[English] 日本語
Yorodumi
- PDB-6ifo: Crystal structure of AcrIIA2-SpyCas9-sgRNA ternary complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ifo
TitleCrystal structure of AcrIIA2-SpyCas9-sgRNA ternary complex
Components
  • AcrIIA2
  • CRISPR-associated endonuclease Cas9/Csn1
  • RNA (99-MER)
KeywordsRNA BINDING PROTEIN/RNA / anti-CRISPR / SpyCas9 / sgRNA / AcrIIA2 / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


maintenance of CRISPR repeat elements / 3'-5' exonuclease activity / DNA endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / DNA binding / RNA binding / metal ion binding
Similarity search - Function
CRISPR-associated endonuclease Cas9, bridge helix / Bridge helix of CRISPR-associated endonuclease Cas9 / CRISPR-associated endonuclease Cas9, PAM-interacting domain / CRISPR-associated endonuclease Cas9, REC lobe / REC lobe of CRISPR-associated endonuclease Cas9 / PAM-interacting domain of CRISPR-associated endonuclease Cas9 / : / Cas9 RuvC domain / HNH endonuclease / CRISPR-associated endonuclease Cas9 ...CRISPR-associated endonuclease Cas9, bridge helix / Bridge helix of CRISPR-associated endonuclease Cas9 / CRISPR-associated endonuclease Cas9, PAM-interacting domain / CRISPR-associated endonuclease Cas9, REC lobe / REC lobe of CRISPR-associated endonuclease Cas9 / PAM-interacting domain of CRISPR-associated endonuclease Cas9 / : / Cas9 RuvC domain / HNH endonuclease / CRISPR-associated endonuclease Cas9 / Cas9-type HNH domain / Cas9-type HNH domain profile. / HNH nuclease / Ribonuclease H superfamily
Similarity search - Domain/homology
RNA / RNA (> 10) / CRISPR-associated endonuclease Cas9/Csn1
Similarity search - Component
Biological speciesStreptococcus pyogenes serotype M1 (bacteria)
Listeria monocytogenes (bacteria)
Streptococcus pyogenes M1 GAS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.313 Å
AuthorsLiu, L. / Wang, Y.
CitationJournal: Mol. Cell / Year: 2019
Title: Phage AcrIIA2 DNA Mimicry: Structural Basis of the CRISPR and Anti-CRISPR Arms Race.
Authors: Liu, L. / Yin, M. / Wang, M. / Wang, Y.
History
DepositionSep 20, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Nov 22, 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: CRISPR-associated endonuclease Cas9/Csn1
C: RNA (99-MER)
B: CRISPR-associated endonuclease Cas9/Csn1
D: RNA (99-MER)
F: AcrIIA2
E: AcrIIA2


Theoretical massNumber of molelcules
Total (without water)409,8996
Polymers409,8996
Non-polymers00
Water00
1
A: CRISPR-associated endonuclease Cas9/Csn1
C: RNA (99-MER)
E: AcrIIA2


Theoretical massNumber of molelcules
Total (without water)204,9493
Polymers204,9493
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CRISPR-associated endonuclease Cas9/Csn1
D: RNA (99-MER)
F: AcrIIA2


Theoretical massNumber of molelcules
Total (without water)204,9493
Polymers204,9493
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.155, 214.567, 131.971
Angle α, β, γ (deg.)90.00, 102.89, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein CRISPR-associated endonuclease Cas9/Csn1 / SpCas9 / SpyCas9


Mass: 158786.922 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes serotype M1 (bacteria)
Gene: cas9, csn1, SPy_1046 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12
References: UniProt: Q99ZW2, Hydrolases; Acting on ester bonds
#2: RNA chain RNA (99-MER)


Mass: 31994.982 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Streptococcus pyogenes M1 GAS (bacteria)
#3: Protein AcrIIA2


Mass: 14167.594 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.57 Å3/Da / Density % sol: 65.59 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.1 M Bis-Tris, pH 6.0, 15% PEG 20000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97775 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Jul 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97775 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 56422 / % possible obs: 98.9 % / Redundancy: 5.1 % / Rpim(I) all: 0.14 / Net I/σ(I): 5.8
Reflection shellResolution: 3.3→3.36 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 1 / Rpim(I) all: 0.623 / % possible all: 96.8

-
Processing

Software
NameVersionClassification
PHENIX(1.14_3247: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZT0

4zt0


Resolution: 3.313→49.51 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 25.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2684 2843 5.04 %
Rwork0.2224 --
obs0.2247 56422 66.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.313→49.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23624 3808 0 0 27432
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01128295
X-RAY DIFFRACTIONf_angle_d1.51839059
X-RAY DIFFRACTIONf_dihedral_angle_d24.63711163
X-RAY DIFFRACTIONf_chiral_restr0.2244535
X-RAY DIFFRACTIONf_plane_restr0.0074357
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3126-3.3697100.65498X-RAY DIFFRACTION1
3.3697-3.431100.32867X-RAY DIFFRACTION1
3.431-3.49690.863920.259951X-RAY DIFFRACTION1
3.4969-3.56830.459170.2956171X-RAY DIFFRACTION4
3.5683-3.64590.264200.2654507X-RAY DIFFRACTION12
3.6459-3.73060.2932470.26211096X-RAY DIFFRACTION27
3.7306-3.82390.3561010.26761835X-RAY DIFFRACTION45
3.8239-3.92730.31161540.26872733X-RAY DIFFRACTION68
3.9273-4.04280.32021650.26353308X-RAY DIFFRACTION82
4.0428-4.17320.29051970.24923667X-RAY DIFFRACTION91
4.1732-4.32230.31022280.24413962X-RAY DIFFRACTION99
4.3223-4.49520.27622200.22774028X-RAY DIFFRACTION99
4.4952-4.69960.2712050.2164047X-RAY DIFFRACTION99
4.6996-4.94720.2672100.21013999X-RAY DIFFRACTION99
4.9472-5.25680.28532000.21124031X-RAY DIFFRACTION99
5.2568-5.66220.26412060.21823992X-RAY DIFFRACTION98
5.6622-6.2310.26792400.22424047X-RAY DIFFRACTION100
6.231-7.13040.27611950.22494045X-RAY DIFFRACTION99
7.1304-8.97480.222320.18914009X-RAY DIFFRACTION99
8.9748-49.51570.2092140.19164036X-RAY DIFFRACTION98

+
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