[English] 日本語
Yorodumi
- PDB-8y08: Crystal structure of LbCas12a in complex with crRNA and 14nt targ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8y08
TitleCrystal structure of LbCas12a in complex with crRNA and 14nt target DNA
Components
  • DNA (5'-D(*CP*GP*TP*CP*CP*TP*TP*TP*AP*TP*T)-3')
  • DNA (5'-D(P*CP*TP*TP*TP*AP*CP*TP*GP*GP*AP*TP*GP*CP*GP*TP*AP*AP*AP*GP*GP*AP*CP*G)-3')
  • LbCas12a
  • RNA (35-MER)
KeywordsRNA BINDING PROTEIN / CRISPR / Cas12a / crRNA / Complex
Function / homology
Function and homology information


: / CRISPR-associated endonuclease Cpf1 PI domain / : / CRISPR-associated endonuclease Cpf1 REC2 domain / CRISPR-associated endonuclease Cas12a / Cas12a, REC1 domain / Cas12a, RuvC nuclease domain / Cas12a, nuclease domain / Alpha helical recognition lobe domain / Nuclease domain / RuvC nuclease domain
Similarity search - Domain/homology
: / DNA / DNA (> 10) / RNA / RNA (> 10) / LbCas12a
Similarity search - Component
Biological speciesLachnospiraceae bacterium ND2006 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.64 Å
AuthorsLin, X. / Chen, J. / Liu, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32022047 China
CitationJournal: Nucleic Acids Res. / Year: 2025
Title: DNA target binding-induced pre-crRNA processing in type II and V CRISPR-Cas systems.
Authors: Chen, J. / Lin, X. / Xiang, W. / Chen, Y. / Zhao, Y. / Huang, L. / Liu, L.
History
DepositionJan 22, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 1, 2025Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.year / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: LbCas12a
B: RNA (35-MER)
C: DNA (5'-D(P*CP*TP*TP*TP*AP*CP*TP*GP*GP*AP*TP*GP*CP*GP*TP*AP*AP*AP*GP*GP*AP*CP*G)-3')
D: DNA (5'-D(*CP*GP*TP*CP*CP*TP*TP*TP*AP*TP*T)-3')
E: LbCas12a
F: RNA (35-MER)
G: DNA (5'-D(P*CP*TP*TP*TP*AP*CP*TP*GP*GP*AP*TP*GP*CP*GP*TP*AP*AP*AP*GP*GP*AP*CP*G)-3')
H: DNA (5'-D(*CP*GP*TP*CP*CP*TP*TP*TP*AP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)334,22811
Polymers334,2088
Non-polymers213
Water181
1
A: LbCas12a
B: RNA (35-MER)
C: DNA (5'-D(P*CP*TP*TP*TP*AP*CP*TP*GP*GP*AP*TP*GP*CP*GP*TP*AP*AP*AP*GP*GP*AP*CP*G)-3')
D: DNA (5'-D(*CP*GP*TP*CP*CP*TP*TP*TP*AP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,1257
Polymers167,1044
Non-polymers213
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15230 Å2
ΔGint-114 kcal/mol
Surface area63970 Å2
MethodPISA
2
E: LbCas12a
F: RNA (35-MER)
G: DNA (5'-D(P*CP*TP*TP*TP*AP*CP*TP*GP*GP*AP*TP*GP*CP*GP*TP*AP*AP*AP*GP*GP*AP*CP*G)-3')
H: DNA (5'-D(*CP*GP*TP*CP*CP*TP*TP*TP*AP*TP*T)-3')


Theoretical massNumber of molelcules
Total (without water)167,1044
Polymers167,1044
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14680 Å2
ΔGint-98 kcal/mol
Surface area64080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.390, 142.292, 208.582
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23
14
24

