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- PDB-5kk5: AsCpf1(E993A)-crRNA-DNA ternary complex -

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Basic information

Entry
Database: PDB / ID: 5kk5
TitleAsCpf1(E993A)-crRNA-DNA ternary complex
Components
  • CRISPR-associated endonuclease Cpf1
  • DNA (28-MER)
  • DNA (8-mer)
  • RNA (40-MER)
KeywordsHydrolase/DNA/RNA / Cpf1 / CRISPR-Cas / crRNA / Hydrolase-DNA-RNA complex
Function / homology
Function and homology information


Bacillus subtilis ribonuclease / deoxyribonuclease I / deoxyribonuclease I activity / defense response to virus / lyase activity / DNA binding / RNA binding
Similarity search - Function
: / 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) / CRISPR-associated endonuclease Cas12a
Similarity search - Component
Biological speciesAcidaminococcus sp.
Acidaminococcus sp. BV3L6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.289 Å
AuthorsGao, P. / Yang, H. / Rajashankar, K.R. / Huang, Z. / Patel, D.J.
CitationJournal: Cell Res. / Year: 2016
Title: Type V CRISPR-Cas Cpf1 endonuclease employs a unique mechanism for crRNA-mediated target DNA recognition.
Authors: Gao, P. / Yang, H. / Rajashankar, K.R. / Huang, Z. / Patel, D.J.
History
DepositionJun 21, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Derived calculations / Refinement description
Category: pdbx_audit_support / pdbx_struct_oper_list / software
Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CRISPR-associated endonuclease Cpf1
B: RNA (40-MER)
C: DNA (28-MER)
D: DNA (8-mer)


Theoretical massNumber of molelcules
Total (without water)178,3304
Polymers178,3304
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14490 Å2
ΔGint-97 kcal/mol
Surface area62980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)195.737, 195.737, 125.206
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein CRISPR-associated endonuclease Cpf1 / AsCpf1


Mass: 151448.000 Da / Num. of mol.: 1 / Mutation: E993A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acidaminococcus sp. (strain BV3L6) (bacteria)
Strain: BV3L6 / Gene: cpf1, HMPREF1246_0236 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL
References: UniProt: U2UMQ6, Hydrolases; Acting on ester bonds
#2: RNA chain RNA (40-MER)


Mass: 14320.470 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Acidaminococcus sp. BV3L6 (bacteria)
#3: DNA chain DNA (28-MER)


Mass: 10168.568 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Acidaminococcus sp. BV3L6 (bacteria)
#4: DNA chain DNA (8-mer)


Mass: 2392.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Acidaminococcus sp. BV3L6 (bacteria)

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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: 3.42 Å3/Da / Density % sol: 64.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Tris, pH 7.0, 30% PEG600, 0.5 M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.289→105.473 Å / Num. obs: 37141 / % possible obs: 99.5 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 14.1
Reflection shellResolution: 3.29→3.43 Å / Redundancy: 5.5 % / Rmerge(I) obs: 1.53 / Mean I/σ(I) obs: 1.36 / % possible all: 96.6

