[English] 日本語
Yorodumi
- PDB-1ea4: TRANSCRIPTIONAL REPRESSOR COPG/22bp dsDNA COMPLEX -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ea4
TitleTRANSCRIPTIONAL REPRESSOR COPG/22bp dsDNA COMPLEX
Components
  • DNA (5'-D(*TP*AP*AP*CP*CP*GP*TP*GP *CP*AP*CP*TP*CP*AP*AP*TP*GP*CP*AP*AP*TP*C)-3')
  • DNA(5'-D(*AP*GP*AP*TP*TP*GP*CP*AP*TP *TP*GP*AP*GP*TP*GP*CP*AP*CP*GP*GP*TP*T)-3')
  • TRANSCRIPTIONAL REPRESSOR COPG
KeywordsGENE REGULATION/DNA / TRANSCRIPTIONAL REPRESSOR / DNA-BINDING PROTEIN / PLASMID / PROTEIN-DNA COMPLEX / GENE REGULATION-DNA complex
Function / homology
Function and homology information


plasmid maintenance / protein-DNA complex / sequence-specific DNA binding / regulation of DNA-templated transcription
Similarity search - Function
Ribbon-helix-helix protein, CopG / Ribbon-helix-helix protein, copG family / Met repressor-like / Arc Repressor Mutant / Arc-type ribbon-helix-helix / Ribbon-helix-helix / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Protein CopG
Similarity search - Component
Biological speciesSTREPTOCOCCUS AGALACTIAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsGomis-Rueth, F.X. / Costa, M. / Sola, M. / Acebo, P. / Eritja, R. / Espinosa, M. / Solar, G.D. / Coll, M.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: Plasmid Transcriptional Repressor Copg Oligomerises to Render Helical Superstructures Unbound and in Complexes with Oligonucleotides
Authors: Costa, M. / Sola, M. / Del, G. / Eritja, R. / Hernaindez-Arriaga, A.M. / Espinosa, M. / Gomis-Rueth, F.X. / Coll, M.
#1: Journal: Embo J. / Year: 1998
Title: The Structure of Plasmid-Encoded Transcriptional Repressor Copg Unliganded and Bound to its Operator
Authors: Gomis-Rueth, F.X. / Sola, M. / Acebo, P. / Parraga, A. / Guasch, A. / Eritja, R. / Gonzalez, A. / Espinosa, M. / Solar, G.D. / Coll, M.
#2: Journal: FEBS Lett. / Year: 1998
Title: Overexpression, Purification, Crystallization and Preliminary X-Ray Diffraction Analysis of the Pmv158-Encoded Plasmid Transcriptional Repressor Protein Copg
Authors: Gomis-Rueth, F.X. / Sola, M. / Perez-Luque, R. / Acebo, P. / Alda, M.T. / Gonzalez, A. / Espinosa, M. / Solar, G.D. / Coll, M.
History
DepositionNov 5, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 5, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq.db_align_beg

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TRANSCRIPTIONAL REPRESSOR COPG
B: TRANSCRIPTIONAL REPRESSOR COPG
D: TRANSCRIPTIONAL REPRESSOR COPG
E: TRANSCRIPTIONAL REPRESSOR COPG
F: TRANSCRIPTIONAL REPRESSOR COPG
G: TRANSCRIPTIONAL REPRESSOR COPG
H: TRANSCRIPTIONAL REPRESSOR COPG
J: TRANSCRIPTIONAL REPRESSOR COPG
K: TRANSCRIPTIONAL REPRESSOR COPG
L: TRANSCRIPTIONAL REPRESSOR COPG
U: DNA (5'-D(*TP*AP*AP*CP*CP*GP*TP*GP *CP*AP*CP*TP*CP*AP*AP*TP*GP*CP*AP*AP*TP*C)-3')
V: DNA(5'-D(*AP*GP*AP*TP*TP*GP*CP*AP*TP *TP*GP*AP*GP*TP*GP*CP*AP*CP*GP*GP*TP*T)-3')
W: DNA (5'-D(*TP*AP*AP*CP*CP*GP*TP*GP *CP*AP*CP*TP*CP*AP*AP*TP*GP*CP*AP*AP*TP*C)-3')
X: DNA(5'-D(*AP*GP*AP*TP*TP*GP*CP*AP*TP *TP*GP*AP*GP*TP*GP*CP*AP*CP*GP*GP*TP*T)-3')
Y: DNA (5'-D(*TP*AP*AP*CP*CP*GP*TP*GP *CP*AP*CP*TP*CP*AP*AP*TP*GP*CP*AP*AP*TP*C)-3')
Z: DNA(5'-D(*AP*GP*AP*TP*TP*GP*CP*AP*TP *TP*GP*AP*GP*TP*GP*CP*AP*CP*GP*GP*TP*T)-3')


