[English] 日本語
Yorodumi
- PDB-5id6: Structure of Cpf1/RNA Complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5id6
TitleStructure of Cpf1/RNA Complex
Components
  • Cpf1
  • RNA (5'-R(P*AP*AP*UP*UP*UP*CP*UP*AP*CP*UP*AP*AP*GP*UP*GP*UP*AP*GP*AP*UP*C)-3')
KeywordsHYDROLASE
Function / homologyCRISPR-associated endonuclease Cas12a / Cas12a, REC1 domain / Cas12a, RuvC nuclease domain / Cas12a, nuclease domain / Alpha helical recognition lobe domain / Nuclease domain / RuvC nuclease domain / Cpf1
Function and homology information
Biological speciesLachnospiraceae bacterium ND2006 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.382 Å
AuthorsDong, D. / Ren, K. / Qiu, X. / Wang, J. / Huang, Z.
CitationJournal: Nature / Year: 2016
Title: The crystal structure of Cpf1 in complex with CRISPR RNA
Authors: Dong, D. / Ren, K. / Qiu, X. / Zheng, J. / Guo, M. / Guan, X. / Liu, H. / Li, N. / Zhang, B. / Yang, D. / Ma, C. / Wang, S. / Wu, D. / Ma, Y. / Fan, S. / Wang, J. / Gao, N. / Huang, Z.
Validation Report
SummaryFull reportAbout validation report
History
DepositionFeb 24, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1May 4, 2016Group: Database references
Revision 1.2May 11, 2016Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cpf1
G: RNA (5'-R(P*AP*AP*UP*UP*UP*CP*UP*AP*CP*UP*AP*AP*GP*UP*GP*UP*AP*GP*AP*UP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,8414
Polymers150,7932
Non-polymers492
Water1086
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5400 Å2
ΔGint-63 kcal/mol
Surface area59820 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)168.352, 83.011, 124.086
Angle α, β, γ (deg.)90.00, 106.72, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein/peptide Cpf1 /


Mass: 144132.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lachnospiraceae bacterium ND2006 (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A182DWE3*PLUS
#2: RNA chain RNA (5'-R(P*AP*AP*UP*UP*UP*CP*UP*AP*CP*UP*AP*AP*GP*UP*GP*UP*AP*GP*AP*UP*C)-3')


Mass: 6659.973 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Magnesium
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O / Water

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.16 M Magnesium acetate, 18%(w/v) Polyethylene glycol 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97776 Å
DetectorType: CCD pilatus CBF / Detector: CCD / Date: Jan 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97776 Å / Relative weight: 1
ReflectionResolution: 2.38→41.51 Å / Num. obs: 64262 / % possible obs: 99.6 % / Redundancy: 3.8 % / Net I/σ(I): 20.67
Reflection shellResolution: 2.38→2.42 Å

-
Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
HKL-2000data scaling
PDB_EXTRACT3.2data extraction
Cootmodel building
RefinementResolution: 2.382→41.506 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2608 3272 5.09 %
Rwork0.2023 --
Obs0.2052 64262 97.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.382→41.506 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9949 443 2 6 10400
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealNumber
f_bond_d0.00910655
f_angle_d1.38814422
f_dihedral_angle_d18.3014098
f_chiral_restr0.1061551
f_plane_restr0.0051762
LS refinement shell

Refinement-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3823-2.41790.34671330.3037255495
2.4179-2.45570.34861360.2906265598
2.4557-2.49590.34261280.2966260297
2.4959-2.53890.32841500.273261797
2.5389-2.58510.34451430.276260196
2.5851-2.63480.27231360.257261998
2.6348-2.68860.29571620.2535265598
2.6886-2.7470.30791440.2517264398
2.747-2.81090.29051230.2342267198
2.8109-2.88120.3321490.248264599
2.8812-2.95910.29881360.2451265498
2.9591-3.04610.29681200.2344265198
3.0461-3.14440.31491560.2306257796
3.1444-3.25680.30721430.2303264098
3.2568-3.38710.27651590.2238267399
3.3871-3.54120.2811580.2115264599
3.5412-3.72780.27211350.2114271499
3.7278-3.96120.26281530.1899266699
3.9612-4.26670.23271490.1801261396
4.2667-4.69560.2151390.1633272199
4.6956-5.37380.23491380.1685269299
5.3738-6.76560.23441420.1976271798
6.7656-41.51180.21551400.1661276598
Refinement TLS params.Method: refined / Origin x: 45.0357 Å / Origin y: 0.6252 Å / Origin z: 26.7772 Å
111213212223313233
T0.4407 Å2-0.0551 Å20.0099 Å2-0.4454 Å2-0.0727 Å2--0.3955 Å2
L0.7168 °2-0.2261 °2-0.6608 °2-0.821 °20.4031 °2--2.113 °2
S-0.0772 Å °-0.3169 Å °-0.0778 Å °0.1007 Å °0.2385 Å °-0.101 Å °0.2242 Å °0.4145 Å °-0.1414 Å °
Refinement TLS groupSelection details: all

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
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.

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