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111METMETARGARGchain 'A'AA1 - 10761 - 1076
121ASNASNSERSERchain 'A'AA1081 - 12251081 - 1225
211METMETARGARGchain 'E'EE1 - 10761 - 1076
221ASNASNSERSERchain 'E'EE1081 - 12251081 - 1225
112AACCchain 'B'BB-20 - 141 - 35
212AACCchain 'F'FF-20 - 141 - 35
113DCDCDGDGchain 'C'CC-13 - 91 - 23
213DCDCDGDGchain 'G'GG-13 - 91 - 23
114DCDCDTDTchain 'D'DD-9 - 11 - 11
214DCDCDTDTchain 'H'HH-9 - 11 - 11

NCS ensembles :
ID
1
2
3
4

-
Components

-
DNA chain , 2 types, 4 molecules CGDH

#3: DNA chain DNA (5'-D(P*CP*TP*TP*TP*AP*CP*TP*GP*GP*AP*TP*GP*CP*GP*TP*AP*AP*AP*GP*GP*AP*CP*G)-3')


Mass: 7120.609 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Lachnospiraceae bacterium ND2006 (bacteria)
#4: DNA chain DNA (5'-D(*CP*GP*TP*CP*CP*TP*TP*TP*AP*TP*T)-3')


Mass: 3290.157 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Lachnospiraceae bacterium ND2006 (bacteria)

-
Protein / RNA chain , 2 types, 4 molecules AEBF

#1: Protein LbCas12a


Mass: 143888.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lachnospiraceae bacterium ND2006 (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A5S8WF58
#2: RNA chain RNA (35-MER)


Mass: 12804.658 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lachnospiraceae bacterium ND2006 (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria)

-
Non-polymers , 2 types, 4 molecules

#5: Chemical ChemComp-LI / LITHIUM ION


Mass: 6.941 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Li
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.36 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Li2SO4, 30 mM Na2HPO4, 43.75 mM citric acid, 13% PEG 1000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 3.64→50 Å / Num. obs: 39629 / % possible obs: 95.9 % / Redundancy: 9.4 % / Biso Wilson estimate: 45.39 Å2 / Rpim(I) all: 0.115 / Net I/σ(I): 6.75
Reflection shellResolution: 3.64→3.71 Å / Redundancy: 9.1 % / Num. unique obs: 1938 / Rpim(I) all: 0.366 / % possible all: 96

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-30007.21data scaling
HKL-30007.21data reduction
Coot0.7.2.1model building
PHENIX1.17.1_3660phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XUZ

5xuz


Resolution: 3.64→26.07 Å / SU ML: 0.5186 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 30.5204
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2849 1871 5.02 %
Rwork0.2515 35380 -
obs0.2532 37251 90.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.36 Å2
Refinement stepCycle: LAST / Resolution: 3.64→26.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19928 2864 3 1 22796
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003723548
X-RAY DIFFRACTIONf_angle_d0.68432346
X-RAY DIFFRACTIONf_chiral_restr0.04353544
X-RAY DIFFRACTIONf_plane_restr0.0043656
X-RAY DIFFRACTIONf_dihedral_angle_d18.63414162
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.64-3.740.3967690.32941529X-RAY DIFFRACTION51.3
3.74-3.850.3531220.30342421X-RAY DIFFRACTION81.19
3.85-3.970.34711410.2792639X-RAY DIFFRACTION89.13
3.97-4.110.31581550.2712767X-RAY DIFFRACTION93.92
4.11-4.270.3291670.25182803X-RAY DIFFRACTION94.89
4.27-4.470.28151460.24532823X-RAY DIFFRACTION94.34
4.47-4.70.28641540.23292827X-RAY DIFFRACTION95
4.7-4.990.24441440.23212873X-RAY DIFFRACTION95.69
5-5.380.2411670.24442849X-RAY DIFFRACTION95.32
5.38-5.910.28171580.24372842X-RAY DIFFRACTION94.64
5.91-6.760.33321450.25422904X-RAY DIFFRACTION95.25
6.76-8.460.23161510.24243001X-RAY DIFFRACTION97.71
8.46-26.070.22011520.21743102X-RAY DIFFRACTION97.08

+
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