[English] 日本語
Yorodumi
- PDB-2kod: A high-resolution NMR structure of the dimeric C-terminal domain ... -

+
Open data


ID or keywords:

Loading...

no data

-
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 / homologyIntegrase, N-terminal zinc-binding domain / Peptidase A2A, retrovirus, catalytic / Retroviral matrix protein / Reverse transcriptase thumb / Reverse transcriptase connection / Retrovirus capsid, N-terminal / Retrovirus capsid, C-terminal / Ribonuclease H domain / Aspartic peptidase, active site / Matrix protein, lentiviral and alpha-retroviral, N-terminal ...Integrase, N-terminal zinc-binding domain / Peptidase A2A, retrovirus, catalytic / Retroviral matrix protein / Reverse transcriptase thumb / Reverse transcriptase connection / Retrovirus capsid, N-terminal / Retrovirus capsid, C-terminal / Ribonuclease H domain / Aspartic peptidase, active site / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Zinc finger, CCHC-type / Integrase, catalytic core / Integrase, C-terminal, retroviral / Retroviral nucleocapsid protein Gag / Reverse transcriptase domain / Immunodeficiency lentiviral matrix, N-terminal / Ribonuclease H-like superfamily / Integrase-like, N-terminal / Reverse transcriptase thumb domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Integrase Zinc binding domain / Integrase core domain / gag gene protein p24 (core nucleocapsid protein) / Integrase DNA binding domain / gag gene protein p17 (matrix protein) / Zinc knuckle / Retroviral aspartyl protease / Retropepsins / |RNase H / Zinc finger, CCHC-type superfamily / Integrase, C-terminal domain superfamily, retroviral / Ribonuclease H superfamily / Retropepsin-like catalytic domain / Aspartic peptidase domain superfamily / Eukaryotic and viral aspartyl proteases active site. / Reverse transcriptase connection domain / Zinc finger CCHC-type profile. / Integrase DNA binding domain profile. / Vpr-mediated nuclear import of PICs / APOBEC3G mediated resistance to HIV-1 infection / Autointegration results in viral DNA circles / Integration of viral DNA into host genomic DNA / Assembly Of The HIV Virion / Binding and entry of HIV virion / 2-LTR circle formation / Plus-strand DNA synthesis / Minus-strand DNA synthesis / Early Phase of HIV Life Cycle / Integration of provirus / Budding and maturation of HIV virion / Uncoating of the HIV Virion / Integrase catalytic domain profile. / Aspartyl protease, retroviral-type family profile. / Zinc finger integrase-type profile. / Reverse transcriptase (RT) catalytic domain profile. / RNase H domain profile. / integrase activity / nuclear transport / viral genome packaging / RNA-dependent DNA biosynthetic process / uncoating of virus / entry into host cell / viral life cycle / induction by virus of host cysteine-type endopeptidase activity involved in apoptotic process / HIV-1 retropepsin / virion assembly / retroviral ribonuclease H / exoribonuclease H activity / exoribonuclease H / host multivesicular body / viral penetration into host nucleus / RNA-directed DNA polymerase / viral genome integration into host DNA / Nucleotidyltransferases / RNA-directed DNA polymerase activity / suppression by virus of host gene expression / RNA-DNA hybrid ribonuclease activity / fusion of virus membrane with host plasma membrane / establishment of integrated proviral latency / peptidase activity / viral nucleocapsid / lipid binding / DNA recombination / Acting on Ester Bonds / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / aspartic-type endopeptidase activity / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / RNA binding / DNA binding / zinc ion binding / identical protein binding / Gag-Pol polyprotein
Function and homology information
Specimen sourceHIV-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 ...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.
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Polyers19,6792
Non-polymers00
Water0
1


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

-
Components

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


Mass: 9839.316 Da / Num. of mol.: 2 / Source: (gene. exp.) HIV-1 M:B_HXB2R (virus) / Plasmid name: pET21 / Production host: Escherichia coli (E. coli) / References: UniProt:P04585

-
Experimental details

-
Experiment

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

-
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.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
2mMDTT1
0.02%sodium azide1
2mMHIV-1 CA C-terminal domain[U-100% 13C; U-100% 15N]2
25mMsodium phosphate2
2mMDTT2
0.02%sodium azide2
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

-
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

+
About Yorodumi

-
News

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • All the functionalities will be ported from the levgacy version.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more