[English] 日本語
Yorodumi
- PDB-1ajy: STRUCTURE AND MOBILITY OF THE PUT3 DIMER: A DNA PINCER, NMR, 13 S... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ajy
TitleSTRUCTURE AND MOBILITY OF THE PUT3 DIMER: A DNA PINCER, NMR, 13 STRUCTURES
ComponentsPUT3
KeywordsTRANSCRIPTION REGULATION / PUT3
Function / homology
Function and homology information


positive regulation of proline catabolic process to glutamate / proline metabolic process / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-templated transcription / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleus
Similarity search - Function
Fungal specific transcription factor domain / Zn(2)-C6 fungal-type DNA-binding domain / Transcription factor domain, fungi / Fungal specific transcription factor domain / Single helix bin / CD2-Gal4 / Zn(2)-C6 fungal-type DNA-binding domain signature. / Fungal Zn(2)-Cys(6) binuclear cluster domain / Zn(2)-C6 fungal-type DNA-binding domain superfamily / Zn(2)-C6 fungal-type DNA-binding domain profile. ...Fungal specific transcription factor domain / Zn(2)-C6 fungal-type DNA-binding domain / Transcription factor domain, fungi / Fungal specific transcription factor domain / Single helix bin / CD2-Gal4 / Zn(2)-C6 fungal-type DNA-binding domain signature. / Fungal Zn(2)-Cys(6) binuclear cluster domain / Zn(2)-C6 fungal-type DNA-binding domain superfamily / Zn(2)-C6 fungal-type DNA-binding domain profile. / GAL4-like Zn(II)2Cys6 (or C6 zinc) binuclear cluster DNA-binding domain / Zn(2)-C6 fungal-type DNA-binding domain / Basic-leucine zipper domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Few Secondary Structures / Irregular / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Proline utilization trans-activator
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / molecular dynamics
AuthorsWalters, K.J. / Dayie, K.T. / Reece, R.J. / Ptashne, M. / Wagner, G.
CitationJournal: Nat.Struct.Biol. / Year: 1997
Title: Structure and mobility of the PUT3 dimer.
Authors: Walters, K.J. / Dayie, K.T. / Reece, R.J. / Ptashne, M. / Wagner, G.
History
DepositionMay 12, 1997Processing site: BNL
Revision 1.0Sep 17, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / 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.process_site / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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
A: PUT3
B: PUT3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4516
Polymers16,1892
Non-polymers2624
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)13 / 50NO VIOLATION ABOVE 0.5 ANGSTROMS AND 5 DEGREE DIHEDRAL ANGLE
Representative

-
Components

#1: Protein PUT3


Mass: 8094.525 Da / Num. of mol.: 2 / Fragment: DNA-BINDING DOMAIN, RESIDUES 31 - 100 / Source method: isolated from a natural source / Details: EXPRESSED IN ESCHERICHIA COLI / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P25502
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY (1H
12113C
13115N)
141TOCSY
151HNHA
161HNHB
171P.COSY

-
Sample preparation

Sample conditionspH: 6.5 / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UP750VarianUP7507501
Bruker AMX600BrukerAMX6006002

-
Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
X-PLOR3.851phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.851BRUNGERrefinement
X-PLOR3.851structure solution
RefinementMethod: molecular dynamics / Software ordinal: 1
Details: PROGRAMS WRITTEN BY MICHAEL NILGES FOR SYMMETRIC DIMERS WERE USED (NILGES, M. PROTEINS 17, 297-309 (1993)). STRUCTURES WERE STARTED FROM AN EXTENDED MONOMER CONFORMATION AND RANDOM ROTATIONS ...Details: PROGRAMS WRITTEN BY MICHAEL NILGES FOR SYMMETRIC DIMERS WERE USED (NILGES, M. PROTEINS 17, 297-309 (1993)). STRUCTURES WERE STARTED FROM AN EXTENDED MONOMER CONFORMATION AND RANDOM ROTATIONS WERE MADE AROUND THE PHI-PSI ANGLES. THE MONOMER WAS THEN DUPLICATED AND MOLECULAR DYNAMICS WAS PERFORMED USING NMR DISTANCE RESTRAINTS AND GENERATED SYMMETRY DISTANCE RESTRAINTS. RMSD CALCULATED BY SUPERIMPOSING STRUCTURES ON LOWEST ENERGY STRUCTURE FOR RESIDUES 33-62 OF EACH MONOMER AND 68-98 OF EACH DIMER. RMSD (ANGSTROMS): ATOMS FOR RESIDUES 33-62: 0.55 ATOMS FOR RESIDUES 33-62: 1.1 BACKBONE ATOMS FOR RESIDUES 68-98: 0.7 HEAVY ATOMS FOR RESIDUES 68-98: 1.5
NMR ensembleConformer selection criteria: NO VIOLATION ABOVE 0.5 ANGSTROMS AND 5 DEGREE DIHEDRAL ANGLE
Conformers calculated total number: 50 / Conformers submitted total number: 13

+
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