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- PDB-6jdq: Crystal structure of Nme1Cas9 in complex with sgRNA -

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Basic information

Entry
Database: PDB / ID: 6jdq
TitleCrystal structure of Nme1Cas9 in complex with sgRNA
Components
  • CRISPR-associated endonuclease Cas9
  • sgRNA
KeywordsHYDROLASE/RNA / CRISPR-Cas9 / NmeCas9 / binary / Nme1Cas9 / hydrolase / HYDROLASE-RNA complex
Function / homology
Function and homology information


maintenance of CRISPR repeat elements / endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / DNA binding / RNA binding / metal ion binding
Similarity search - Function
RuvC endonuclease subdomain 3 / RuvC endonuclease subdomain 3 / HNH endonuclease / CRISPR-associated endonuclease Cas9 / Cas9-type HNH domain / Cas9-type HNH domain profile. / HNH nuclease / Ribonuclease H superfamily
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / CRISPR-associated endonuclease Cas9
Similarity search - Component
Biological speciesNeisseria meningitidis serogroup C (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsSun, W. / Yang, J. / Cheng, Z. / Liu, C. / Wang, K. / Huang, X. / Wang, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31725008 China
CitationJournal: Mol.Cell / Year: 2019
Title: Structures of Neisseria meningitidis Cas9 Complexes in Catalytically Poised and Anti-CRISPR-Inhibited States.
Authors: Sun, W. / Yang, J. / Cheng, Z. / Amrani, N. / Liu, C. / Wang, K. / Ibraheim, R. / Edraki, A. / Huang, X. / Wang, M. / Wang, J. / Liu, L. / Sheng, G. / Yang, Y. / Lou, J. / Sontheimer, E.J. / Wang, Y.
History
DepositionFeb 2, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 8, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CRISPR-associated endonuclease Cas9
B: sgRNA


Theoretical massNumber of molelcules
Total (without water)168,9952
Polymers168,9952
Non-polymers00
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10810 Å2
ΔGint-112 kcal/mol
Surface area65160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.080, 122.452, 238.074
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CRISPR-associated endonuclease Cas9


Mass: 125935.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis serogroup C (strain 8013) (bacteria)
Strain: 8013 / Gene: cas9, NMV_1993 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: C9X1G5, Hydrolases; Acting on ester bonds
#2: RNA chain sgRNA


Mass: 43059.352 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 3.11 Å3/Da / Density % sol: 60.43 %
Crystal growTemperature: 289 K / Method: evaporation / pH: 8.5 / Details: 0.1M tris pH 8.5, 0.12M K2SO4, 18.5% PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.95→50 Å / Num. obs: 45932 / % possible obs: 100 % / Redundancy: 7.3 % / CC1/2: 0.973 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.039 / Rrim(I) all: 0.104 / Χ2: 0.949 / Net I/σ(I): 19.9
Reflection shellResolution: 2.95→3 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2270 / CC1/2: 0.619 / Rpim(I) all: 0.455 / Χ2: 0.855 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.14_3247: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JDV

6jdv


Resolution: 2.95→48.914 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2896 2241 5.01 %
Rwork0.2554 --
obs0.2571 44724 98.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.95→48.914 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8338 2473 0 19 10830
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01611288
X-RAY DIFFRACTIONf_angle_d1.50915813
X-RAY DIFFRACTIONf_dihedral_angle_d23.4764584
X-RAY DIFFRACTIONf_chiral_restr0.1081849
X-RAY DIFFRACTIONf_plane_restr0.0071632
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-3.01420.35461170.35942286X-RAY DIFFRACTION85
3.0142-3.08430.39071310.33452494X-RAY DIFFRACTION95
3.0843-3.16140.3591510.32632644X-RAY DIFFRACTION100
3.1614-3.24680.34631280.32032638X-RAY DIFFRACTION100
3.2468-3.34240.36181260.29632672X-RAY DIFFRACTION100
3.3424-3.45020.31771470.29532664X-RAY DIFFRACTION100
3.4502-3.57350.32141680.28852622X-RAY DIFFRACTION100
3.5735-3.71650.3211270.26062686X-RAY DIFFRACTION100
3.7165-3.88560.26011370.24442659X-RAY DIFFRACTION100
3.8856-4.09040.26931490.24342669X-RAY DIFFRACTION100
4.0904-4.34650.27971350.22042686X-RAY DIFFRACTION100
4.3465-4.68180.24751500.21492691X-RAY DIFFRACTION100
4.6818-5.15250.29731560.21672701X-RAY DIFFRACTION100
5.1525-5.8970.24941280.22732735X-RAY DIFFRACTION100
5.897-7.42550.27851470.24752755X-RAY DIFFRACTION100
7.4255-48.92110.2361440.23882881X-RAY DIFFRACTION99

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