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- PDB-3x1l: Crystal Structure of the CRISPR-Cas RNA Silencing Cmr Complex Bou... -

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Basic information

Entry
Database: PDB / ID: 3x1l
TitleCrystal Structure of the CRISPR-Cas RNA Silencing Cmr Complex Bound to a Target Analog
Components
  • (CRISPR system Cmr subunit ...) x 3
  • Cmr4
  • Cmr6
  • DNA (5'-D(*TP*GP*CP*TP*CP*TP*CP*AP*GP*CP*CP*GP*CP*AP*AP*GP*GP*AP*CP*CP*GP*CP*AP*TP*AP*CP*TP*AP*CP*AP*A)-3')
  • RNA (32-MER)
KeywordsRNA BINDING PROTEIN/RNA/DNA / RNA-recognition motif / RNA silencing / RNA binding / RNA BINDING PROTEIN-RNA-DNA complex
Function / homology
Function and homology information


defense response to virus / nucleotide binding / RNA binding / metal ion binding / cytoplasm
Similarity search - Function
AF1862-like domain / Immunoglobulin-like - #4350 / Carboxypeptidase Inhibitor; Chain A - #70 / : / : / CRISPR RNA silencing complex Cmr2 subunit, first helical domain / CRISPR RNA silencing complex Cmr2 subunit, Zn-binding domain / CRISPR-associated protein (Cas_Cmr5) / CRISPR-associated protein, TM1793 / CRISPR-associated protein, TM1791 ...AF1862-like domain / Immunoglobulin-like - #4350 / Carboxypeptidase Inhibitor; Chain A - #70 / : / : / CRISPR RNA silencing complex Cmr2 subunit, first helical domain / CRISPR RNA silencing complex Cmr2 subunit, Zn-binding domain / CRISPR-associated protein (Cas_Cmr5) / CRISPR-associated protein, TM1793 / CRISPR-associated protein, TM1791 / CRISPR-associated protein, Cmr3 / CRISPR-associated protein (Cas_Cmr3) / Carboxypeptidase Inhibitor; Chain A / CRISPR-associated protein, Cmr5 / CRISPR-associated RAMP Cmr4 / AF1862-like domain superfamily / CRISPR-associated protein Cmr2 / CRISPR-associated protein Cmr2, N-terminal / CRISPR-Cas system, Cmr2 subunit, D1 domain, cysteine cluster / CRISPR-associated protein Cmr2, N-terminal / : / CRISPR RNA silencing complex Cmr2 subunit, second helical domain / CRISPR type III-associated protein / RAMP superfamily / GGDEF domain profile. / GGDEF domain / Peroxidase; domain 1 / Reverse transcriptase/Diguanylate cyclase domain / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / DNA / DNA (> 10) / RNA / RNA (> 10) / Uncharacterized protein / CRISPR system Cmr subunit Cmr5 / Uncharacterized protein / CRISPR system Cmr subunit Cmr2 / CRISPR system Cmr subunit Cmr3
Similarity search - Component
Biological speciesPyrococcus furiosus DSM 3638 (archaea)
Archaeoglobus fulgidus DSM 4304 (archaea)
Pyrococcus furiosus COM1 (archaea)
synthetic (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.096 Å
AuthorsOsawa, T. / Numata, T.
CitationJournal: Mol.Cell / Year: 2015
Title: Crystal structure of the CRISPR-Cas RNA silencing Cmr complex bound to a target analog.
Authors: Osawa, T. / Inanaga, H. / Sato, C. / Numata, T.
History
DepositionNov 20, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 13, 2015Provider: repository / Type: Initial release
Revision 1.1May 20, 2015Group: Structure summary
Revision 1.2Aug 24, 2022Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CRISPR system Cmr subunit Cmr2
B: CRISPR system Cmr subunit Cmr3
C: Cmr4
D: Cmr4
E: Cmr4
F: CRISPR system Cmr subunit Cmr5
G: CRISPR system Cmr subunit Cmr5
H: Cmr6
I: RNA (32-MER)
J: DNA (5'-D(*TP*GP*CP*TP*CP*TP*CP*AP*GP*CP*CP*GP*CP*AP*AP*GP*GP*AP*CP*CP*GP*CP*AP*TP*AP*CP*TP*AP*CP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)331,45012
Polymers331,36010
Non-polymers902
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area45130 Å2
ΔGint-243 kcal/mol
Surface area84880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.489, 76.215, 139.188
Angle α, β, γ (deg.)90.32, 104.83, 118.58
Int Tables number1
Space group name H-MP1

