[English] 日本語
Yorodumi
- PDB-3rln: Structural Basis of Cytosolic DNA Recognition by Innate Immune Re... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3rln
TitleStructural Basis of Cytosolic DNA Recognition by Innate Immune Receptors
ComponentsGamma-interferon-inducible protein 16
KeywordsDNA BINDING PROTEIN / HIN200/OB fold/DNA binding / cytosolic DNA sensor/DNA binding / DNA / cytosol
Function / homology
Function and homology information


negative regulation of AIM2 inflammasome complex assembly / myeloid cell differentiation / STING mediated induction of host immune responses / IRF3-mediated induction of type I IFN / negative regulation of DNA binding / negative regulation of viral genome replication / negative regulation of gene expression, epigenetic / transcription factor binding / intrinsic apoptotic signaling pathway by p53 class mediator / monocyte differentiation ...negative regulation of AIM2 inflammasome complex assembly / myeloid cell differentiation / STING mediated induction of host immune responses / IRF3-mediated induction of type I IFN / negative regulation of DNA binding / negative regulation of viral genome replication / negative regulation of gene expression, epigenetic / transcription factor binding / intrinsic apoptotic signaling pathway by p53 class mediator / monocyte differentiation / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / cellular response to interferon-beta / cellular response to glucose starvation / activation of innate immune response / negative regulation of innate immune response / positive regulation of interleukin-1 beta production / positive regulation of cytokine production / cellular response to ionizing radiation / autophagy / double-stranded DNA binding / regulation of inflammatory response / defense response to virus / regulation of autophagy / nuclear speck / inflammatory response / innate immune response / negative regulation of DNA-templated transcription / nucleolus / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / identical protein binding / nucleus / membrane / cytosol / cytoplasm
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
Gamma-interferon-inducible protein 16
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.251 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 19, 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 / 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: Gamma-interferon-inducible protein 16


Theoretical massNumber of molelcules
Total (without water)22,4091
Polymers22,4091
Non-polymers00
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)128.673, 128.673, 67.772
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-12-

HOH

21A-51-

HOH

-
Components

#1: Protein Gamma-interferon-inducible protein 16 / Ifi-16 / Interferon-inducible myeloid differentiation transcriptional activator


Mass: 22408.717 Da / Num. of mol.: 1 / Fragment: unp residues 571-766 / Mutation: K663A, R667A, N710A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IFI16, IFNGIP1 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q16666
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.41 Å3/Da / Density % sol: 48.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2 M KCl, 20% PEG3350, pH 7.0, 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: Oct 13, 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: 2.25→50 Å / Num. all: 10327 / Num. obs: 10296 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.8 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 23.48
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.599 / Mean I/σ(I) obs: 2.76 / Num. unique all: 499 / % possible all: 96.7

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: dev_723)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3RLO

