[English] 日本語
Yorodumi
- PDB-2lf4: Structure of a monomeric mutant of the HIV-1 capsid protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2lf4
TitleStructure of a monomeric mutant of the HIV-1 capsid protein
ComponentsGag polyprotein
KeywordsPROTEIN TRANSPORT / fullerene
Function / homology
Function and homology information


viral budding via host ESCRT complex / 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 budding via host ESCRT complex / 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 / viral penetration into host nucleus / symbiont-mediated suppression of host gene expression / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / viral nucleocapsid / DNA recombination / host cell cytoplasm / 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 / RNA binding / zinc ion binding / membrane / cytoplasm
Similarity search - Function
Retrovirus capsid C-terminal domain / Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / Gag protein p6 / Gag protein p6 / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / : / gag protein p24 N-terminal domain / Reverse transcriptase connection / Reverse transcriptase connection domain ...Retrovirus capsid C-terminal domain / Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / Gag protein p6 / Gag protein p6 / 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 / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / RNase H type-1 domain profile. / Ribonuclease H domain / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / 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. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H 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 / Gag polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model 4
AuthorsShin, R.S. / Tzou, Y. / Krishna, N.
CitationJournal: Biochemistry / Year: 2011
Title: Structure of a Monomeric Mutant of the HIV-1 Capsid Protein.
Authors: Shin, R. / Tzou, Y.M. / Krishna, N.R.
History
DepositionJun 28, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Gag polyprotein


Theoretical massNumber of molelcules
Total (without water)26,6441
Polymers26,6441
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 500target function
RepresentativeModel #1closest to the average

-
Components

#1: Protein Gag polyprotein


Mass: 26643.502 Da / Num. of mol.: 1 / Mutation: W184A, M185A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: gag / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 / Variant (production host): Rosetta 2 / References: UniProt: Q72497, UniProt: P12497*PLUS

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1262D 1H-15N SOFAST HMQC
1332D 1H-13C HSQC
1423D CBCA(CO)NH
1523D HNCO
1623D HNCA
1743D HN(CA)CB
1833D (H)CCH-TOCSY
1953D (H)CCH-TOCSY
11033D (H)CCH-COSY
11153D (H)CCH-COSY
11213D 1H-15N NOESY
11333D 1H-13C NOESY

-
Sample preparation

Details
Solution-IDContentsSolvent system
12 mM [U-98% 15N] HIV-1 CA, 25 mM sodium chloride, 25 mM [U-99% 2H] sodium acetate, 10 mM [U-99% 2H] DTT, 0.02 % sodium azide, 0.1 mM AEBSF protease inhibitor, 1 mM [U-99% 2H] EDTA, 90% H2O/10% D2O90% H2O/10% D2O
22 mM [U-98% 13C; U-98% 15N] HIV-1 CA, 25 mM sodium chloride, 25 mM [U-99% 2H] sodium acetate, 10 mM [U-99% 2H] DTT, 0.02 % sodium azide, 0.1 mM AEBSF protease inhibitor, 1 mM [U-99% 2H] EDTA, 90% H2O/10% D2O90% H2O/10% D2O
32 mM [U-98% 13C; U-98% 15N] HIV-1 CA, 25 mM sodium chloride, 25 mM [U-99% 2H] sodium acetate, 10 mM [U-99% 2H] DTT, 0.02 % sodium azide, 0.1 mM AEBSF protease inhibitor, 1 mM [U-99% 2H] EDTA, 100% D2O100% D2O
42 mM [U-98% 13C; U-98% 15N] HIV-1 CA, 25 mM sodium chloride, 25 mM [U-99% 2H] sodium acetate, 10 mM [U-99% 2H] DTT, 0.02 % sodium azide, 0.1 mM AEBSF protease inhibitor, 1 mM [U-99% 2H] EDTA, 90% H2O/10% D2O90% H2O/10% D2O
52 mM [U-98% 13C; U-98% 15N] HIV-1 CA, 25 mM sodium chloride, 25 mM [U-99% 2H] sodium acetate, 10 mM [U-99% 2H] DTT, 0.02 % sodium azide, 0.1 mM AEBSF protease inhibitor, 1 mM [U-99% 2H] EDTA, 100% D2O100% D2O
62 mM [U-98% 13C; U-98% 15N] HIV-1 CA, 25 mM sodium chloride, 25 mM [U-99% 2H] sodium acetate, 10 mM [U-99% 2H] DTT, 0.02 % sodium azide, 0.1 mM AEBSF protease inhibitor, 1 mM [U-99% 2H] EDTA, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 mMHIV-1 CA-1[U-98% 15N]1
25 mMsodium chloride-21
25 mMsodium acetate-3[U-99% 2H]1
10 mMDTT-4[U-99% 2H]1
0.02 %sodium azide-51
0.1 mMAEBSF protease inhibitor-61
1 mMEDTA-7[U-99% 2H]1
2 mMHIV-1 CA-8[U-98% 13C; U-98% 15N]2
25 mMsodium chloride-92
25 mMsodium acetate-10[U-99% 2H]2
10 mMDTT-11[U-99% 2H]2
0.02 %sodium azide-122
0.1 mMAEBSF protease inhibitor-132
1 mMEDTA-14[U-99% 2H]2
2 mMHIV-1 CA-15[U-98% 13C; U-98% 15N]3
25 mMsodium chloride-163
25 mMsodium acetate-17[U-99% 2H]3
10 mMDTT-18[U-99% 2H]3
0.02 %sodium azide-193
0.1 mMAEBSF protease inhibitor-203
1 mMEDTA-21[U-99% 2H]3
2 mMHIV-1 CA-22[U-98% 13C; U-98% 15N]4
25 mMsodium chloride-234
25 mMsodium acetate-24[U-99% 2H]4
10 mMDTT-25[U-99% 2H]4
0.02 %sodium azide-264
0.1 mMAEBSF protease inhibitor-274
1 mMEDTA-28[U-99% 2H]4
2 mMHIV-1 CA-29[U-98% 13C; U-98% 15N]5
25 mMsodium chloride-305
25 mMsodium acetate-31[U-99% 2H]5
10 mMDTT-32[U-99% 2H]5
0.02 %sodium azide-335
0.1 mMAEBSF protease inhibitor-345
1 mMEDTA-35[U-99% 2H]5
2 mMHIV-1 CA-36[U-98% 13C; U-98% 15N]6
25 mMsodium chloride-376
25 mMsodium acetate-38[U-99% 2H]6
10 mMDTT-39[U-99% 2H]6
0.02 %sodium azide-406
0.1 mMAEBSF protease inhibitor-416
1 mMEDTA-42[U-99% 2H]6
Sample conditionspH: 5.5 / Pressure: ambient / Temperature: 303 K

-
NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
TopSpin1.3Bruker Biospindata analysis
TopSpin1.3Bruker Biospinprocessing
TopSpin1.3Bruker Biospincollection
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
XEASYBartels et al.chemical shift assignment
XEASYBartels et al.data analysis
XEASYBartels et al.peak picking
CYANA2.1Guntert, Mumenthaler and Wuthrichchemical shift assignment
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: 50,000 steps
NMR constraintsNOE constraints total: 3052 / NOE intraresidue total count: 1005 / NOE long range total count: 420 / NOE medium range total count: 720 / NOE sequential total count: 907 / Hydrogen bond constraints total count: 190 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 1 / Protein phi angle constraints total count: 192 / Protein psi angle constraints total count: 193
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 500 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 2.54 ° / Maximum upper distance constraint violation: 0.1 Å

+
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