[English] 日本語
Yorodumi
- PDB-2ont: A swapped dimer of the HIV-1 capsid C-terminal domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ont
TitleA swapped dimer of the HIV-1 capsid C-terminal domain
ComponentsCapsid protein p24
KeywordsVIRAL PROTEIN / HIV / capsid / GAG / domain swap
Function / homology
Function and homology information


viral process / HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase ...viral process / HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / symbiont-mediated suppression of host gene expression / viral penetration into host nucleus / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / viral capsid / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / viral translational frameshifting / lipid binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / DNA binding / zinc ion binding / membrane
Similarity search - Function
Retrovirus capsid C-terminal domain / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / : / gag protein p24 N-terminal domain / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. ...Retrovirus capsid C-terminal domain / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / : / gag protein p24 N-terminal domain / 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. / Retropepsin-like catalytic domain / RNase H type-1 domain profile. / Ribonuclease H domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase (RNA-dependent DNA polymerase) / Retroviral matrix protein / Retrovirus capsid, C-terminal / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Ribonuclease H superfamily / 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
Gag-Pol polyprotein / p24
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsIvanov, D. / Tsodikov, O.V. / Kasanov, J. / Ellenberger, T. / Wagner, G. / Collins, T.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Domain-swapped dimerization of the HIV-1 capsid C-terminal domain
Authors: Ivanov, D. / Tsodikov, O.V. / Kasanov, J. / Ellenberger, T. / Wagner, G. / Collins, T.
History
DepositionJan 24, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Capsid protein p24


Theoretical massNumber of molelcules
Total (without water)8,5411
Polymers8,5411
Non-polymers00
Water34219
1
A: Capsid protein p24

A: Capsid protein p24


Theoretical massNumber of molelcules
Total (without water)17,0812
Polymers17,0812
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3060 Å2
ΔGint-25 kcal/mol
Surface area8530 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)40.129, 40.129, 105.322
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
DetailsThe biological unit is a swapped dimer. The structure consists of one monomer per asymmetric unit. The second monomer to complete the dimer is obtained by applying the following crystallographic symmetry transformation matrix to the given monomer: 0.0000000 1.0000000 0.0000001 1.0000000 0.0000000 0.0000000 0.0000000 0.0000001 -1.0000000

-
Components

#1: Protein Capsid protein p24


Mass: 8540.737 Da / Num. of mol.: 1 / Fragment: capsid C-terminal domain, residues 278-353 / Mutation: deletion of Ala177
Source method: isolated from a genetically manipulated source
Details: Ala177 deleted
Source: (gene. exp.) Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)
Genus: Lentivirus / Species: Human immunodeficiency virus 1 / Strain: isolate NY5 group M subtype B / Gene: gag-pol / Plasmid: pGEX2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P12497, UniProt: Q9IVQ4*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.42 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.75
Details: Reservoir: 0.1 M Sodium phosphate pH 6.75, 28% v/v PEG 1500, 15% v/v glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 15, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 4176 / % possible obs: 98 % / Observed criterion σ(I): 2.5 / Redundancy: 6.9 % / Rmerge(I) obs: 0.046
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 5 / % possible all: 89.6

-
Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
ADSCQUANTUMdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: the structure of the wild-type CA-CTD monomer (1A8O). In the above search model, the linker region and a part of helix 2 (residues 174-188 of the capsid) were removed to avoid ...Starting model: the structure of the wild-type CA-CTD monomer (1A8O). In the above search model, the linker region and a part of helix 2 (residues 174-188 of the capsid) were removed to avoid introducing a bias in the possible mode of dimerization

1a8o


Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.903 / SU B: 31.999 / SU ML: 0.303 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.41 / ESU R Free: 0.291 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.294 175 4.7 %RANDOM
Rwork0.243 ---
obs0.246 3715 99.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.636 Å2
Baniso -1Baniso -2Baniso -3
1--2.43 Å20 Å20 Å2
2---2.43 Å20 Å2
3---4.85 Å2
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms561 0 0 19 580
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.022570
X-RAY DIFFRACTIONr_angle_refined_deg1.7551.973773
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.981572
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.00424.825
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.8641598
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.839154
X-RAY DIFFRACTIONr_chiral_restr0.1030.289
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02428
X-RAY DIFFRACTIONr_nbd_refined0.2650.2274
X-RAY DIFFRACTIONr_nbtor_refined0.3060.2393
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2430.227
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2350.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3070.28
X-RAY DIFFRACTIONr_mcbond_it0.6511.5375
X-RAY DIFFRACTIONr_mcangle_it1.1522584
X-RAY DIFFRACTIONr_scbond_it2.0343223
X-RAY DIFFRACTIONr_scangle_it3.44.5189
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.512 11 -
Rwork0.338 259 -
obs-270 100 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
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.
  • 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

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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