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Open data
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Basic information
Entry | Database: PDB / ID: 4cmq | ||||||
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Title | Crystal structure of Mn-bound S.pyogenes Cas9 | ||||||
![]() | CRISPR-ASSOCIATED ENDONUCLEASE CAS9/CSN1 | ||||||
![]() | HYDROLASE / DNASE / ENDONUCLEASE / RNA-GUIDED / IMMUNITY / CRRNA / GENOME EDITING | ||||||
Function / homology | ![]() maintenance of CRISPR repeat elements / 3'-5' exonuclease activity / DNA endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / DNA binding / RNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jinek, M. / Jiang, F. / Taylor, D.W. / Sternberg, S.H. / Kaya, E. / Ma, E. / Anders, C. / Hauer, M. / Zhou, K. / Lin, S. ...Jinek, M. / Jiang, F. / Taylor, D.W. / Sternberg, S.H. / Kaya, E. / Ma, E. / Anders, C. / Hauer, M. / Zhou, K. / Lin, S. / Kaplan, M. / Iavarone, A.T. / Charpentier, E. / Nogales, E. / Doudna, J.A. | ||||||
![]() | ![]() Title: Structures of Cas9 endonucleases reveal RNA-mediated conformational activation. Authors: Martin Jinek / Fuguo Jiang / David W Taylor / Samuel H Sternberg / Emine Kaya / Enbo Ma / Carolin Anders / Michael Hauer / Kaihong Zhou / Steven Lin / Matias Kaplan / Anthony T Iavarone / ...Authors: Martin Jinek / Fuguo Jiang / David W Taylor / Samuel H Sternberg / Emine Kaya / Enbo Ma / Carolin Anders / Michael Hauer / Kaihong Zhou / Steven Lin / Matias Kaplan / Anthony T Iavarone / Emmanuelle Charpentier / Eva Nogales / Jennifer A Doudna / ![]() Abstract: Type II CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated) systems use an RNA-guided DNA endonuclease, Cas9, to generate double-strand breaks in invasive DNA ...Type II CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated) systems use an RNA-guided DNA endonuclease, Cas9, to generate double-strand breaks in invasive DNA during an adaptive bacterial immune response. Cas9 has been harnessed as a powerful tool for genome editing and gene regulation in many eukaryotic organisms. We report 2.6 and 2.2 angstrom resolution crystal structures of two major Cas9 enzyme subtypes, revealing the structural core shared by all Cas9 family members. The architectures of Cas9 enzymes define nucleic acid binding clefts, and single-particle electron microscopy reconstructions show that the two structural lobes harboring these clefts undergo guide RNA-induced reorientation to form a central channel where DNA substrates are bound. The observation that extensive structural rearrangements occur before target DNA duplex binding implicates guide RNA loading as a key step in Cas9 activation. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 943.7 KB | Display | ![]() |
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PDB format | ![]() | 777.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5858C ![]() 5859C ![]() 5860C ![]() 4cmpSC ![]() 4ogcC ![]() 4ogeC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.99971, -0.0238, 0.0032), Vector: |
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Components
#1: Protein | Mass: 158986.109 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q99ZW2, Hydrolases; Acting on ester bonds #2: Chemical | ChemComp-MN / #3: Chemical | ChemComp-SO4 / Sequence details | M-TERMINAL GAAS IS DERIVED FROM THE EXPRESSION | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 49 % / Description: NONE |
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Crystal grow | pH: 8.5 Details: 0.1 M TRIS 8.5, 0.3 M LITHIUM SULFATE, 15% PEG 3350 SOAKED IN MOTHER LIQUOR SUPPLEMENTED WITH 20 MM MNCL2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 28, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.09→47.53 Å / Num. obs: 56200 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 19.1 |
Reflection shell | Resolution: 3.09→3.18 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.94 / Mean I/σ(I) obs: 2.3 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4CMP Resolution: 3.09→47.528 Å / SU ML: 0.45 / σ(F): 1.36 / Phase error: 28.75 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.09→47.528 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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