Theoretical massNumber of molelcules
Total (without water)91,74916
Polymers91,74916
Non-polymers00
Water1,820101
1
A: TRANSCRIPTIONAL REPRESSOR COPG
B: TRANSCRIPTIONAL REPRESSOR COPG
D: TRANSCRIPTIONAL REPRESSOR COPG
E: TRANSCRIPTIONAL REPRESSOR COPG
F: TRANSCRIPTIONAL REPRESSOR COPG
G: TRANSCRIPTIONAL REPRESSOR COPG
H: TRANSCRIPTIONAL REPRESSOR COPG
J: TRANSCRIPTIONAL REPRESSOR COPG
K: TRANSCRIPTIONAL REPRESSOR COPG
L: TRANSCRIPTIONAL REPRESSOR COPG
U: DNA (5'-D(*TP*AP*AP*CP*CP*GP*TP*GP *CP*AP*CP*TP*CP*AP*AP*TP*GP*CP*AP*AP*TP*C)-3')
V: DNA(5'-D(*AP*GP*AP*TP*TP*GP*CP*AP*TP *TP*GP*AP*GP*TP*GP*CP*AP*CP*GP*GP*TP*T)-3')
W: DNA (5'-D(*TP*AP*AP*CP*CP*GP*TP*GP *CP*AP*CP*TP*CP*AP*AP*TP*GP*CP*AP*AP*TP*C)-3')
X: DNA(5'-D(*AP*GP*AP*TP*TP*GP*CP*AP*TP *TP*GP*AP*GP*TP*GP*CP*AP*CP*GP*GP*TP*T)-3')
Y: DNA (5'-D(*TP*AP*AP*CP*CP*GP*TP*GP *CP*AP*CP*TP*CP*AP*AP*TP*GP*CP*AP*AP*TP*C)-3')
Z: DNA(5'-D(*AP*GP*AP*TP*TP*GP*CP*AP*TP *TP*GP*AP*GP*TP*GP*CP*AP*CP*GP*GP*TP*T)-3')

A: TRANSCRIPTIONAL REPRESSOR COPG
B: TRANSCRIPTIONAL REPRESSOR COPG
D: TRANSCRIPTIONAL REPRESSOR COPG
E: TRANSCRIPTIONAL REPRESSOR COPG
F: TRANSCRIPTIONAL REPRESSOR COPG
G: TRANSCRIPTIONAL REPRESSOR COPG
H: TRANSCRIPTIONAL REPRESSOR COPG
J: TRANSCRIPTIONAL REPRESSOR COPG
K: TRANSCRIPTIONAL REPRESSOR COPG
L: TRANSCRIPTIONAL REPRESSOR COPG
U: DNA (5'-D(*TP*AP*AP*CP*CP*GP*TP*GP *CP*AP*CP*TP*CP*AP*AP*TP*GP*CP*AP*AP*TP*C)-3')
V: DNA(5'-D(*AP*GP*AP*TP*TP*GP*CP*AP*TP *TP*GP*AP*GP*TP*GP*CP*AP*CP*GP*GP*TP*T)-3')
W: DNA (5'-D(*TP*AP*AP*CP*CP*GP*TP*GP *CP*AP*CP*TP*CP*AP*AP*TP*GP*CP*AP*AP*TP*C)-3')
X: DNA(5'-D(*AP*GP*AP*TP*TP*GP*CP*AP*TP *TP*GP*AP*GP*TP*GP*CP*AP*CP*GP*GP*TP*T)-3')
Y: DNA (5'-D(*TP*AP*AP*CP*CP*GP*TP*GP *CP*AP*CP*TP*CP*AP*AP*TP*GP*CP*AP*AP*TP*C)-3')
Z: DNA(5'-D(*AP*GP*AP*TP*TP*GP*CP*AP*TP *TP*GP*AP*GP*TP*GP*CP*AP*CP*GP*GP*TP*T)-3')