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
XDSdata scaling
XDSdata reduction
AutoSolphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 3.289→105.473 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2548 1998 5.38 %
Rwork0.2161 --
obs0.2182 37141 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.289→105.473 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9646 1555 0 0 11201
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00511601
X-RAY DIFFRACTIONf_angle_d1.07116038
X-RAY DIFFRACTIONf_dihedral_angle_d18.3896733
X-RAY DIFFRACTIONf_chiral_restr0.0561816
X-RAY DIFFRACTIONf_plane_restr0.0061799
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.57510.4622-0.11311.6665-0.01621.1156-0.01130.11820.0088-0.1237-0.02390.0925-0.1259-0.1053-0.02460.84890.06120.04510.77910.00420.8154-50.891732.4718-54.0965
20.69471.0296-0.7613.3748-1.18811.4832-0.17430.0116-0.3065-0.3370.1435-0.28060.54080.2460.00271.38590.0406-0.02771.0601-0.11521.078-54.28256.8201-58.4673
32.75460.41130.25212.2654-0.4190.5999-0.22250.0945-0.5673-0.6966-0.0556-0.6110.37660.46380.25731.53070.18410.19380.902-0.02891.2211-35.09431.2795-66.2477
40.7453-0.68440.6331.4555-0.66212.4125-0.6264-0.440.50651.5377-0.3077-1.3139-0.69260.83670.16742.3424-0.86-0.87082.30040.37522.71740.258834.5967-56.3605
52.72381.5225-0.77812.224-1.50451.1899-0.58980.83130.5241.1823-0.3422-2.2189-1.4059-0.00160.23132.1297-0.0481-0.33121.64670.13681.8344-7.744519.6609-56.124
69.616-1.46993.02553.00372.36483.921-0.49611.5564-0.4395-0.82720.2916-0.48490.31260.3353-0.73221.9211-0.310.23491.4536-0.25541.8038-42.23081.9769-82.6874
76.20590.45060.20024.30342.14853.1460.19521.2318-1.2671-1.33370.4601-1.16840.52610.5939-0.2792.12280.13480.5241.3901-0.30421.7023-35.20620.0943-80.8466
81.66121.21550.97255.15920.4960.88820.61780.0289-0.5284-0.667-1.48740.03650.76220.39830.47081.21340.21910.15691.0357-0.09650.9712-47.019325.3915-62.1939
91.8945-0.4360.49518.31193.07748.34650.20730.35140.0954-1.9159-0.2885-0.5018-0.8461.13370.69371.0612-0.0480.15541.1466-0.07281.1146-35.249751.9524-59.517
109.93331.1891-3.73890.8181-1.63283.49260.35431.33880.6669-3.9795-0.3023-1.03780.90111.63451.04612.02550.2790.33041.19190.11660.9922-33.659944.0133-63.4406
112.10971.7178-0.76753.4117-2.90882.8257-0.14810.1185-0.2074-0.4587-0.5275-0.57540.31930.58520.61281.137-0.00380.11120.9099-0.06110.9302-47.328120.9048-59.7991
126.19041.3111-0.2329.57921.20728.6204-0.4764-0.07190.56271.3670.14360.4492-0.9322-1.47080.33061.66370.1634-0.00511.31150.07821.2846-67.7461-8.4713-49.578
130.1679-0.43730.00891.2674-0.02690.0004-0.0874-0.01580.0521-0.0425-0.0442-0.02380.0074-0.0205-0.00342.85890.65210.09893.3475-0.13953.1628-83.433-4.3724-52.0838
148.79497.0881-0.76496.1722-0.64650.2288-1.54421.2304-0.0592-0.6411.10061.26521.4788-0.60420.20871.6501-0.3146-0.39331.20750.13652.1328-70.9655-5.9799-52.2126
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 428 )
2X-RAY DIFFRACTION2chain 'A' and (resid 429 through 725 )
3X-RAY DIFFRACTION3chain 'A' and (resid 726 through 1066 )
4X-RAY DIFFRACTION4chain 'A' and (resid 1067 through 1208 )
5X-RAY DIFFRACTION5chain 'A' and (resid 1209 through 1307 )
6X-RAY DIFFRACTION6chain 'B' and (resid -19 through -15 )
7X-RAY DIFFRACTION7chain 'B' and (resid -14 through 0 )
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 15 )
9X-RAY DIFFRACTION9chain 'B' and (resid 16 through 20 )
10X-RAY DIFFRACTION10chain 'C' and (resid -19 through -15 )
11X-RAY DIFFRACTION11chain 'C' and (resid -14 through 0 )
12X-RAY DIFFRACTION12chain 'C' and (resid 1 through 7 )
13X-RAY DIFFRACTION13chain 'C' and (resid 8 through 8 )
14X-RAY DIFFRACTION14chain 'D' and (resid -8 through -1 )

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