[English] 日本語
Yorodumi
- PDB-8q40: Crystal structure of cA4 activated Can2 in complex with a cleaved... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8q40
TitleCrystal structure of cA4 activated Can2 in complex with a cleaved DNA substrate
Components
  • Cyclic tetraadenosine monophosphate (cA4)
  • DNA (5'-D(*TP*CP*A)-3')
  • DUF1887 family protein
KeywordsDNA BINDING PROTEIN / Can2 / cyclic oligoadenylates / cA4 / CARF / CRISPR ancillary nuclease / Protein-DNA complex
Function / homologytRNA endonuclease-like domain superfamily / Restriction endonuclease type II-like / nucleic acid binding / metal ion binding / : / : / DNA / RNA / DUF1887 family protein
Function and homology information
Biological speciesThermoanaerobacter brockii subsp. finnii Ako-1 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsJungfer, K. / Sigg, A. / Jinek, M.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)ERC-CoG-820152European Union
CitationJournal: Nucleic Acids Res. / Year: 2024
Title: Substrate selectivity and catalytic activation of the type III CRISPR ancillary nuclease Can2.
Authors: Jungfer, K. / Sigg, A. / Jinek, M.
History
DepositionAug 4, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DUF1887 family protein
B: DUF1887 family protein
D: DNA (5'-D(*TP*CP*A)-3')
C: DNA (5'-D(*TP*CP*A)-3')
X: Cyclic tetraadenosine monophosphate (cA4)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,76310
Polymers109,4885
Non-polymers2755
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, protein:ligand complex
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9140 Å2
ΔGint-35 kcal/mol
Surface area35510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.696, 79.062, 94.579
Angle α, β, γ (deg.)90.000, 95.360, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein DUF1887 family protein


Mass: 51400.473 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacter brockii subsp. finnii Ako-1 (bacteria)
Gene: Thebr_0943 / Production host: Escherichia coli (E. coli) / References: UniProt: E8URK0
#2: DNA chain DNA (5'-D(*TP*CP*A)-3')


Mass: 2707.826 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Thermoanaerobacter brockii subsp. finnii Ako-1 (bacteria)
#3: RNA chain Cyclic tetraadenosine monophosphate (cA4)


Type: Polycyclic / Class: Antiviral / Mass: 1271.866 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Cyclic oligoadenylates such as c-tetraAMP were found to be novel bacterial second messengers. Antiviral in context of signalling for Type III CRISPR-Cas systems.
Source: (synth.) synthetic construct (others) / References: BIRD: PRD_002431
#4: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCRISPR-Cas systems provide bacteria with adaptive immunity against bacteriophages. Cyclic ...CRISPR-Cas systems provide bacteria with adaptive immunity against bacteriophages. Cyclic oligoadenylate signaling was found to be essential for the type III system against the jumbo phage.
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.98 Å3/Da / Density % sol: 38.02 % / Description: plate-shaped crystals
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 50 mM Tris pH 8, 17.1% (v/v) PEG 550 MME, 4.3% (w/v) PEG 2000

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.21→47.12 Å / Num. obs: 37882 / % possible obs: 88.65 % / Redundancy: 6.4 % / Biso Wilson estimate: 40.4 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06794 / Rpim(I) all: 0.0291 / Rrim(I) all: 0.07404 / Net I/σ(I): 16.52
Reflection shellResolution: 2.21→2.289 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.7591 / Mean I/σ(I) obs: 2.24 / Num. unique obs: 2076 / CC1/2: 0.867 / Rpim(I) all: 0.3229 / Rrim(I) all: 0.8267 / % possible all: 48.97

