[English] 日本語
Yorodumi
- PDB-7vyx: Crystal structure of the selenomethionine(SeMet)-derived Cas12c1 ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7vyx
TitleCrystal structure of the selenomethionine(SeMet)-derived Cas12c1 (D969A) ternary complex
Components
  • Non-target DNA strand
  • Selenomethionine (SeMet)-labeled Cas12c1 D969A mutant
  • Target DNA strand
  • sgRNA
KeywordsRNA BINDING PROTEIN/RNA/DNA / Cas12c / Cas12c1 / CRISPR / RNA BINDING PROTEIN-RNA-DNA COMPLEX
Function / homologyDNA / DNA (> 10) / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesParasutterella muris (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.2 Å
AuthorsZhang, B. / Lin, J.Y. / Perculija, V. / OuYang, S.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31770948 China
CitationJournal: Nucleic Acids Res. / Year: 2022
Title: Structural insights into target DNA recognition and cleavage by the CRISPR-Cas12c1 system
Authors: Zhang, B. / Lin, J. / Perculija, V. / Li, Y. / Lu, Q. / Chen, J. / Ouyang, S.
History
DepositionNov 15, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1May 24, 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jun 14, 2023Group: Source and taxonomy / Structure summary / Category: entity / entity_src_gen
Item: _entity.details / _entity.pdbx_mutation ..._entity.details / _entity.pdbx_mutation / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Selenomethionine (SeMet)-labeled Cas12c1 D969A mutant
B: Selenomethionine (SeMet)-labeled Cas12c1 D969A mutant
C: sgRNA
D: sgRNA
E: Target DNA strand
F: Target DNA strand
G: Non-target DNA strand
H: Non-target DNA strand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)421,27910
Polymers421,1498
Non-polymers1312
Water00
1
A: Selenomethionine (SeMet)-labeled Cas12c1 D969A mutant
C: sgRNA
E: Target DNA strand
G: Non-target DNA strand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,6405
Polymers210,5744
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13910 Å2
ΔGint-120 kcal/mol
Surface area76090 Å2
MethodPISA
2
B: Selenomethionine (SeMet)-labeled Cas12c1 D969A mutant
D: sgRNA
F: Target DNA strand
H: Non-target DNA strand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,6405
Polymers210,5744
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13730 Å2
ΔGint-112 kcal/mol
Surface area74850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.127, 149.850, 173.246
Angle α, β, γ (deg.)90.000, 91.590, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Selenomethionine (SeMet)-labeled Cas12c1 D969A mutant


Mass: 150174.516 Da / Num. of mol.: 2 / Mutation: D969A
Source method: isolated from a genetically manipulated source
Details: WP_251451673.1 / Source: (gene. exp.) Parasutterella muris (bacteria) / Production host: Escherichia coli (E. coli)
#2: RNA chain sgRNA


Mass: 43743.930 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#3: DNA chain Target DNA strand


Mass: 9548.153 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#4: DNA chain Non-target DNA strand


Mass: 7107.680 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.97 Å3/Da / Density % sol: 58.61 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris-HCl (pH 8.2), 16% polyethylene glycol 3350 (w/v), 0.02 M citric acid, 0.05 M lithium acetate dihydrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 78406 / % possible obs: 99.9 % / Redundancy: 6.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.13 / Net I/σ(I): 14.8
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 7 % / Rmerge(I) obs: 1.634 / Mean I/σ(I) obs: 1.18 / Num. unique obs: 7804 / CC1/2: 0.493 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.13-2998phasing
RefinementMethod to determine structure: SAD / Resolution: 3.2→49.73 Å / Cor.coef. Fo:Fc: 0.823 / Cor.coef. Fo:Fc free: 0.802 / SU B: 0.003 / SU ML: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.577 / ESU R Free: 0.66 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2924 2973 4.8 %RANDOM
Rwork0.2557 ---
obs0.2575 59278 79.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 200 Å2 / Biso mean: 73.493 Å2 / Biso min: 8.64 Å2
Baniso -1Baniso -2Baniso -3
1--1.73 Å2-0 Å20.22 Å2
2--1.63 Å20 Å2
3---0.09 Å2
Refinement stepCycle: final / Resolution: 3.2→49.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18902 5561 2 0 24465
Biso mean--70.51 --
Num. residues----2668
LS refinement shellResolution: 3.2→3.283 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 30 -
Rwork0.308 715 -
all-745 -
obs--13.02 %

+
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://pdbjlc1.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