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Basic information

Entry
Database: PDB / ID: 6j9m
TitleNmeBH+AcrIIC2
Components
  • AcrIIC2
  • CRISPR-associated endonuclease Cas9
KeywordsHYDROLASE/HYDROLASE INHIBITOR / AcrIIC2 / HYDROLASE-HYDROLASE INHIBITOR 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 / CRISPR-associated endonuclease Cas9 / HNH endonuclease / Cas9-type HNH domain / Cas9-type HNH domain profile. / HNH nuclease / Ribonuclease H superfamily
Similarity search - Domain/homology
: / : / Phage associated protein / CRISPR-associated endonuclease Cas9
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.394 Å
AuthorsZhu, Y.L. / Gao, A. / Serganov, A. / Gao, P.
Funding support United States, China, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01GM112940 United States
National Science Foundation (China)91753133 China
National Science Foundation (China)31670903 China
CitationJournal: Mol. Cell / Year: 2019
Title: Diverse Mechanisms of CRISPR-Cas9 Inhibition by Type IIC Anti-CRISPR Proteins.
Authors: Zhu, Y. / Gao, A. / Zhan, Q. / Wang, Y. / Feng, H. / Liu, S. / Gao, G. / Serganov, A. / Gao, P.
History
DepositionJan 23, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 1, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 23, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.4Nov 22, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CRISPR-associated endonuclease Cas9
B: AcrIIC2
C: AcrIIC2
D: AcrIIC2
E: AcrIIC2
F: CRISPR-associated endonuclease Cas9


Theoretical massNumber of molelcules
Total (without water)74,1426
Polymers74,1426
Non-polymers00
Water1,67593
1
A: CRISPR-associated endonuclease Cas9
C: AcrIIC2
D: AcrIIC2


Theoretical massNumber of molelcules
Total (without water)37,0713
Polymers37,0713
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-12 kcal/mol
Surface area13780 Å2
MethodPISA
2
B: AcrIIC2
E: AcrIIC2
F: CRISPR-associated endonuclease Cas9


Theoretical massNumber of molelcules
Total (without water)37,0713
Polymers37,0713
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5180 Å2
ΔGint-13 kcal/mol
Surface area13510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.385, 81.996, 76.063
Angle α, β, γ (deg.)90.00, 96.44, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CRISPR-associated endonuclease Cas9


Mass: 8535.054 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Gene: cas9, A6J54_04955 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A1V0G6B2, UniProt: C9X1G5*PLUS, Hydrolases; Acting on ester bonds
#2: Protein
AcrIIC2


Mass: 14267.906 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Gene: CIJ84_02100 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3E2QCQ3, UniProt: A0A425B3G2*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSequence of AcrIIC2 was based on protein sequence of published literature (Pawluk et al., PMID: ...Sequence of AcrIIC2 was based on protein sequence of published literature (Pawluk et al., PMID: 27984730), in which reisdues 'MA' at terminal were reported.

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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: 1.94 Å3/Da / Density % sol: 36.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M CHES, ethanol

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Data collection

DiffractionMean temperature: 193 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.39→50 Å / Num. obs: 22256 / % possible obs: 99.8 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 29.6
Reflection shellResolution: 2.39→2.43 Å / Rmerge(I) obs: 0.274 / Num. unique obs: 1113

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-3000data scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6J9K

