[English] 日本語
Yorodumi
- PDB-3rn5: Structural basis of cytosolic DNA recognition by innate immune re... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3rn5
TitleStructural basis of cytosolic DNA recognition by innate immune receptors
Components
  • DNA (5'-D(*CP*CP*AP*TP*CP*AP*AP*AP*GP*AP*GP*AP*GP*AP*AP*AP*GP*AP*G)-3')
  • DNA (5'-D(*GP*CP*TP*CP*TP*TP*TP*CP*TP*CP*TP*CP*TP*TP*TP*GP*AP*TP*G)-3')
  • Interferon-inducible protein AIM2
KeywordsImmune system/DNA / OB FOLD / DNA BINDING / CYTOSOLIC / Immune system-DNA complex
Function / homology
Function and homology information


pyroptosome complex assembly / AIM2 inflammasome complex assembly / The AIM2 inflammasome / AIM2 inflammasome complex / regulation of behavior / cysteine-type endopeptidase activator activity / Cytosolic sensors of pathogen-associated DNA / pattern recognition receptor signaling pathway / negative regulation of NF-kappaB transcription factor activity / pattern recognition receptor activity ...pyroptosome complex assembly / AIM2 inflammasome complex assembly / The AIM2 inflammasome / AIM2 inflammasome complex / regulation of behavior / cysteine-type endopeptidase activator activity / Cytosolic sensors of pathogen-associated DNA / pattern recognition receptor signaling pathway / negative regulation of NF-kappaB transcription factor activity / pattern recognition receptor activity / pyroptotic inflammatory response / T cell homeostasis / cellular response to interferon-beta / positive regulation of defense response to virus by host / signaling adaptor activity / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / activation of innate immune response / positive regulation of interleukin-1 beta production / tumor necrosis factor-mediated signaling pathway / positive regulation of NF-kappaB transcription factor activity / brain development / neuron cellular homeostasis / cellular response to xenobiotic stimulus / positive regulation of inflammatory response / site of double-strand break / double-stranded DNA binding / defense response to virus / immune response / innate immune response / DNA damage response / mitochondrion / nucleoplasm / identical protein binding / cytoplasm / cytosol
Similarity search - Function
HIN-200/IF120x / HIN-200 family / HIN-200/IF120x domain / HIN-200 A and B domains profile. / DAPIN domain / DAPIN domain profile. / PAAD/DAPIN/Pyrin domain / PAAD/DAPIN/Pyrin domain / Death-like domain superfamily / Nucleic acid-binding proteins ...HIN-200/IF120x / HIN-200 family / HIN-200/IF120x domain / HIN-200 A and B domains profile. / DAPIN domain / DAPIN domain profile. / PAAD/DAPIN/Pyrin domain / PAAD/DAPIN/Pyrin domain / Death-like domain superfamily / 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-inducible protein AIM2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsJin, T.C. / Xiao, T.
CitationJournal: Immunity / Year: 2012
Title: Structures of the HIN Domain:DNA Complexes Reveal Ligand Binding and Activation Mechanisms of the AIM2 Inflammasome and IFI16 Receptor.
Authors: Jin, T. / Perry, A. / Jiang, J. / Smith, P. / Curry, J.A. / Unterholzner, L. / Jiang, Z. / Horvath, G. / Rathinam, V.A. / Johnstone, R.W. / Hornung, V. / Latz, E. / Bowie, A.G. / Fitzgerald, K.A. / Xiao, T.S.
History
DepositionApr 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1May 9, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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
A: Interferon-inducible protein AIM2
B: Interferon-inducible protein AIM2
C: Interferon-inducible protein AIM2
D: Interferon-inducible protein AIM2
K: DNA (5'-D(*CP*CP*AP*TP*CP*AP*AP*AP*GP*AP*GP*AP*GP*AP*AP*AP*GP*AP*G)-3')
L: DNA (5'-D(*GP*CP*TP*CP*TP*TP*TP*CP*TP*CP*TP*CP*TP*TP*TP*GP*AP*TP*G)-3')
M: DNA (5'-D(*CP*CP*AP*TP*CP*AP*AP*AP*GP*AP*GP*AP*GP*AP*AP*AP*GP*AP*G)-3')
N: DNA (5'-D(*GP*CP*TP*CP*TP*TP*TP*CP*TP*CP*TP*CP*TP*TP*TP*GP*AP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,77817
Polymers117,2198
Non-polymers5599
Water2,936163
1
A: Interferon-inducible protein AIM2
B: Interferon-inducible protein AIM2
K: DNA (5'-D(*CP*CP*AP*TP*CP*AP*AP*AP*GP*AP*GP*AP*GP*AP*AP*AP*GP*AP*G)-3')
L: DNA (5'-D(*GP*CP*TP*CP*TP*TP*TP*CP*TP*CP*TP*CP*TP*TP*TP*GP*AP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8588
Polymers58,6104
Non-polymers2484
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-23 kcal/mol
Surface area27850 Å2
MethodPISA
2
C: Interferon-inducible protein AIM2
D: Interferon-inducible protein AIM2
M: DNA (5'-D(*CP*CP*AP*TP*CP*AP*AP*AP*GP*AP*GP*AP*GP*AP*AP*AP*GP*AP*G)-3')
N: DNA (5'-D(*GP*CP*TP*CP*TP*TP*TP*CP*TP*CP*TP*CP*TP*TP*TP*GP*AP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9209
Polymers58,6104
Non-polymers3105
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint-4 kcal/mol
Surface area28500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.360, 136.360, 77.040
Angle α, β, γ (deg.)90.00, 89.98, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Interferon-inducible protein AIM2 / Absent in melanoma 2