3rlo


Resolution: 2.251→37.145 Å / SU ML: 0.67 / σ(F): 0 / Phase error: 24.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2291 496 4.83 %random
Rwork0.1773 ---
all0.1798 10327 --
obs0.1798 10296 99.44 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.301 Å2 / ksol: 0.342 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å2-0 Å2
2--0.17 Å2-0 Å2
3----0.3399 Å2
Refinement stepCycle: LAST / Resolution: 2.251→37.145 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1490 0 0 86 1576
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071533
X-RAY DIFFRACTIONf_angle_d1.1242069
X-RAY DIFFRACTIONf_dihedral_angle_d13.771574
X-RAY DIFFRACTIONf_chiral_restr0.083240
X-RAY DIFFRACTIONf_plane_restr0.005264
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2505-2.4770.34581230.25692391X-RAY DIFFRACTION99
2.477-2.83530.28911190.21342428X-RAY DIFFRACTION100
2.8353-3.57170.25771230.17452445X-RAY DIFFRACTION100
3.5717-37.14970.1811310.15472506X-RAY DIFFRACTION100
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)
12.9388-2.9292-0.99814.08341.37931.2162-0.2243-0.27320.37810.48160.01930.87560.1602-0.0992-0.0710.27360.1654-0.04490.1632-0.33610.99795.168713.02221.0855
22.8427-1.7553-1.89836.49052.4574.0201-0.31210.05330.4214-0.41650.09380.37270.19750.48350.14350.3489-0.0399-0.00170.34960.02570.259525.38667.030110.9586
36.7365-1.6814-2.1325.85731.13735.6342-0.2578-0.61691.02280.1422-0.15570.13660.1295-0.3999-0.0550.1637-0.0211-0.06210.3013-0.16580.458713.565812.145819.1073
46.2243-1.655-0.8576.92581.07794.1833-0.0495-0.19041.1483-0.3026-0.02280.36820.1359-0.25940.05210.1558-0.0213-0.01860.264-0.04160.389212.76411.269916.3833
53.1522-0.4565-0.58216.0019-0.51862.6470.0213-0.19941.2962-0.3397-0.15930.799-0.2004-0.17210.12890.2239-0.0241-0.08210.262-0.05310.60395.725513.096216.4428
67.15352.7342.74036.33591.15716.59780.0384-1.5022-0.26870.74050.36360.33130.5522-0.00280.060.24510.04220.05530.54570.03390.266114.58083.309824.1759
75.52810.4211-0.24566.85661.62445.52670.09770.0761-0.1066-0.2547-0.14690.45180.4122-0.26610.13450.2106-0.0489-0.00410.2110.04750.24649.58593.052814.119
80.2029-0.14620.4181.2175-1.72082.66960.222-0.61981.9918-0.0455-0.64411.4152-1.6359-1.80280.56160.56640.3723-0.16160.8129-0.11.3476-2.91817.172713.1205
97.0232-5.3594-1.00046.55860.2014.53680.36850.6897-0.435-0.4138-0.39211.149-0.1683-0.61010.45070.60910.229-0.11441.1406-0.71511.8399-1.421421.893822.2654
100.6009-0.81091.24321.2015-1.92553.13510.11490.01611.0293-0.3554-0.72720.8655-0.1707-0.18810.61940.38660.0718-0.06720.7116-0.43231.129111.045822.96628.8595
115.22580.3552-1.05414.3675-0.77.0068-0.2269-1.780.21641.14480.27280.33850.2399-0.2827-0.31420.42560.01070.03440.7954-0.01780.329926.327615.614837.3835
124.2398-0.46030.86292.4088-0.72247.8667-0.1969-1.2064-0.3060.47520.60580.63850.5475-0.9214-0.36720.391-0.0587-0.0420.73130.15650.294722.91058.955631.2144
135.6888-1.4231-1.78175.002-2.0912.65660.3557-1.41131.25320.14730.158-0.2471-0.58370.6431-0.2960.2656-0.04120.0310.4972-0.19850.406834.310222.020228.5566
142.2738-1.4371-1.74523.6110.2033.21420.1602-0.60230.24910.01880.0845-0.8590.52071.0112-0.09390.24310.1207-0.00430.4721-0.05450.321444.042811.325523.0687
155.0954-1.9552-2.78015.05920.55342.2971-0.0048-0.85560.40360.2347-0.0679-0.07410.61770.3769-0.05620.24110.0295-0.07790.4849-0.01990.320939.577612.771625.9665
164.7999-2.5629-3.43945.0582.98963.1205-0.073-1.1160.85090.24270.4201-0.35270.17330.0721-0.14280.28930.0664-0.04010.6344-0.1440.304234.519116.619231.5553
178.6349-2.9031-5.3693.63550.4364.04490.19320.6050.1638-0.0535-0.11330.25240.4514-0.3337-0.24440.2602-0.0525-0.01830.4354-0.02730.259635.063111.519615.8279
183.71480.16942.19717.1432-0.02356.5501-0.1113-0.79960.27820.1975-0.0452-0.2006-0.0620.350.07940.15450.00010.02720.3919-0.00750.264932.105115.362326.679
192.89870.33141.95656.93511.01617.65240.0695-0.7172-0.42460.46340.3764-0.02690.59220.2807-0.18220.2190.030.01350.43580.10680.244630.08269.090926.5146
204.91771.8744-0.32362.29162.21837.2346-0.5617-0.13080.9501-0.75590.1314-0.2026-1.58760.82510.34170.5892-0.1598-0.03720.360.0130.513331.908125.904419.0752
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 575:584)
2X-RAY DIFFRACTION2(chain A and resid 585:596)
3X-RAY DIFFRACTION3(chain A and resid 597:608)
4X-RAY DIFFRACTION4(chain A and resid 609:624)
5X-RAY DIFFRACTION5(chain A and resid 625:635)
6X-RAY DIFFRACTION6(chain A and resid 636:642)
7X-RAY DIFFRACTION7(chain A and resid 643:650)
8X-RAY DIFFRACTION8(chain A and resid 651:656)
9X-RAY DIFFRACTION9(chain A and resid 657:661)
10X-RAY DIFFRACTION10(chain A and resid 662:670)
11X-RAY DIFFRACTION11(chain A and resid 671:682)
12X-RAY DIFFRACTION12(chain A and resid 683:688)
13X-RAY DIFFRACTION13(chain A and resid 689:695)
14X-RAY DIFFRACTION14(chain A and resid 696:701)
15X-RAY DIFFRACTION15(chain A and resid 702:706)
16X-RAY DIFFRACTION16(chain A and resid 707:719)
17X-RAY DIFFRACTION17(chain A and resid 720:725)
18X-RAY DIFFRACTION18(chain A and resid 726:745)
19X-RAY DIFFRACTION19(chain A and resid 746:758)
20X-RAY DIFFRACTION20(chain A and resid 759:764)

+
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