[English] 日本語
Yorodumi
- PDB-2lvh: Solution structure of the zinc finger AFV1p06 protein from the hy... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2lvh
TitleSolution structure of the zinc finger AFV1p06 protein from the hyperthermophilic archaeal virus AFV1
ComponentsPutative zinc finger protein ORF59a
KeywordsMETAL BINDING PROTEIN / Zinc finger
Function / homologyClassic Zinc Finger / Double Stranded RNA Binding Domain / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2-type / 2-Layer Sandwich / zinc ion binding / Alpha Beta / Putative zinc finger protein ORF59a
Function and homology information
Biological speciesAcidianus filamentous virus 1
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
Model detailslowest energy, model 1
AuthorsGuilliere, F. / Sezonov, G. / Prangishvili, D. / Delepierre, M. / Guijarro, J.
CitationJournal: Plos One / Year: 2013
Title: Solution structure of an archaeal DNA binding protein with an eukaryotic zinc finger fold.
Authors: Guilliere, F. / Danioux, C. / Jaubert, C. / Desnoues, N. / Delepierre, M. / Prangishvili, D. / Sezonov, G. / Guijarro, J.I.
History
DepositionJul 5, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_conn_angle / struct_conn / struct_site
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_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.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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: Putative zinc finger protein ORF59a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,0762
Polymers7,0101
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 150structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Putative zinc finger protein ORF59a


Mass: 7010.232 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acidianus filamentous virus 1 / Strain: Yellowstone / Gene: ORF59a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q70LE5
#2: 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 1H-15N HSQC
1212D 1H-13C HSQC
1312D 1H-13C HSQC aliphatic
1413D CBCA(CO)NH
1513D HN(CA)CB
1613D HNCO
1713D C(CO)NH
1813D H(CCO)NH
1913D HNHA
11013D 1H-15N NOESY
11112D 1H-13C HSQC aliphatic
11212D 1H-13C HSQC aromatic
11312D (HB)CB(CGCD)HD aromatic
11412D (HB)CB(CGCDCE)HE aromatic
11513D 1H-13C NOESY aliphatic
11613D 1H-13C NOESY aromatic

-
Sample preparation

DetailsContents: 0.8-1 mM [U-98% 13C; U-98% 15N] AFV1p06, 88% H2O/12% D2O
Solvent system: 88% H2O/12% D2O
SampleUnits: mM / Component: AFV1p06-1 / Isotopic labeling: [U-98% 13C; U-98% 15N] / Conc. range: 0.8-1
Sample conditionsIonic strength: 200 / pH: 7.4 / Pressure: ambient / Temperature: 298.15 K

-
NMR measurement

NMR spectrometerType: Varian NMR System / Manufacturer: Varian / Model: NMR System / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
VnmrJ2.3AVariancollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRView5.3Johnson, One Moon Scientificdata analysis
NMRView5.3Johnson, One Moon Scientificpeak picking
NMRView5.3Johnson, One Moon Scientificchemical shift assignment
ARIA2.2Linge, O'Donoghue and Nilgesautomated noe assignment
ARIA2.2Linge, O'Donoghue and Nilgesstructure solution
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
TALOSCornilescu, Delaglio and Baxdihedral constraints
Procheck3.5.4Laskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thostructure analysis
WhatCheckVriendstructure analysis
MOLMOL2K.2Koradi, Billeter and Wuthrichdata analysis
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 959 / NOE intraresidue total count: 380 / NOE long range total count: 220 / NOE medium range total count: 157 / NOE sequential total count: 202 / Hydrogen bond constraints total count: 19 / Protein phi angle constraints total count: 40 / Protein psi angle constraints total count: 37
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 150 / Conformers submitted total number: 10
NMR ensemble rmsDistance rms dev: 0.0194 Å / Distance rms dev error: 0.0037 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