Mass: 23480.465 Da / Num. of mol.: 4 / Fragment: unp residues 144-343
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AIM2 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O14862
#2: DNA chain DNA (5'-D(*CP*CP*AP*TP*CP*AP*AP*AP*GP*AP*GP*AP*GP*AP*AP*AP*GP*AP*G)-3')


Mass: 5904.879 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DNA 19mer
#3: DNA chain DNA (5'-D(*GP*CP*TP*CP*TP*TP*TP*CP*TP*CP*TP*CP*TP*TP*TP*GP*AP*TP*G)-3')


Mass: 5743.705 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DNA 19mer
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2.79 Å3/Da / Density % sol: 55.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 8% PEG1000, 0.1 M KCl, 10 mM MgCl2, 0.1 M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 16, 2010
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 44491 / Num. obs: 44323 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.42 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 19.26
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 4.45 % / Rmerge(I) obs: 0.621 / Mean I/σ(I) obs: 3.29 / Num. unique all: 4442 / % possible all: 100

-
Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: dev_736)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3RLO

3rlo


Resolution: 2.5→46.015 Å / σ(F): 0 / σ(I): 0 / Phase error: 31.72 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2411 2239 5.05 %Random
Rwork0.2006 ---
obs0.2021 44323 99.64 %-
all-44491 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.103 Å2 / ksol: 0.313 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.0707 Å2-0 Å2-1.3488 Å2
2---9.0616 Å20 Å2
3---8.9909 Å2
Refinement stepCycle: LAST / Resolution: 2.5→46.015 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6199 1546 36 163 7944
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088143
X-RAY DIFFRACTIONf_angle_d0.96511124
X-RAY DIFFRACTIONf_dihedral_angle_d20.3353185
X-RAY DIFFRACTIONf_chiral_restr0.0651283
X-RAY DIFFRACTIONf_plane_restr0.0041134
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5013-2.55570.39631420.33732618X-RAY DIFFRACTION95
2.5557-2.61510.36391410.32162620X-RAY DIFFRACTION95
2.6151-2.68050.32651290.322651X-RAY DIFFRACTION95
2.6805-2.7530.38231340.3062619X-RAY DIFFRACTION95
2.753-2.8340.33681500.31492625X-RAY DIFFRACTION94
2.834-2.92540.29391220.3082603X-RAY DIFFRACTION95
2.9254-3.02990.34511470.28212643X-RAY DIFFRACTION95
3.0299-3.15120.32781430.2682592X-RAY DIFFRACTION95
3.1512-3.29460.261370.24282644X-RAY DIFFRACTION94
3.2946-3.46820.25761450.2122615X-RAY DIFFRACTION95
3.4682-3.68530.23991460.20122632X-RAY DIFFRACTION94
3.6853-3.96960.2521320.19092614X-RAY DIFFRACTION95
3.9696-4.36860.21881330.15592640X-RAY DIFFRACTION95
4.3686-4.99970.16791390.13622655X-RAY DIFFRACTION95
4.9997-6.2950.21551390.15842653X-RAY DIFFRACTION95
6.295-39.50450.19171550.15982599X-RAY DIFFRACTION92
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.2525-0.45692.55665.6539-4.73516.88930.17851.08610.2666-1.1982-0.30941.16990.72070.19220.08320.63780.157-0.16520.34110.02860.6743.492643.7933-8.0397
21.807-0.98741.39923.28420.09673.33030.04570.18350.5441-0.4779-0.24810.018-0.78660.06550.08050.47240.12230.05030.1420.13070.646113.426450.9262-3.9401
34.2445-1.46120.44747.7215-3.68726.41920.19080.4520.4158-0.7245-0.20511.0925-0.3485-0.5467-0.06650.62820.1172-0.10540.25460.01350.73482.657546.4184-4.7275
47.80730.49830.43830.1122-0.01580.30620.02640.0732-0.8433-0.0623-0.04720.29350.3026-0.03490.03070.4590.00190.02370.1340.04890.602218.115431.25561.8484
