[English] 日本語
Yorodumi
- PDB-1pyi: CRYSTAL STRUCTURE OF A PPR1-DNA COMPLEX: DNA RECOGNITION BY PROTE... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1pyi
TitleCRYSTAL STRUCTURE OF A PPR1-DNA COMPLEX: DNA RECOGNITION BY PROTEINS CONTAINING A ZN2CYS6 BINUCLEAR CLUSTER
Components
  • DNA (5'-D(*TP*CP*GP*GP*CP*AP*AP*TP*TP*GP*CP*CP*GP*A)-3')
  • PROTEIN (PYRIMIDINE PATHWAY REGULATOR 1)
KeywordsTRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / TRANSCRIPTION-DNA COMPLEX / GAL4 / ZINC FINGER / ZN2CYS6 / BINUCLEAR CLUSTER / TRANSCRIPTION FACTOR
Function / homology
Function and homology information


positive regulation of pyrimidine nucleotide biosynthetic process / pyrimidine nucleotide biosynthetic process / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / 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 / 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 / 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 / Few Secondary Structures / Irregular
Similarity search - Domain/homology
DNA / DNA (> 10) / Pyrimidine pathway regulatory protein 1 / Pyrimidine pathway regulatory protein 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / Resolution: 3.2 Å
AuthorsMarmorstein, R. / Harrison, S.C.
Citation
Journal: Genes Dev. / Year: 1994
Title: Crystal structure of a PPR1-DNA complex: DNA recognition by proteins containing a Zn2Cys6 binuclear cluster.
Authors: Marmorstein, R. / Harrison, S.C.
#1: Journal: Nature / Year: 1992
Title: DNA Recognition by GAL4: Structure of a Protein-DNA Complex
Authors: Marmorstein, R. / Carey, M. / Ptashne, M. / Harrison, S.C.
History
DepositionJan 4, 1995Deposition site: BNL / Processing site: BNL
Revision 1.0Feb 27, 1995Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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_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_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
D: DNA (5'-D(*TP*CP*GP*GP*CP*AP*AP*TP*TP*GP*CP*CP*GP*A)-3')
E: DNA (5'-D(*TP*CP*GP*GP*CP*AP*AP*TP*TP*GP*CP*CP*GP*A)-3')
A: PROTEIN (PYRIMIDINE PATHWAY REGULATOR 1)
B: PROTEIN (PYRIMIDINE PATHWAY REGULATOR 1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7378
Polymers30,4754
Non-polymers2624
Water181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.800, 92.600, 174.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Atom site foot note1: CIS PROLINE - PRO A 49 / 2: CIS PROLINE - PRO B 49

-
Components

#1: DNA chain DNA (5'-D(*TP*CP*GP*GP*CP*AP*AP*TP*TP*GP*CP*CP*GP*A)-3')


Mass: 4280.792 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein PROTEIN (PYRIMIDINE PATHWAY REGULATOR 1)


Mass: 10956.896 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: YSCPPR1 (ACCESSION X01739) / Plasmid: PRSETA / Cell (production host): BL21 (PLYSS) / Gene (production host): YSCPPR1 (ACCESSION X01739) / Production host: Escherichia coli (E. coli) / References: UniProt: PPR1_YEAST, UniProt: P07272*PLUS
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.53 Å3/Da / Density % sol: 55 %
Crystal
*PLUS
Density % sol: 55 %
Crystal grow
*PLUS
pH: 6.8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
10.6 mMprotein dimer1drop
20.7 mMDNA duplex1drop
37 %PEG35001drop
41 %MPD1drop
587.5 mM1dropNaCl
662.5 mM1dropCaCl2
70.050 mMzinc acetate1drop
80.010 mMsodium cacodylate1droppH6.8
915 %PEG35001reservoir
102 %MPD1reservoir
11125 mM1reservoirCaCl2
120.100 mMzinc acetate1reservoir
1320 mMsodium cacodylate1reservoirpH6.8

-
Data collection

DetectorType: XENTRONICS / Detector: AREA DETECTOR / Date: Oct 9, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 7096 / Observed criterion σ(I): 4 / Redundancy: 4.6 % / Rmerge(I) obs: 0.064
Reflection
*PLUS
Observed criterion σ(I): 4 / Redundancy: 4.6 % / Rmerge(I) obs: 0.064

-
Processing

SoftwareName: XDS / Classification: data reduction
RefinementResolution: 3.2→10 Å / σ(F): 0 /
RfactorNum. reflection
Rfree0.33 -
obs0.245 35480
Refinement stepCycle: LAST / Resolution: 3.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1253 568 4 1 1826
Refinement
*PLUS
Highest resolution: 3.2 Å / Lowest resolution: 10 Å / σ(F): 0 / Rfactor obs: 0.245 / Rfactor Rfree: 0.33 / Rfactor Rwork: 0.245
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 29.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.017
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_deg3.7

+
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