[English] 日本語
Yorodumi
- PDB-1k1a: Crystal structure of the ankyrin repeat domain of Bcl-3: a unique... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1k1a
TitleCrystal structure of the ankyrin repeat domain of Bcl-3: a unique member of the IkappaB protein family
ComponentsB-cell lymphoma 3-encoded protein
KeywordsTRANSCRIPTION / Bcl-3 / NF-kappaB transcription factors / IkappaB proteins
Function / homology
Function and homology information


Bcl3-Bcl10 complex / follicular dendritic cell differentiation / Bcl3/NF-kappaB2 complex / regulation of DNA binding / marginal zone B cell differentiation / regulation of non-canonical NF-kappaB signal transduction / humoral immune response mediated by circulating immunoglobulin / negative regulation of interleukin-8 production / T cell apoptotic process / negative regulation of receptor signaling pathway via JAK-STAT ...Bcl3-Bcl10 complex / follicular dendritic cell differentiation / Bcl3/NF-kappaB2 complex / regulation of DNA binding / marginal zone B cell differentiation / regulation of non-canonical NF-kappaB signal transduction / humoral immune response mediated by circulating immunoglobulin / negative regulation of interleukin-8 production / T cell apoptotic process / negative regulation of receptor signaling pathway via JAK-STAT / negative regulation of T cell apoptotic process / antimicrobial humoral response / germinal center formation / response to UV-C / T-helper 2 cell differentiation / T-helper 1 type immune response / negative regulation of NF-kappaB transcription factor activity / defense response to protozoan / positive regulation of interleukin-10 production / negative regulation of tumor necrosis factor production / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / canonical NF-kappaB signal transduction / spleen development / extracellular matrix organization / positive regulation of translation / DNA damage response, signal transduction by p53 class mediator / response to virus / histone deacetylase binding / positive regulation of type II interferon production / protein import into nucleus / transcription corepressor activity / midbody / regulation of apoptotic process / protein-macromolecule adaptor activity / DNA-binding transcription factor binding / transcription coactivator activity / defense response to bacterium / ciliary basal body / negative regulation of DNA-templated transcription / intracellular membrane-bounded organelle / DNA damage response / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
: / Ankyrin repeat-containing domain / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat ...: / Ankyrin repeat-containing domain / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
B-cell lymphoma 3 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsMichel, F. / Soler-Lopez, M. / Petosa, C. / Cramer, P. / Siebenlist, U. / Mueller, C.W.
CitationJournal: EMBO J. / Year: 2001
Title: Crystal structure of the ankyrin repeat domain of Bcl-3: a unique member of the IkappaB protein family.
Authors: Michel, F. / Soler-Lopez, M. / Petosa, C. / Cramer, P. / Siebenlist, U. / Muller, C.W.
History
DepositionSep 24, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: B-cell lymphoma 3-encoded protein


Theoretical massNumber of molelcules
Total (without water)25,8291
Polymers25,8291
Non-polymers00
Water3,513195
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.703, 51.218, 64.680
Angle α, β, γ (deg.)90.00, 102.01, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein B-cell lymphoma 3-encoded protein / BCL3 / BCL-3 protein


Mass: 25829.451 Da / Num. of mol.: 1 / Fragment: ankyrin repeat domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P20749
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.99 Å3/Da / Density % sol: 38.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 6000, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 5.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mMMES1drop
2350 mM1dropNaCl
35 mMdithiothreitol1drop
43-10 mg/mlprotein1drop
55 %PEG60001reservoir
6100 mMMES1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 28, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.8→40 Å / Num. all: 17021 / Num. obs: 17021 / % possible obs: 89.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rsym value: 0.072 / Net I/σ(I): 10.5
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 1.73 % / Mean I/σ(I) obs: 1.65 / Num. unique all: 1479 / Rsym value: 0.697 / % possible all: 77.8
Reflection
*PLUS
Lowest resolution: 40 Å / Redundancy: 2.71 % / Num. measured all: 46088 / Rmerge(I) obs: 0.072
Reflection shell
*PLUS
% possible obs: 77.8 % / Rmerge(I) obs: 0.697

-
Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ikn

1ikn


Resolution: 1.86→20 Å / SU B: 3.68115 / SU ML: 0.11055 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.18488 / ESU R Free: 0.15154 / Stereochemistry target values: Engh & Huber
Details: RESIDUES SER178,VAL179,LEU182,GLN251,ARG269,SER307 PRESENT DOUBLE CONFORMATIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22859 828 5 %RANDOM
Rwork0.19899 ---
all0.2004 16328 --
obs0.2004 16328 89.8 %-
Displacement parametersBiso mean: 21.105 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å2-0.04 Å2
2---1.27 Å20 Å2
3---1.35 Å2
Refinement stepCycle: LAST / Resolution: 1.86→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1729 0 0 195 1924
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0070.021
X-RAY DIFFRACTIONp_mcbond_it0.5781.5
X-RAY DIFFRACTIONp_mcangle_it1.1042
X-RAY DIFFRACTIONp_scbond_it1.7893
X-RAY DIFFRACTIONp_scangle_it3.1034.5
X-RAY DIFFRACTIONp_plane_restr0.0040.02
X-RAY DIFFRACTIONp_chiral_restr0.070.2
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.199
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg0.94

+
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