[English] 日本語
Yorodumi
- PDB-5u0a: CRISPR RNA-guided surveillance complex -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 5u0a
TitleCRISPR RNA-guided surveillance complex
DescriptorCRISPR RNA-guided surveillance complex
KeywordsIMMUNE SYSTEM / CRISPR-Cas / Cascacde / surveillance
Specimen sourceThermobifida fusca (strain yx) / bacteria / thermophilic
Thermobifida fusca yx / bacteria / thermophilic
MethodElectron microscopy (3.3 Å resolution / Particle / Single particle)
AuthorsXiao, Y. / Luo, M. / Hayes, R.P. / Kim, J. / Ng, S. / Ding, F. / Liao, M. / Ke, A.
CitationCell, 2017, 170, 48-60.e11

Cell, 2017, 170, 48-60.e11 Yorodumi Papers
Structure Basis for Directional R-loop Formation and Substrate Handover Mechanisms in Type I CRISPR-Cas System.
Yibei Xiao / Min Luo / Robert P Hayes / Jonathan Kim / Sherwin Ng / Fang Ding / Maofu Liao / Ailong Ke

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 23, 2016 / Release: Aug 9, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Aug 9, 2017Structure modelrepositoryInitial release
1.1Aug 16, 2017Structure modelDatabase referencescitation_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_PubMed / _citation.title

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
3D viewer


View / / Stereo:
Center
Zoom
Scale
Slabnear <=> far

fix: /
Orientation
Orientation Rotation
Misc. /
Show/hide

Downloads & links

-
Assembly

Deposited unit
A: CRISPR-associated protein, Cse3 family
C: CRISPR-associated protein, Cse1 family
D: CRISPR-associated protein, Cse4 family
E: CRISPR-associated protein, Cse4 family
F: CRISPR-associated protein, Cse4 family
G: CRISPR-associated protein, Cse4 family
H: CRISPR-associated protein, Cse4 family
I: CRISPR-associated protein, Cse4 family
J: Cse2
K: crRNA
L: Cse2
M: Target Strand
N: CRISPR-associated protein, Cas5e family
O: Nontarget Strand


Theoretical massNumber of molelcules
Total (without water)464,31114
Polyers464,31114
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

-
CRISPR-associated protein, ... , 4 types, 9 molecules ACDEFGHIN

#1: Polypeptide(L)CRISPR-associated protein, Cse3 family


Mass: 26327.938 Da / Num. of mol.: 1 / Source: (gene. exp.) Thermobifida fusca (strain YX) / References: UniProt: Q47PJ5
#2: Polypeptide(L)CRISPR-associated protein, Cse1 family


Mass: 61433.297 Da / Num. of mol.: 1 / Source: (gene. exp.) Thermobifida fusca (strain YX) / References: UniProt: Q47PJ1
#3: Polypeptide(L)
CRISPR-associated protein, Cse4 family / Cas7


Mass: 41043.043 Da / Num. of mol.: 6 / Source: (gene. exp.) Thermobifida fusca (strain YX) / References: UniProt: Q47PJ3
#7: Polypeptide(L)CRISPR-associated protein, Cas5e family


Mass: 28279.260 Da / Num. of mol.: 1 / Source: (gene. exp.) Thermobifida fusca (strain YX) / References: UniProt: Q47PJ4

Molecular function

Biological process

-
DNA chain , 2 types, 2 molecules MO

#6: DNA chainTarget Strand


Mass: 15251.741 Da / Num. of mol.: 1 / Source: (synth.) Thermobifida fusca YX
#8: DNA chainNontarget Strand


Mass: 12076.723 Da / Num. of mol.: 1 / Source: (synth.) Thermobifida fusca YX

-
Polypeptide(L) / RNA chain , 2 types, 3 molecules JLK

#4: Polypeptide(L)Cse2


Mass: 27446.613 Da / Num. of mol.: 2 / Source: (gene. exp.) Thermobifida fusca (strain YX) / References: UniProt: Q47PJ2

Molecular function

#5: RNA chaincrRNA


Mass: 19790.793 Da / Num. of mol.: 1 / Source: (synth.) Thermobifida fusca YX

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

-
Sample preparation

ComponentName: CRISPR RNA-guided surveillance complex / Type: COMPLEX / Entity ID: 1, 2, 3, 4, 5, 6, 7, 8 / Source: RECOMBINANT
Source (natural)Organism: Thermobifida fusca (strain YX)
Source (recombinant)Organism: Escherichia coli BL21(DE3) / Plasmid: pcdf
Buffer solutionDetails: 10 mM HEPES pH 7.5, 150 mM NaCl, 5 mM DTT / pH: 7.5
SpecimenConc.: 0.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: 400 mesh Quantifoil holey carbon grid
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Humidity: 85 %

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 31000 / Calibrated defocus min: 1000 nm / Calibrated defocus max: 21000 nm / Cs: 2 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: GATAN LIQUID NITROGEN / Temperature (max): 105 kelvins / Temperature (min): 80 kelvins
Image recordingElectron dose: 8 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of real images: 1072

-
Processing

SoftwareName: PHENIX / Version: 1.11.1-2575_1692: / Classification: refinement
EM software
IDNameVersionCategoryImage processing IDImaging IDFitting ID
1SpiderPARTICLE SELECTION1
2SAMUELPARTICLE SELECTION1
3UcsfImager4IMAGE ACQUISITION1
5RELION1.4CTF CORRECTION1
8COOT0.8.1MODEL FITTING1
10SPIDERINITIAL EULER ASSIGNMENT1
11RELION1.4FINAL EULER ASSIGNMENT1
12RELION1.4CLASSIFICATION1
13RELION1.4RECONSTRUCTION1
14PHENIX1.11.1MODEL REFINEMENT1
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNumber of particles selected: 303301
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 131292 / Symmetry type: POINT
Atomic model buildingRef protocol: OTHER
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01330167
ELECTRON MICROSCOPYf_angle_d1.42041600
ELECTRON MICROSCOPYf_dihedral_angle_d18.35417710
ELECTRON MICROSCOPYf_chiral_restr0.0794700
ELECTRON MICROSCOPYf_plane_restr0.0084928

+
About Yorodumi

-
News

-
Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

  • Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
  • Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
  • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

External links: The 2017 Nobel Prize in Chemistry - Press Release

-
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 / EM Navigator (legacy version) / Yorodumi (legacy version)

+
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 / EM Navigator (legacy version) / Yorodumi (legacy version)

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • All the functionalities will be ported from the levgacy version.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi

Read more