-
Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
autoPROC20230726data scaling
XDS20220110data reduction
Coot0.9.8.9model building
PHASER2.7.16phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.21→47.12 Å / SU ML: 0.2508 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.0748
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2359 1864 4.92 %
Rwork0.1962 36018 -
obs0.1983 37882 88.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.63 Å2
Refinement stepCycle: LAST / Resolution: 2.21→47.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7230 82 93 175 7580
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00347574
X-RAY DIFFRACTIONf_angle_d0.628710220
X-RAY DIFFRACTIONf_chiral_restr0.04581106
X-RAY DIFFRACTIONf_plane_restr0.00311260
X-RAY DIFFRACTIONf_dihedral_angle_d11.73652842
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.21-2.270.4706400.28861068X-RAY DIFFRACTION33.94
2.27-2.330.29151530.24523116X-RAY DIFFRACTION99.88
2.33-2.410.27251610.23123122X-RAY DIFFRACTION99.85
2.41-2.50.28251600.23383094X-RAY DIFFRACTION99.97
2.5-2.590.29751540.24873106X-RAY DIFFRACTION99.97
2.6-2.710.3111110.25812033X-RAY DIFFRACTION65.47
2.71-2.860.32511660.2473097X-RAY DIFFRACTION99.91
2.86-3.040.26571470.23573152X-RAY DIFFRACTION99.91
3.04-3.270.26371690.23073075X-RAY DIFFRACTION100
3.27-3.60.25651450.20612613X-RAY DIFFRACTION83.12
3.6-4.120.23781290.17442222X-RAY DIFFRACTION71.2
4.12-5.190.17271580.14613127X-RAY DIFFRACTION99.91
5.19-47.120.18481710.16493193X-RAY DIFFRACTION99.82
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)
11.0599007-0.346365246578-0.4317368417041.43677407745-0.6445322160651.632309099620.101191431344-0.354647209237-0.04523145994840.320520565864-0.29542964572-0.1410267507760.07084324319290.160953436195-0.0816530995250.250664993636-0.0306032487367-0.070585748790.3865616101130.08385531075160.27179715201926.7744457447-7.7521196219850.5317164792
20.6085115795990.193261695612-0.4997137587280.1934424767260.2260620777041.18580500088-0.040277331270.0702340748213-0.0835445524301-0.03072413452470.09504015288390.00172981592726-0.172699193386-0.125803906306-0.01045424588160.2617012510590.04211481048170.02427806540170.3143810479150.06946231028610.33936827992730.8668808738-3.157466766493.98577237488
31.040783176690.0843783733947-0.2148315736990.1746873550510.2706554147471.20065625462-0.06971632547240.08474786764560.026467236249-0.0363980850070.00262083946076-0.0252093518066-0.2042158542950.111061562095-7.44325000023E-50.401745199390.05419751814230.01418941318760.305720897690.06827409214370.36223872360827.3096818970.3953768097519.87323477482
41.199634171820.2991203931930.1951147691380.7590419558730.08937347745681.426757450490.107533210541-0.2998490936430.08451422596360.110793288-0.2075298621890.118994400236-0.0456633787016-0.219367376966-0.001644315627580.249857593940.04048649451120.03113972767420.375360932668-0.06577641396310.3543109797851.32010839768-1.8300505684643.4081033134
50.8201261949710.1887704523280.5397842036621.182055431340.9557288794681.788382153740.03339305762240.4403317985210.0424373309047-0.373833423157-0.00432511918653-0.00186754129461-0.116457942878-0.08566467646170.0002243157686690.4878740832580.0227260263754-0.003973542907730.395334855646-0.002246040274940.3857238663320.84829453814-19.3685941221-6.37527878339
61.272281353710.253066484281-0.2688893331531.330582406310.3740719986741.48040093604-0.117424266538-0.0439411695919-0.158073112691-0.01145546748660.004204464498460.02058771553750.1461700011990.0228566905857-1.96434518364E-80.3352043004760.0490257870099-0.01766750915860.2697937752020.02431516975520.2984232274055.29415734519-17.279991275721.5127152023
70.2690357753720.1292988624870.1186455195660.124442461498-0.05612624450520.31060649344-0.2110621580760.224461307637-0.390881847872-0.01035077594180.05627257572640.2689440439650.4606603872530.0715947866695-0.02053603883991.427213426650.04663588061250.2951061194150.5688130514030.04974963336391.1317763203923.0765799536-6.853761020815.35074449096
80.02048368319860.005039533820980.008135015805750.0240068788855-0.01772476571570.0195847294219-0.684668839718-0.01283756040620.2604222200910.273707285237-0.5685338873530.188805189113-0.0851094978307-0.131881987185.7827397446E-51.080857478190.1393080411110.09552765100590.8867359239390.08763195177190.8981455448887.52697338906-12.72472978426.59332839078
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 146 )AA1 - 1461 - 146
22chain 'A' and (resid 147 through 242 )AA147 - 242147 - 242
33chain 'A' and (resid 243 through 437 )AA243 - 437243 - 437
44chain 'B' and (resid 1 through 184 )BB1 - 1841 - 184
55chain 'B' and (resid 185 through 300 )BB185 - 300185 - 300
66chain 'B' and (resid 301 through 437 )BB301 - 437301 - 437
77chain 'D' and (resid 1 through 3 )DF1 - 3
88chain 'C' and (resid 1 through 3 )CH1 - 3

+
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