[English] 日本語
Yorodumi
- PDB-2m9u: Solution NMR structure of the C-terminal domain (CTD) of Moloney ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2m9u
TitleSolution NMR structure of the C-terminal domain (CTD) of Moloney murine leukemia virus integrase, Northeast Structural Genomics Target OR41A
ComponentsIntegrase p46
KeywordsVIRAL PROTEIN / SH3 domain / NESG / OR41A-15.1 / PSI-Biology / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


retroviral 3' processing activity / host cell late endosome membrane / DNA catabolic process / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / virion assembly / protein-DNA complex / host multivesicular body / RNA-directed DNA polymerase / viral genome integration into host DNA ...retroviral 3' processing activity / host cell late endosome membrane / DNA catabolic process / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / virion assembly / protein-DNA complex / host multivesicular body / RNA-directed DNA polymerase / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / viral nucleocapsid / DNA recombination / structural constituent of virion / 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 / host cell plasma membrane / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane
Similarity search - Function
SH3 type barrels. - #850 / Gag-Pol polyprotein, Zinc-finger like domain / Murine leukemia virus integrase, C-terminal / Zinc-finger like, probable DNA-binding / Murine leukemia virus (MLV) integrase (IN) C-terminal domain / Gamma-retroviral matrix protein / Gag polyprotein, inner coat protein p12 / Core shell protein Gag P30 / Matrix protein (MA), p15 / Gag polyprotein, inner coat protein p12 ...SH3 type barrels. - #850 / Gag-Pol polyprotein, Zinc-finger like domain / Murine leukemia virus integrase, C-terminal / Zinc-finger like, probable DNA-binding / Murine leukemia virus (MLV) integrase (IN) C-terminal domain / Gamma-retroviral matrix protein / Gag polyprotein, inner coat protein p12 / Core shell protein Gag P30 / Matrix protein (MA), p15 / Gag polyprotein, inner coat protein p12 / Gag P30 core shell protein / Gamma-retroviral matrix domain superfamily / Reverse transcriptase/retrotransposon-derived protein, RNase H-like domain / RNase H-like domain found in reverse transcriptase / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / SH3 type barrels. / 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 / 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. / Ribonuclease H superfamily / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Roll / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / Mainly Beta
Similarity search - Domain/homology
Biological speciesMoloney murine leukemia virus isolate Shinnick
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsAiyer, S. / Rossi, P. / Schneider, W.M. / Chander, A. / Roth, M.J. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: Altering murine leukemia virus integration through disruption of the integrase and BET protein family interaction.
Authors: Aiyer, S. / Swapna, G.V. / Malani, N. / Aramini, J.M. / Schneider, W.M. / Plumb, M.R. / Ghanem, M. / Larue, R.C. / Sharma, A. / Studamire, B. / Kvaratskhelia, M. / Bushman, F.D. / Montelione, G.T. / Roth, M.J.
History
DepositionJun 19, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 18, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2014Group: Database references
Revision 1.2Jun 4, 2014Group: Database references
Revision 1.3Jun 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 / 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.pdbx_seq_one_letter_code / _struct_ref_seq_dif.details
Revision 1.4May 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: Integrase p46


Theoretical massNumber of molelcules
Total (without water)10,1321
Polymers10,1321
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)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Integrase p46 / IN


Mass: 10131.592 Da / Num. of mol.: 1
Fragment: DNA binding C terminal domain (CTD) residues 1659-1738
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moloney murine leukemia virus isolate Shinnick
Gene: gag-pol / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03355

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCO
1413D CBCA(CO)NH
1513D HN(CA)CB
1613D HBHA(CO)NH
1713D (H)CCH-TOCSY
1813D 13C-edited NOESY
1913D 1H-15N NOESY
11013D 13C-edited NOESY
11122D 1H-15N HSQC
11222D 1H-13C HSQC

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-100% 13C; U-100% 15N] MLV IN CTD, 90% H2O/10% D2O90% H2O/10% D2O
20.5 mM [U-10% 13C; U-100% 15N] MLV IN CTD, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMMLV IN CTD-1[U-100% 13C; U-100% 15N]1
0.5 mMMLV IN CTD-2[U-10% 13C; U-100% 15N]2
Sample conditionsIonic strength: 50mM K-glutamate, 100mM NaCl / pH: 6.5 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
AutoAssign2.2.1Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
AutoStructure2.2.1Huang, Tejero, Powers and Montelionechemical shift assignment
AutoStructure2.2.1Huang, Tejero, Powers and Montelionestructure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichgeometry optimization
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CNS2.0.6Brunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
CNS2.0.6Brunger, Adams, Clore, Gros, Nilges and Readrefinement
Sparky2.1Goddardpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structure was determined using triple resonance NMR spectroscopy. Automated backbone assignments were made using AutoAssign software. Sidechain assignments were completed manually. ...Details: The structure was determined using triple resonance NMR spectroscopy. Automated backbone assignments were made using AutoAssign software. Sidechain assignments were completed manually. Initial NOESY assignments for the monomer were made using AutoStructure and CYANA-2.1. The oligomeric state was confirmed to be a monomer by measuring the correlation time using 1D T1 and T2 experiments. A total of 100 structures were calculated and 20 best conformers were then refined in a shell of water using CNS. Final structure quality factors were determined using the PSVS server: ordered residues are defined as (7-18 and 24-61). (a) RMSD (ordered residues) all backbone atoms: 0.6A; all heavy atoms: 0.9A. (b) Ramachandran statistics for all ordered residues: Most favoured region: 87.2%; additionally allowed region: 12.4%; generously allowed region: 0.3% and disallowed region: 0.0%. (c) Procheck scores for all ordered residues (Raw/Z) phi/psi -0.81/-2.87; all dihedral angles: -0.45/-2.66. (d) MolProbity clash score (Raw/Z): 13.47/-0.79. (e) RPF scores for the goodness of fit to NOESY data:- Recall: 0.888; precision: 0.968; F-measure: 0.926; DP score: 0.821
NMR constraintsHydrogen bond constraints total count: 44
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 8.7 °
NMR ensemble rmsDistance rms dev: 0.02 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