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Components

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CRISPR system Cmr subunit ... , 3 types, 4 molecules ABFG

#1: Protein CRISPR system Cmr subunit Cmr2 / CRISPR-associated protein Cas10/Cmr2 / subtype III-B


Mass: 78226.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus DSM 3638 (archaea) / Gene: cmr2, PF1129 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8U1S6
#2: Protein CRISPR system Cmr subunit Cmr3 / CRISPR type III-B/RAMP module-associated protein Cmr3


Mass: 36366.379 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus DSM 3638 (archaea) / Gene: cmr3, PF1128 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8U1S7
#4: Protein CRISPR system Cmr subunit Cmr5 / CRISPR type III-B/RAMP module-associated protein Cmr5


Mass: 17407.707 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus DSM 4304 (archaea)
Gene: AF_1861 / Production host: Escherichia coli (E. coli) / References: UniProt: O28417

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Protein , 2 types, 4 molecules CDEH

#3: Protein Cmr4


Mass: 39865.824 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus DSM 4304 (archaea)
Gene: AF_1863 / Production host: Escherichia coli (E. coli) / References: UniProt: O28416
#5: Protein Cmr6


Mass: 40298.773 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus DSM 4304 (archaea)
Gene: AF_1861 / Production host: Escherichia coli (E. coli) / References: UniProt: O28418

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RNA chain / DNA chain , 2 types, 2 molecules IJ

#6: RNA chain RNA (32-MER)


Mass: 12604.483 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Pyrococcus furiosus COM1 (archaea) / References: GenBank: CP003685
#7: DNA chain DNA (5'-D(*TP*GP*CP*TP*CP*TP*CP*AP*GP*CP*CP*GP*CP*AP*AP*GP*GP*AP*CP*CP*GP*CP*AP*TP*AP*CP*TP*AP*CP*AP*A)-3')


Mass: 9451.103 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence is complementary to entity_id 6 / Source: (synth.) synthetic (others)

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Non-polymers , 3 types, 132 molecules

#8: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#9: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 39.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 13-15% (w/v) PEG 3350, 100mM succinic acid, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.096→50 Å / Num. obs: 148845 / % possible obs: 97.4 %
Reflection shellResolution: 2.1→2.22 Å / % possible all: 94.4

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Processing

Software
NameVersionClassification
XDSdata scaling
PHENIXmodel building
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.096→44.338 Å / SU ML: 0.24 / σ(F): 1.93 / Phase error: 27.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2464 7442 5 %
Rwork0.2082 --
obs0.2101 148827 97.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.096→44.338 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18693 1127 2 130 19952
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00320309
X-RAY DIFFRACTIONf_angle_d0.62727782
X-RAY DIFFRACTIONf_dihedral_angle_d11.9287305
X-RAY DIFFRACTIONf_chiral_restr0.0253277
X-RAY DIFFRACTIONf_plane_restr0.0033314
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0961-2.120.3392130.2741402884
2.12-2.14490.29452460.2455469197
2.1449-2.1710.28952510.2392475997
2.171-2.19850.29642440.237463597
2.1985-2.22750.30382500.2382475997
2.2275-2.2580.28332450.2368464597
2.258-2.29020.3042510.2426476697
2.2902-2.32440.27622470.2347469598
2.3244-2.36070.31212500.2366475498
2.3607-2.39940.30722480.2351471898
2.3994-2.44080.29042490.2358473398
2.4408-2.48520.28072490.2298472698
2.4852-2.5330.27532480.2272472498
2.533-2.58470.27252510.2314476098
2.5847-2.64090.29112490.2436472598
2.6409-2.70230.29912500.2402476598
2.7023-2.76990.29242510.241476898
2.7699-2.84470.28922500.2509474698
2.8447-2.92840.27512510.2457476498
2.9284-3.02290.28012510.2392476798
3.0229-3.13090.27712490.234474299
3.1309-3.25630.26952530.2248480299
3.2563-3.40440.26422510.2137476999
3.4044-3.58380.22032530.1982479699
3.5838-3.80830.20442520.1882479199
3.8083-4.10210.21722510.1774478499
4.1021-4.51460.21112540.1636481199
4.5146-5.1670.19852520.1638480299
5.167-6.50650.20772530.1881479799
6.5065-44.34750.18682300.188436390

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