceBrukerAvance7003
Bruker AvanceBrukerAvance6004

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Processing

NMR software
NameVersionDeveloperClassification
TOPSPIN2.1Brukercollection
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
RefinementMethod: 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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