[English] 日本語
Yorodumi
- PDB-1u6p: NMR Structure of the MLV encapsidation signal bound to the Nucleo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1u6p
TitleNMR Structure of the MLV encapsidation signal bound to the Nucleocapsid protein
Components
  • 101-MER
  • Gag polyproteinGroup-specific antigen
KeywordsViral protein/RNA / MLV / A-MINOR K-TURN / STEM LOOP / BULGE / G-U MISMATCH / G-A MISMATCH / U-U MISMATCH / A-C MISMATCH / Zinc finger / NC / Viral protein-RNA COMPLEX
Function / homology
Function and homology information


host cell uropod / host cell late endosome membrane / viral budding via host ESCRT complex / host multivesicular body / viral nucleocapsid / structural constituent of virion / host cell plasma membrane / RNA binding / zinc ion binding / membrane
Similarity search - Function
Zinc finger, CCHC-type / HIV-1 Nucleocapsid Protein / 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 / Retroviral matrix protein ...Zinc finger, CCHC-type / HIV-1 Nucleocapsid Protein / 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 / Retroviral matrix protein / Few Secondary Structures / Irregular / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile.
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / Gag polyprotein
Similarity search - Component
Biological speciesMoloney murine leukemia virus
MethodSOLUTION NMR / TORSION ANGLE DYNAMICS, SIMULATED ANNEALING
AuthorsD'Souza, V. / Summers, M.F.
CitationJournal: Nature / Year: 2004
Title: Structural basis for packaging the dimeric genome of Moloney murine leukaemia virus
Authors: D'Souza, V. / Summers, M.F.
History
DepositionJul 30, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2004Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: 101-MER
A: Gag polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1473
Polymers39,0822
Non-polymers651
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 / -structures with the least restraint violations
RepresentativeModel #1lowest energy

-
Components

#1: RNA chain 101-MER


Mass: 32704.438 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: THIS SEQUENCE WAS SYNTHESIZED BY IN VITRO TRANSCRIPTION USING A LINEARIZED DNA PLASMID AS TEMPLATE
#2: Protein Gag polyprotein / Group-specific antigen / MMLV nucleocapsid protein


Mass: 6377.248 Da / Num. of mol.: 1 / Fragment: Nucleoprotein p10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moloney murine leukemia virus / Genus: Gammaretrovirus / Species: Murine leukemia virus / Gene: GAG / Plasmid: pGEX-6p1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 plysS / References: UniProt: P03332
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
1313D 13C-separated NOESY
1413D 15N-separated NOESY
1514D 13C/15N-separated NOESY
1614D 13C-separated NOESY

-
Sample preparation

Details
Solution-IDContentsSolvent system
11.2MM PSI MONOMERIC RNA GUA-15N,13C;10MM TRIS, 100% D2O10MM TRIS, 100% D2O
21.2MM PSI MONOMERIC RNA ADE-15N,13C; 10MM TRIS, 100% D2O10MM TRIS, 100% D2O
31.2MM PSI MONOMERIC RNA CYT-15N,13C; 10MM TRIS, 100% D2O10MM TRIS, 100% D2O
41.2MM PSI MONOMERIC RNA URA-15N,13C; 10MM TRIS, 100% D2O10MM TRIS, 100% D2O
51.2MM PSI MONOMERIC RNA GUA-URA-CYT-2H, 10MM TRIS, 100% D2O;10MM TRIS, 100% D2O
61.2MM PSI MONOMERIC RNA GUA-ADE-CYT-2H, 10MM TRIS, 100% D2O;10MM TRIS, 100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
110 mM Nacl 7.0 AMBIENT 308 K
210 mM Nacl 7.0 AMBIENT 308 K
310 mM Nacl 7.0 AMBIENT 308 K
410 mM Nacl 7.0 AMBIENT 308 K
510 mM Nacl 7.0 AMBIENT 308 K
610 mM Nacl 7.0 AMBIENT 308 K

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 800 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6brukercollection
NMRPipe2.1Delaglio F et.alprocessing
NMRView5.0.3Johnson Bdata analysis
CYANAGuntertrefinement
RefinementMethod: TORSION ANGLE DYNAMICS, SIMULATED ANNEALING / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers submitted total number: 20

+
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