[English] 日本語
Yorodumi
- PDB-4jbk: Molecular basis for abrogation of activation of pro-inflammatory ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4jbk
TitleMolecular basis for abrogation of activation of pro-inflammatory cytokines
Components
  • DNA (5'-D(P*GP*GP*AP*AP*TP*TP*AP*TP*AP*AP*TP*TP*CP*C)-3')
  • Interferon-activable protein 202
KeywordsDNA BINDING PROTEIN/DNA / OB fold / DNA / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


negative regulation of AIM2 inflammasome complex assembly / cellular response to interferon-beta / activation of innate immune response / negative regulation of innate immune response / protein homooligomerization / double-stranded DNA binding / protein homotetramerization / molecular adaptor activity / inflammatory response / innate immune response ...negative regulation of AIM2 inflammasome complex assembly / cellular response to interferon-beta / activation of innate immune response / negative regulation of innate immune response / protein homooligomerization / double-stranded DNA binding / protein homotetramerization / molecular adaptor activity / inflammatory response / innate immune response / nucleus / cytoplasm
Similarity search - Function
HIN-200/IF120x / HIN-200/IF120x domain / HIN-200 A and B domains profile. / HIN-200 family / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Interferon-activable protein 202
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.963 Å
AuthorsRu, H. / Ni, X. / Crowley, C. / Zhao, L. / Ding, W. / Hung, L.-W. / Shaw, N. / Cheng, G. / Liu, Z.-J.
CitationJournal: Cell Res. / Year: 2013
Title: Structural basis for termination of AIM2-mediated signaling by p202
Authors: Ru, H. / Ni, X. / Zhao, L. / Crowley, C. / Ding, W. / Hung, L.-W. / Shaw, N. / Cheng, G. / Liu, Z.-J.
History
DepositionFeb 19, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 26, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Interferon-activable protein 202
B: Interferon-activable protein 202
C: Interferon-activable protein 202
D: Interferon-activable protein 202
E: DNA (5'-D(P*GP*GP*AP*AP*TP*TP*AP*TP*AP*AP*TP*TP*CP*C)-3')
F: DNA (5'-D(P*GP*GP*AP*AP*TP*TP*AP*TP*AP*AP*TP*TP*CP*C)-3')
G: DNA (5'-D(P*GP*GP*AP*AP*TP*TP*AP*TP*AP*AP*TP*TP*CP*C)-3')
H: DNA (5'-D(P*GP*GP*AP*AP*TP*TP*AP*TP*AP*AP*TP*TP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)107,9368
Polymers107,9368
Non-polymers00
Water00
1
A: Interferon-activable protein 202
D: Interferon-activable protein 202
E: DNA (5'-D(P*GP*GP*AP*AP*TP*TP*AP*TP*AP*AP*TP*TP*CP*C)-3')
F: DNA (5'-D(P*GP*GP*AP*AP*TP*TP*AP*TP*AP*AP*TP*TP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)53,9684
Polymers53,9684
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3400 Å2
ΔGint-36 kcal/mol
Surface area24890 Å2
MethodPISA
2
B: Interferon-activable protein 202
G: DNA (5'-D(P*GP*GP*AP*AP*TP*TP*AP*TP*AP*AP*TP*TP*CP*C)-3')

B: Interferon-activable protein 202
G: DNA (5'-D(P*GP*GP*AP*AP*TP*TP*AP*TP*AP*AP*TP*TP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)53,9684
Polymers53,9684
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
Buried area3430 Å2
ΔGint-39 kcal/mol
Surface area24550 Å2
MethodPISA
3
C: Interferon-activable protein 202
H: DNA (5'-D(P*GP*GP*AP*AP*TP*TP*AP*TP*AP*AP*TP*TP*CP*C)-3')

C: Interferon-activable protein 202
H: DNA (5'-D(P*GP*GP*AP*AP*TP*TP*AP*TP*AP*AP*TP*TP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)53,9684
Polymers53,9684
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_756-x+2,y,-z+11
Buried area3550 Å2
ΔGint-39 kcal/mol
Surface area24500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.304, 109.940, 106.137
Angle α, β, γ (deg.)90.00, 120.03, 90.00
Int Tables number5
Space group name H-MC121
DetailsAUTHOR STATES THAT THE BIOLOGICAL ASSEMBLY IS UNKNOWN.

