[English] 日本語
Yorodumi
- PDB-6je9: Crystal structure of Nme1Cas9-sgRNA dimer mediated by double prot... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6je9
TitleCrystal structure of Nme1Cas9-sgRNA dimer mediated by double protein inhibitor AcrIIC3 monomers
Components
  • AcrIIC3
  • CRISPR-associated endonuclease Cas9
  • sgRNA
KeywordsHYDROLASE/HYDROLASE INHIBITOR/RNA / CRISPR-Cas9 / NmeCas9 / Nme1Cas9 / AcrIIC3 / anti-CRISPR / hydrolase / dimer / HYDROLASE-HYDROLASE INHIBITOR-RNA complex
Function / homology
Function and homology information


maintenance of CRISPR repeat elements / endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / DNA binding / RNA binding / metal ion binding
Similarity search - Function
RuvC endonuclease subdomain 3 / RuvC endonuclease subdomain 3 / 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) / RNA (> 100) / : / Uncharacterized protein / CRISPR-associated endonuclease Cas9
Similarity search - Component
Biological speciesNeisseria meningitidis 8013 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.46 Å
AuthorsSun, W. / Yang, J. / Cheng, Z. / Liu, C. / Wang, K. / Huang, X. / Wang, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31725008 China
CitationJournal: Mol.Cell / Year: 2019
Title: Structures of Neisseria meningitidis Cas9 Complexes in Catalytically Poised and Anti-CRISPR-Inhibited States.
Authors: Sun, W. / Yang, J. / Cheng, Z. / Amrani, N. / Liu, C. / Wang, K. / Ibraheim, R. / Edraki, A. / Huang, X. / Wang, M. / Wang, J. / Liu, L. / Sheng, G. / Yang, Y. / Lou, J. / Sontheimer, E.J. / Wang, Y.
History
DepositionFeb 4, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 8, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Nov 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
B: sgRNA
C: CRISPR-associated endonuclease Cas9
D: sgRNA
E: AcrIIC3
F: AcrIIC3


Theoretical massNumber of molelcules
Total (without water)364,9046
Polymers364,9046
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27490 Å2
ΔGint-257 kcal/mol
Surface area136260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.844, 156.196, 151.600
Angle α, β, γ (deg.)90.00, 108.58, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein CRISPR-associated endonuclease Cas9


Mass: 125935.195 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis 8013 (bacteria) / Gene: cas9, NMV_1993 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: C9X1G5, Hydrolases; Acting on ester bonds
#2: RNA chain sgRNA


Mass: 43059.352 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Protein AcrIIC3


Mass: 13457.375 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis 8013 (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A3E2QDI5, UniProt: A0A425B395*PLUS

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.47 Å3/Da / Density % sol: 64.56 %
Crystal growTemperature: 289 K / Method: evaporation / pH: 5.5
Details: 0.21M NaAc, 0.1 M NaAc pH 5.5, 0.04M tris HCl pH 7.5, 32% pentaerythritol propoxylate (5/4 PO/OH)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.97892 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97892 Å / Relative weight: 1
ReflectionResolution: 3.46→50 Å / Num. obs: 65468 / % possible obs: 99.5 % / Redundancy: 4.3 % / CC1/2: 0.993 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.042 / Rrim(I) all: 0.088 / Net I/σ(I): 15.5
Reflection shellResolution: 3.46→3.52 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.952 / Mean I/σ(I) obs: 1 / Num. unique obs: 3286 / CC1/2: 0.138 / Rpim(I) all: 0.567 / Rrim(I) all: 1.113 / % possible all: 99.4

-
Processing

Software
NameVersionClassification
PHENIX(1.14_3247: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JDQ

6jdq


Resolution: 3.46→45.597 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 24.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2605 2462 4.89 %
Rwork0.2209 --
obs0.2229 50326 77.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.46→45.597 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17332 4826 0 0 22158
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00423039
X-RAY DIFFRACTIONf_angle_d0.86932339
X-RAY DIFFRACTIONf_dihedral_angle_d11.18413330
X-RAY DIFFRACTIONf_chiral_restr0.0483852
X-RAY DIFFRACTIONf_plane_restr0.0053393
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4601-3.52670.5257100.2709263X-RAY DIFFRACTION8
3.5267-3.59860.3779330.281457X-RAY DIFFRACTION14
3.5986-3.67680.3108480.2926657X-RAY DIFFRACTION20
3.6768-3.76230.3283610.2621098X-RAY DIFFRACTION32
3.7623-3.85640.3247750.25521679X-RAY DIFFRACTION49
3.8564-3.96060.32991550.26652533X-RAY DIFFRACTION75
3.9606-4.0770.3081870.24453302X-RAY DIFFRACTION97
4.077-4.20860.26841570.23513428X-RAY DIFFRACTION99
4.2086-4.35890.26441570.21843451X-RAY DIFFRACTION100
4.3589-4.53320.24661570.20573439X-RAY DIFFRACTION100
4.5332-4.73930.23061690.20653453X-RAY DIFFRACTION100
4.7393-4.98890.23551930.20013352X-RAY DIFFRACTION100
4.9889-5.30110.2271750.20523454X-RAY DIFFRACTION100
5.3011-5.70960.26581850.21813417X-RAY DIFFRACTION100
5.7096-6.28290.24051810.22293462X-RAY DIFFRACTION100
6.2829-7.1890.26141860.22543442X-RAY DIFFRACTION100
7.189-9.04580.22841710.19923458X-RAY DIFFRACTION100
9.0458-45.6010.22341620.20433519X-RAY DIFFRACTION99

+
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