54.51474.6463-0.43165.5205-2.07773.65990.26980.4834-0.4537-0.46470.1073-1.59960.1630.5117-0.28760.44360.00190.17480.2633-0.02990.747429.307438.8238-0.5656
62.92582.03812.8611.42051.99622.81680.08270.39630.3389-0.4293-0.012-0.6838-0.23690.5116-0.02150.30240.00450.21590.34480.08860.987334.999640.562-1.1171
70.6644-0.0342-0.62883.2303-1.14675.65660.10620.18780.6705-0.254-0.1989-1.1306-0.10780.7846-0.01970.38590.0780.14590.36940.13540.919829.976544.23441.2269
82.68270.95390.90085.0183-0.33662.6988-0.2853-0.1810.54320.20280.0941-0.601-0.61530.0332-0.08370.5387-0.049-0.10760.1237-0.08130.609322.290235.333340.5334
92.202-0.70520.00654.360.25562.7137-0.1068-0.28530.02340.47690.06360.1587-0.195-0.20380.0720.37370.03880.05340.0797-0.04690.37588.521727.811939.0925
102.8346-0.339-0.92356.7606-0.50063.33130.0027-0.4164-0.65970.3797-0.19740.67920.19690.01020.0910.3884-0.08110.08960.16980.09780.55649.644-10.624542.4149
111.36170.571-0.58650.3658-0.3470.3330.2019-0.3037-0.25370.2546-0.14180.22810.4735-0.18790.07070.8364-0.16230.07870.35530.2380.81967.0453-10.602149.5292
121.42311.7847-0.54154.2176-0.70653.6642-0.0601-0.04790.39070.285-0.04220.59630.1184-0.40440.11120.28890.0191-0.00920.15850.04760.653312.48653.180938.8277
133.1231-2.09950.36751.59540.78215.81340.1083-0.6959-0.32070.2597-0.025-0.87060.36121.0330.00230.25160.0027-0.18530.43550.09290.859935.0393-2.644737.8795
143.9783-2.5927-1.15725.729-0.62378.71030.0382-0.4808-0.36190.26980.1557-0.96980.3960.8468-0.13490.26270.0732-0.14340.35860.10620.698530.2784-6.307637.5261
152.43140.8194-0.81083.87020.49080.8132-0.30250.138-0.7836-0.5840.1163-0.88770.20710.0880.0490.42060.04330.23710.1945-0.02640.727821.98762.9122-1.9872
162.44380.56450.30663.87410.37383.04-0.12570.3614-0.2969-0.56860.07480.19150.09-0.28840.05390.3286-0.11020.00230.1666-0.07980.38.372310.2132-0.6713
171.98820.43610.16281.9219-0.55461.14420.2302-0.00560.5081-0.0602-0.4016-0.2598-0.47470.11910.15640.90360.10070.05310.1138-0.03360.690414.089245.749218.6116
181.647-0.56380.93492.2229-0.94351.21660.74510.04340.70971.0483-1.2381-0.0309-0.96110.11390.33321.18530.00080.39630.55410.18760.876315.308947.515418.4651
190.48720.2253-0.02792.98170.55880.1168-0.11290.0819-0.24480.0784-0.2401-0.1040.280.0148-0.84380.87260.0219-0.00880.0853-0.01920.870915.2596-15.633220.6434
200.60280.47780.23034.1341-0.79110.33790.32370.2209-0.2521-0.5394-0.5850.42230.408-0.04090.16350.9640.0514-0.09520.185-0.05120.902515.0659-13.934619.4274
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 147:161)
2X-RAY DIFFRACTION2chain 'A' and (resseq 162:199)
3X-RAY DIFFRACTION3chain 'A' and (resseq 200:239)
4X-RAY DIFFRACTION4chain 'A' and (resseq 240:257)
5X-RAY DIFFRACTION5chain 'A' and (resseq 258:275)
6X-RAY DIFFRACTION6chain 'A' and (resseq 276:296)
7X-RAY DIFFRACTION7chain 'A' and (resseq 297:340)
8X-RAY DIFFRACTION8chain 'B' and (resseq 147:210)
9X-RAY DIFFRACTION9chain 'B' and (resseq 211:340)
10X-RAY DIFFRACTION10chain 'C' and (resseq 147:210)
11X-RAY DIFFRACTION11chain 'C' and (resseq 211:229)
12X-RAY DIFFRACTION12chain 'C' and (resseq 230:265)
13X-RAY DIFFRACTION13chain 'C' and (resseq 266:296)
14X-RAY DIFFRACTION14chain 'C' and (resseq 297:340)
15X-RAY DIFFRACTION15chain 'D' and (resseq 147:210)
16X-RAY DIFFRACTION16chain 'D' and (resseq 211:340)
17X-RAY DIFFRACTION17chain 'K'
18X-RAY DIFFRACTION18chain 'L'
19X-RAY DIFFRACTION19chain 'M'
20X-RAY DIFFRACTION20chain 'N'

+
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