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- PDB-5u07: CRISPR RNA-guided surveillance complex -

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Basic information

Database: PDB / ID: 5u07
TitleCRISPR RNA-guided surveillance complex
DescriptorCRISPR RNA-guided surveillance complex
KeywordsIMMUNE SYSTEM / CRISPR-Cas / Cascade
Specimen sourceThermobifida fusca yx / bacteria / thermophilic
MethodElectron microscopy (3.8 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

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Deposited unit
A: CRISPR-associated protein, Cse3 family
B: Cse2
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
M: Target Strand
N: CRISPR-associated protein, Cas5e family
O: Nontarget Strand

Theoretical massNumber of molelcules
Total (without water)447,35014

TypeNameSymmetry operationNumber
identity operation1_555x,y,z1


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 YX / References: UniProt: Q47PJ5
#3: Polypeptide(L)CRISPR-associated protein, Cse1 family

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

Mass: 41043.043 Da / Num. of mol.: 6 / Source: (gene. exp.) Thermobifida fusca 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 YX / References: UniProt: Q47PJ4

Molecular function

Biological process

DNA chain , 2 types, 2 molecules MO

#6: DNA chainTarget Strand

Mass: 6381.106 Da / Num. of mol.: 1 / Source: (synth.) Thermobifida fusca YX
#8: DNA chainNontarget Strand

Mass: 3986.600 Da / Num. of mol.: 1 / Source: (synth.) Thermobifida fusca YX

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

#2: Polypeptide(L)Cse2

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

Molecular function

#5: RNA chaincrRNA

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

Experimental details


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, 9, 10, 11, 12 / Source: RECOMBINANT
Source (natural)Organism: Thermobifida fusca (strain YX)
Source (recombinant)Organism: Escherichia coli BL21(DE3) / Plasmid: pcdf
Buffer solutionDetails: 10 mM Hepes, 150 mM NaCl, 5 mM DTT, pH 7.5 / 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
VitrificationCryogen 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: 2300 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: 1305


SoftwareName: PHENIX / Version: 1.11.1-2575_1692: / Classification: refinement
EM software
IDNameVersionCategoryImage processing IDImaging IDFitting ID
Particle selectionNumber of particles selected: 582497
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.5 CUT-OFF / Number of particles: 70222 / Symmetry type: POINT
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01128773
ELECTRON MICROSCOPYf_angle_d1.41839495
ELECTRON MICROSCOPYf_dihedral_angle_d14.74817066
ELECTRON MICROSCOPYf_chiral_restr0.0734464
ELECTRON MICROSCOPYf_plane_restr0.0084837

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