[English] 日本語
Yorodumi
- PDB-1q3z: NMR structure of the Cys28His mutant (E form) of the nucleocapsid... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1q3z
TitleNMR structure of the Cys28His mutant (E form) of the nucleocapsid protein NCp7 of HIV-1.
ComponentsGAG proteinHIV-1 protease
KeywordsVIRAL PROTEIN / CCHC zinc knuckle / CCHH zinc knuckle
Function / homologyZinc finger, CCHC-type / HIV-1 Nucleocapsid Protein / Few Secondary Structures / Irregular / :
Function and homology information
MethodSOLUTION NMR / distance geometry, simulated annealing, molecular dynamics
AuthorsRamboarina, S. / Druillennec, S. / Morellet, N. / Bouaziz, S. / Roques, B.P.
Citation
Journal: J.Virol. / Year: 2004
Title: Target specificity of human immunodeficiency virus type 1 NCp7 requires an intact conformation of its CCHC N-terminal zinc finger.
Authors: Ramboarina, S. / Druillennec, S. / Morellet, N. / Bouaziz, S. / Roques, B.P.
#1: Journal: Biochemistry / Year: 1999
Title: Structural investigation on the requirement of CCHH zinc finger type in nucleocapsid protein of human immunodeficiency virus 1.
Authors: Ramboarina, S. / Morellet, N. / Fournie-Zaluski, M.C. / Roques, B.P.
History
DepositionAug 1, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE The sequence here corresponds to a strain different than that found in the sequence ...SEQUENCE The sequence here corresponds to a strain different than that found in the sequence database (GenBank accession CAB98186).

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GAG protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,0033
Polymers4,8731
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 100structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #1fewest violations,lowest energy

-
Components

#1: Protein/peptide GAG protein / HIV-1 protease


Mass: 4872.646 Da / Num. of mol.: 1 / Fragment: RESIDUES 390-431 / Mutation: C28H / Source method: obtained synthetically
Details: Two peptides have been chemically synthesized with and without a 15N/13C labelled Histidine residue at position 28
References: UniProt: Q9PY17
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D TOCSY
1212D NOESY
1311H-15N HSQC
1422D TOCSY
1522D NOESY
NMR detailsText: The structure was determined using standard 2D homonuclear experiments and 1H-15N HSQC experiments.

-
Sample preparation

Details
Solution-IDContentsSolvent system
12 mM His28(12-53)NCp7 90% H2O, 10% D2O with 3 equivalents of zinc90% H2O, 10% D2O, pH 6.6 from 278K to 323K
22 mM His28(12-53)NCp7 100% D2O with 3 equivalents of zinc100% D2O, pH 6.6 from 278K to 323K
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
16 mM ZnSO4 6.6 ambient 278 K
26 mM ZnSO4 6.6 ambient 293 K

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AMX / Manufacturer: Bruker / Model: AMX / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
XwinNMRVersion 3.0Brukercollection
XwinNMRVersion 3.0Brukerprocessing
FelixVersion 98.0Accelrysdata analysis
X-PLORVersion 3.851Brungerrefinement
RefinementMethod: distance geometry, simulated annealing, molecular dynamics
Software ordinal: 1
Details: The structure has been calculated using 339 NOE derived distance restraints.
NMR representativeSelection criteria: fewest violations,lowest energy
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 1

+
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