Theoretical massNumber of molelcules
Total (without water)183,49832
Polymers183,49832
Non-polymers00
Water57632
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
MethodPQS
2
D: TRANSCRIPTIONAL REPRESSOR COPG
E: TRANSCRIPTIONAL REPRESSOR COPG
F: TRANSCRIPTIONAL REPRESSOR COPG
G: TRANSCRIPTIONAL REPRESSOR COPG
W: DNA (5'-D(*TP*AP*AP*CP*CP*GP*TP*GP *CP*AP*CP*TP*CP*AP*AP*TP*GP*CP*AP*AP*TP*C)-3')
X: DNA(5'-D(*AP*GP*AP*TP*TP*GP*CP*AP*TP *TP*GP*AP*GP*TP*GP*CP*AP*CP*GP*GP*TP*T)-3')


Theoretical massNumber of molelcules
Total (without water)33,9996
Polymers33,9996
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
H: TRANSCRIPTIONAL REPRESSOR COPG
J: TRANSCRIPTIONAL REPRESSOR COPG
K: TRANSCRIPTIONAL REPRESSOR COPG
L: TRANSCRIPTIONAL REPRESSOR COPG
U: DNA (5'-D(*TP*AP*AP*CP*CP*GP*TP*GP *CP*AP*CP*TP*CP*AP*AP*TP*GP*CP*AP*AP*TP*C)-3')
V: DNA(5'-D(*AP*GP*AP*TP*TP*GP*CP*AP*TP *TP*GP*AP*GP*TP*GP*CP*AP*CP*GP*GP*TP*T)-3')


Theoretical massNumber of molelcules
Total (without water)33,9996
Polymers33,9996
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
A: TRANSCRIPTIONAL REPRESSOR COPG
B: TRANSCRIPTIONAL REPRESSOR COPG
Y: DNA (5'-D(*TP*AP*AP*CP*CP*GP*TP*GP *CP*AP*CP*TP*CP*AP*AP*TP*GP*CP*AP*AP*TP*C)-3')
Z: DNA(5'-D(*AP*GP*AP*TP*TP*GP*CP*AP*TP *TP*GP*AP*GP*TP*GP*CP*AP*CP*GP*GP*TP*T)-3')

A: TRANSCRIPTIONAL REPRESSOR COPG
B: TRANSCRIPTIONAL REPRESSOR COPG
Y: DNA (5'-D(*TP*AP*AP*CP*CP*GP*TP*GP *CP*AP*CP*TP*CP*AP*AP*TP*GP*CP*AP*AP*TP*C)-3')
Z: DNA(5'-D(*AP*GP*AP*TP*TP*GP*CP*AP*TP *TP*GP*AP*GP*TP*GP*CP*AP*CP*GP*GP*TP*T)-3')


Theoretical massNumber of molelcules
Total (without water)47,5028
Polymers47,5028
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
MethodPQS
Unit cell
Length a, b, c (Å)213.400, 76.040, 50.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsFUNCTIONAL TETRAMERS (EACH ONE CONTACTING A 22BP DSDNA)ARE DEFG, HJKL, AND ABA'B' (A' AND B' ARE SYMMETRYEQUIVALENT MOLECULES).TETRAMER DEFG CONTACTS DSDNA WX, HJKL PAIRS UV, ANDABA'B' INTERACTS WITH YZ(DOUBLE OCCUPANCY DUE TO CRYSTALLOGRAPHIC TWOFOLD AXIS)THE BIOMOLECULE 1 IS THE SUPERHELICAL STRUCTURE AND THETETRAMERS CAN BE GENERATED USING THE MATRICES GIVENFOR BIOMOLECULES 2 , 3 AND 4