-
Components

#1: Protein
Interferon-activable protein 202 / Ifi-202 / Interferon-inducible protein p202 / Lupus susceptibility protein p202


Mass: 22705.160 Da / Num. of mol.: 4 / Fragment: HINa domain, UNP residues 46-242
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ifi202a / Production host: Escherichia coli (E. coli) / References: UniProt: Q9R002
#2: DNA chain
DNA (5'-D(P*GP*GP*AP*AP*TP*TP*AP*TP*AP*AP*TP*TP*CP*C)-3')


Mass: 4278.815 Da / Num. of mol.: 4 / Source method: obtained synthetically
Sequence detailsTHIS SEQUECE WAS CAUSED BY STRAIN AKR.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.55 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2M calcium acetate, 0.1M Tris-HCl, 20%(w/v) polyethylene glycol 3000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 12, 2012
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.963→50 Å / Num. all: 22039 / Num. obs: 21825 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 57.95 Å2
Reflection shellResolution: 3→3.11 Å / % possible all: 99.9

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JBM

4jbm


Resolution: 2.963→47.173 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7756 / SU ML: 0.41 / σ(F): 1.36 / Phase error: 29.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2532 1990 9.12 %RANDOM
Rwork0.2203 ---
all0.2219 22039 --
obs0.2234 21825 99.03 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 214.43 Å2 / Biso mean: 77.3168 Å2 / Biso min: 37.07 Å2
Refinement stepCycle: LAST / Resolution: 2.963→47.173 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6087 1148 0 0 7235
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067482
X-RAY DIFFRACTIONf_angle_d1.31510279
X-RAY DIFFRACTIONf_chiral_restr0.0881154
X-RAY DIFFRACTIONf_plane_restr0.0051096
X-RAY DIFFRACTIONf_dihedral_angle_d18.5262909
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9633-3.03740.38761370.34451319145694
3.0374-3.11950.3551340.299114451579100
3.1195-3.21130.37321340.27531412154699
3.2113-3.31490.3131500.27231374152498
3.3149-3.43330.32971490.25221408155799
3.4333-3.57080.27621270.240114141541100
3.5708-3.73320.28361460.23021410155699
3.7332-3.92990.2951460.222314421588100
3.9299-4.1760.24181390.213714291568100
4.176-4.49820.24761420.178214401582100
4.4982-4.95050.19621430.177214161559100
4.9505-5.66580.21251540.195114301584100
5.6658-7.13430.23621370.21414551592100
7.1343-47.17940.19241520.20851441159399
Refinement TLS params.Method: refined / Origin x: 40.4911 Å / Origin y: 11.4431 Å / Origin z: 70.615 Å
111213212223313233
T0.5107 Å20.0264 Å20.008 Å2-0.6014 Å2-0.0049 Å2--0.4829 Å2
L0.3415 °20.078 °2-0.2681 °2-0.2265 °2-0.0123 °2--0.1946 °2
S-0.0714 Å °-0.0953 Å °0.0444 Å °-0.0263 Å °0.0446 Å °-0.0508 Å °0.091 Å °0.1693 Å °0.043 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA3 - 199
2X-RAY DIFFRACTION1ALLB3 - 199
3X-RAY DIFFRACTION1ALLC3 - 199
4X-RAY DIFFRACTION1ALLD3 - 199
5X-RAY DIFFRACTION1ALLE1 - 14
6X-RAY DIFFRACTION1ALLF1 - 14
7X-RAY DIFFRACTION1ALLG1 - 14
8X-RAY DIFFRACTION1ALLH1 - 14

+
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