6j9k


Resolution: 2.394→41.475 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 25.39
RfactorNum. reflection% reflection
Rfree0.2223 1131 5.09 %
Rwork0.1794 --
obs0.1817 22215 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.394→41.475 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4111 0 0 93 4204
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064200
X-RAY DIFFRACTIONf_angle_d1.1855656
X-RAY DIFFRACTIONf_dihedral_angle_d15.1991614
X-RAY DIFFRACTIONf_chiral_restr0.049586
X-RAY DIFFRACTIONf_plane_restr0.005760
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3938-2.50270.28611510.21552476X-RAY DIFFRACTION94
2.5027-2.63460.29781230.21652662X-RAY DIFFRACTION100
2.6346-2.79960.30191430.2242640X-RAY DIFFRACTION100
2.7996-3.01570.27651510.21352651X-RAY DIFFRACTION100
3.0157-3.31910.24651370.20162656X-RAY DIFFRACTION100
3.3191-3.79910.20731410.17512646X-RAY DIFFRACTION100
3.7991-4.78540.18831400.1472656X-RAY DIFFRACTION100
4.7854-41.48140.18021450.162697X-RAY DIFFRACTION99
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)
14.24120.35622.40124.32023.09973.3463-0.14620.0350.7471-0.1508-0.1695-0.257-0.32990.41070.03710.3628-0.0428-0.02660.42360.20080.3733-5.7685.555196.7763
23.43733.2918-1.9195.7013-1.23040.9784-0.25550.4063-0.37240.27950.32380.2086-0.182-0.7216-0.02710.33690.07170.08090.3133-0.01710.3159-14.3393-15.4197100.581
33.4061-0.3322-2.10081.2001-1.31414.7723-0.0025-1.0666-0.31631.0507-0.10010.67570.1739-1.14350.1570.530.02620.08331.1574-0.00410.5051-32.6133-14.500785.3924
41.74960.6682-0.8241.73550.86963.1719-0.2567-0.5369-0.2074-0.11680.3332-0.11520.1910.0279-0.0570.3350.031-0.01750.29090.01670.3149-25.6624-16.716967.4613
52.6006-0.14630.33731.67020.49592.8764-0.0604-0.51410.14540.2842-0.2020.09310.4995-0.86170.17270.3581-0.09350.03850.4688-0.0350.2783-33.0141-20.135170.5081
67.7037-0.1487-1.03682.3966-0.8444.91960.03980.2046-0.0859-0.4474-0.3650.1122-0.2132-1.38920.28520.40330.0727-0.14780.7782-0.14260.3572-40.1371-16.141554.6937
75.207-0.71080.7683.8335-0.32874.5339-0.045-0.0538-1.21450.15270.25030.46831.2389-0.7478-0.17980.5573-0.2159-0.02040.7038-0.1260.4661-38.49-29.036762.7208
83.8811.3042-1.05860.4871-0.41530.336-0.3345-0.6933-0.34111.0043-0.39971.16311.4607-1.22040.2880.7793-0.22720.15870.92120.06520.6233-38.0987-27.432478.9437
93.7276-0.22320.41743.82262.15582.82830.148-0.74230.4421-0.025-0.37420.4664-0.2102-1.2228-0.00430.288-0.0239-0.03730.82-0.15040.3766-40.5351-17.414367.4098
104.11690.4603-1.85882.0152-0.98922.99560.067-0.1876-0.07890.1939-0.15390.0121-0.03070.0351-0.00950.210.0359-0.03320.1957-0.01250.2256-21.089-7.8933116.8057
113.894-1.0825-2.09336.32643.8047.57740.06260.932-0.2378-0.1747-0.46110.3274-0.2953-0.74290.21040.19320.0723-0.00440.1827-0.07070.3066-26.2002-6.7879112.0753
123.9457-4.54510.64527.2712-3.22933.10970.0022-0.875-0.06410.79060.31150.20940.1043-0.38020.19840.33620.0769-0.00120.66180.1540.2839-7.837-7.3572125.3395
131.56461.0197-0.49760.8966-0.45721.4072-0.30910.03770.222-0.13410.02230.00360.19880.10850.03060.27320.0683-0.01290.25140.03970.271-11.364-5.6348107.1922
144.1411-0.9870.69191.06450.07280.71780.02720.3121-0.1087-0.1654-0.057-0.2891-0.03740.4312-0.06920.29660.02250.03360.3358-0.02450.3384-0.497-3.2519105.6798
150.8635-0.36631.34012.0984-0.55662.7795-0.04790.405-0.0946-0.8340.03620.1427-0.28850.3129-0.03070.2324-0.0411-0.00470.240.03810.36621.597211.2751106.3545
162.4027-0.13150.2862.5462-0.15871.26650.1392-0.28970.62280.17180.1329-0.2301-0.55910.5375-0.22840.2717-0.03870.00540.2831-0.0680.402-0.51344.2804113.2243
175.2122.10990.99146.88993.10997.040.2646-0.2835-0.21690.3708-0.0513-0.20320.36470.7487-0.20210.25410.03430.00290.38210.03190.35213.5132-3.1544110.7348
183.5598-1.39131.11762.46891.96316.28080.1018-0.08320.10540.1328-0.0333-0.17590.11760.2263-0.02730.31220.06450.00410.3482-0.00070.3062-18.728-15.559774.3167
194.18990.16540.96793.3662-0.00883.9471-0.0683-0.1905-0.08720.05950.2221-0.20620.3739-0.0303-0.06560.28540.0435-0.04940.3165-0.04440.2059-15.4262-15.103581.503
204.137-1.0912-1.64830.57970.99765.5277-0.3431-0.0596-1.0440.6149-0.0320.19370.9704-0.00140.13350.5462-0.03370.08970.222-0.09820.5035-29.5385-27.850356.5111
213.8610.84620.14936.44083.51636.32270.15750.10030.19520.41880.3279-0.4026-0.75530.2452-0.13880.51350.0319-0.00670.23070.02380.2873-21.5325-8.514560.4178
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 50:55 )A50 - 55
2X-RAY DIFFRACTION2( CHAIN A AND RESID 56:79 )A56 - 79
3X-RAY DIFFRACTION3( CHAIN B AND RESID 3:10 )B3 - 10
4X-RAY DIFFRACTION4( CHAIN B AND RESID 11:24 )B11 - 24
5X-RAY DIFFRACTION5( CHAIN B AND RESID 25:41 )B25 - 41
6X-RAY DIFFRACTION6( CHAIN B AND RESID 42:56 )B42 - 56
7X-RAY DIFFRACTION7( CHAIN B AND RESID 57:78 )B57 - 78
8X-RAY DIFFRACTION8( CHAIN B AND RESID 79:90 )B79 - 90
9X-RAY DIFFRACTION9( CHAIN B AND RESID 91:115 )B91 - 115
10X-RAY DIFFRACTION10( CHAIN C AND RESID 6:90 )C6 - 90
11X-RAY DIFFRACTION11( CHAIN C AND RESID 91:118 )C91 - 118
12X-RAY DIFFRACTION12( CHAIN D AND RESID 5:10 )D5 - 10
13X-RAY DIFFRACTION13( CHAIN D AND RESID 11:24 )D11 - 24
14X-RAY DIFFRACTION14( CHAIN D AND RESID 25:56 )D25 - 56
15X-RAY DIFFRACTION15( CHAIN D AND RESID 57:70 )D57 - 70
16X-RAY DIFFRACTION16( CHAIN D AND RESID 71:90 )D71 - 90
17X-RAY DIFFRACTION17( CHAIN D AND RESID 91:114 )D91 - 114
18X-RAY DIFFRACTION18( CHAIN E AND RESID 4:56 )E4 - 56
19X-RAY DIFFRACTION19( CHAIN E AND RESID 57:119 )E57 - 119
20X-RAY DIFFRACTION20( CHAIN F AND RESID 50:55 )F50 - 55
21X-RAY DIFFRACTION21( CHAIN F AND RESID 56:77 )F56 - 77

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