-
Components

#1: Protein/peptide
TRANSCRIPTIONAL REPRESSOR COPG / REPA PROTEIN


Mass: 5124.092 Da / Num. of mol.: 10 / Fragment: DNA-BINDING PROTEIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOCOCCUS AGALACTIAE (bacteria) / Cellular location: PLASMID PMV158 / Plasmid: PMV158 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P13920
#2: DNA chain DNA (5'-D(*TP*AP*AP*CP*CP*GP*TP*GP *CP*AP*CP*TP*CP*AP*AP*TP*GP*CP*AP*AP*TP*C)-3')


Mass: 6680.344 Da / Num. of mol.: 3 / Fragment: 22BP SSDNA - FIRST STRAND / Source method: obtained synthetically
#3: DNA chain DNA(5'-D(*AP*GP*AP*TP*TP*GP*CP*AP*TP *TP*GP*AP*GP*TP*GP*CP*AP*CP*GP*GP*TP*T)-3')


Mass: 6822.412 Da / Num. of mol.: 3 / Fragment: 22BP SSDNA - SECOND STRAND / Source method: obtained synthetically
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O
Compound detailsREGULATES THE PLASMID COPY NUMBER BY BINDING TO THE REPAB PROMOTER THUS CONTROLING THE SYNTHESIS OF ...REGULATES THE PLASMID COPY NUMBER BY BINDING TO THE REPAB PROMOTER THUS CONTROLING THE SYNTHESIS OF THE PLASMID REPLICATION INITIATOR PROTEIN REPB AND ITS OWN ONE.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.94 %
Description: ONE COPG DIMER/ 9BP DSDNA MODEL WAS USED AS SEARCHING MODEL.
Crystal growpH: 4.6 / Details: MPD, NACL, NAACO, pH 4.60
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
230 %(w/v)MPD1reservoir
30.2 M1reservoirNaCl
40.1 Msodium acetate1reservoir

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.0527
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0527 Å / Relative weight: 1
ReflectionResolution: 2.92→43.85 Å / Num. obs: 17592 / % possible obs: 93.6 % / Redundancy: 5.9 % / Biso Wilson estimate: 80.8 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 5.9
Reflection
*PLUS
Num. measured all: 103432
Reflection shell
*PLUS
Highest resolution: 2.92 Å / Lowest resolution: 3.07 Å / % possible obs: 58.6 % / Rmerge(I) obs: 0.471

-
Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1B01

1b01


Resolution: 2.95→40 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: NOE RESTRAINTS FOR WATSON & CRICK BASE PAIRING. THE COMPLEX SET UP FOR CRYSTALLIZATION WAS MADE UP BY A COPG DIMER-OF-HOMODIMERS AND A 22-BP DSDNA. THERE ARE 2,5 OF THOSE COMPLEXES IN THE ...Details: NOE RESTRAINTS FOR WATSON & CRICK BASE PAIRING. THE COMPLEX SET UP FOR CRYSTALLIZATION WAS MADE UP BY A COPG DIMER-OF-HOMODIMERS AND A 22-BP DSDNA. THERE ARE 2,5 OF THOSE COMPLEXES IN THE ASYMMETRIC UNIT, DEFG+WX (PROTEIN + DNA), HJKL+UV, AND ABA'B'+YZ. THE LATTER REPRESENTS THE "HALF" COMPLEX. THE OTHER HALF IS CREATED BY A CRYSTALLOGRAPHIC TWOFOLD (RENDERING A' AND B'). THE DNA PART HAS BEEN MODELLED WITH THE TWO OBSERVED ORIENTATIONS, EACH WITH OCCUPANCY 0.5. THERE ARE NCS RESTRAINTS, BUT SO MANY THAT THE MATRICES AND TRANSLATIONS HAVE NOT BEEN INCLUDED IN THIS ENTRY. ESSENTIALLY, ALL PROTEIN CHAINS AND ALL DNA STRANDS HAVE BEEN SUBJECTED TO RESTRAINTS.
RfactorNum. reflection% reflectionSelection details
Rfree0.307 -7 %RANDOM
Rwork0.23 ---
obs0.23 17507 96.9 %-
Displacement parametersBiso mean: 66.3 Å2
Refinement stepCycle: LAST / Resolution: 2.95→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3377 2535 0 101 6013
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.34
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS
Software
*PLUS
Name: CNS / Version: 0.9/1.0 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.23 / Rfactor Rwork: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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