[English] 日本語
Yorodumi
- PDB-1gji: Crystal structure of c-Rel bound to DNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1gji
TitleCrystal structure of c-Rel bound to DNA
Components
  • (IL-2 CD28RE DNA) x 2
  • C-REL PROTO-ONCOGENE PROTEIN
KeywordsTRANSCRIPTION/DNA / NF-kB-DNA COMPLEX / TRANSCRIPTION FACTOR / c-Rel HOMODIMER / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


apoptotic DNA fragmentation / non-canonical NF-kappaB signal transduction / canonical NF-kappaB signal transduction / response to cytokine / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / inflammatory response / innate immune response / positive regulation of transcription by RNA polymerase II ...apoptotic DNA fragmentation / non-canonical NF-kappaB signal transduction / canonical NF-kappaB signal transduction / response to cytokine / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / inflammatory response / innate immune response / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus / cytoplasm
Similarity search - Function
Proto-oncogene c-Rel, RHD, N-terminal subdomain / Rel homology domain (RHD), DNA-binding domain / NF-kappa-B/Dorsal / Rel homology domain, conserved site / NFkappaB IPT domain / NF-kappa-B/Rel/dorsal domain signature. / Rel homology domain (RHD), DNA-binding domain / Rel homology dimerisation domain / Rel homology DNA-binding domain / Rel homology dimerisation domain ...Proto-oncogene c-Rel, RHD, N-terminal subdomain / Rel homology domain (RHD), DNA-binding domain / NF-kappa-B/Dorsal / Rel homology domain, conserved site / NFkappaB IPT domain / NF-kappa-B/Rel/dorsal domain signature. / Rel homology domain (RHD), DNA-binding domain / Rel homology dimerisation domain / Rel homology DNA-binding domain / Rel homology dimerisation domain / NF-kappa-B/Rel/dorsal domain profile. / Rel homology domain (RHD), DNA-binding domain superfamily / ig-like, plexins, transcription factors / IPT domain / p53-like transcription factor, DNA-binding / Immunoglobulin E-set / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Proto-oncogene c-Rel
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / molecular replacement, MIR / Resolution: 2.85 Å
AuthorsHuang, D.B. / Chen, Y.Q. / Ruetsche, M. / Phelps, C.B. / Ghosh, G.
CitationJournal: Structure / Year: 2001
Title: X-ray crystal structure of proto-oncogene product c-Rel bound to the CD28 response element of IL-2.
Authors: Huang, D.B. / Chen, Y.Q. / Ruetsche, M. / Phelps, C.B. / Ghosh, G.
History
DepositionMay 30, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: IL-2 CD28RE DNA
D: IL-2 CD28RE DNA
A: C-REL PROTO-ONCOGENE PROTEIN
B: C-REL PROTO-ONCOGENE PROTEIN


Theoretical massNumber of molelcules
Total (without water)76,0544
Polymers76,0544
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.320, 99.320, 196.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: DNA chain IL-2 CD28RE DNA


Mass: 6206.054 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain IL-2 CD28RE DNA


Mass: 6058.939 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein C-REL PROTO-ONCOGENE PROTEIN / C-REL PROTEIN


Mass: 31894.316 Da / Num. of mol.: 2 / Fragment: Rel homology region
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / References: UniProt: P16236

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.16 Å3/Da / Density % sol: 63 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 7.5
Details: PEG 4000, spermine, DTT, pH 7.5, EVAPORATION, temperature 298.0K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 400011
2spermine11
3DTT11
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein1drop
220 %(w/v)PEG40001reservoir
3100 mMHEPES1reservoirpH7.5
41 mMspermine1reservoir
52 mMdithiothreitol1reservoir
60.01 %beta-octylglucoside1reservoir

-
Data collection

DiffractionMean temperature: 168 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Feb 14, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.85→25 Å / Num. all: 21455 / Num. obs: 18723 / % possible obs: 90.8 % / Observed criterion σ(F): 2 / Redundancy: 10 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 7.8
Reflection shellResolution: 2.85→2.95 Å / Redundancy: 7 % / Rmerge(I) obs: 0.424 / Num. unique all: 1159 / % possible all: 46
Reflection
*PLUS
Num. obs: 21455 / % possible obs: 90 % / Num. measured all: 215187 / Rmerge(I) obs: 0.086
Reflection shell
*PLUS
% possible obs: 48 % / Rmerge(I) obs: 0.424 / Mean I/σ(I) obs: 1.8

-
Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: molecular replacement, MIR
Starting model: p65/DNA complex

Resolution: 2.85→25 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
Details: The DNA molecule has alternate conformations. Two sets of coordinates for the DNA molecule were refined with 0.5 occupancy each.
RfactorNum. reflection% reflection
Rfree0.279 897 5 %
Rwork0.227 --
all-21455 -
obs-18732 79.2 %
Refinement stepCycle: LAST / Resolution: 2.85→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4486 1628 0 0 6114
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.32
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor obs: 0.227 / Rfactor Rfree: 0.279 / Rfactor Rwork: 0.227
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_bond_d / Dev ideal: 0.0079

+
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