PDB-5b2s: Crystal structure of the Streptococcus pyogenes Cas9 EQR variant ...

ID or keywords:

Entry

Database: PDB / ID: 5b2s

Title

Crystal structure of the Streptococcus pyogenes Cas9 EQR variant in complex with sgRNA and target DNA (TGAG PAM)

Components

CRISPR-associated endonuclease Cas9
Guide RNA
Non-target DNA, DNA (5'-D(*TP*GP*AP*GP*AP*TP*TP*G)-3')
Target DNA

Keywords

HYDROLASE/RNA/DNA / CRISPR-Cas9 / genome engineering / HYDROLASE-RNA-DNA complex

Function / homology

Function and homology information

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

Streptococcus pyogenes serotype M1 (bacteria)

Streptococcus pyogenes (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Hirano, S. / Nishimasu, H. / Ishitani, R. / Nureki, O.

Citation

Journal: Mol.Cell / Year: 2016
Title: Structural Basis for the Altered PAM Specificities of Engineered CRISPR-Cas9
Authors: Hirano, S. / Nishimasu, H. / Ishitani, R. / Nureki, O.

History

Deposition	Feb 2, 2016	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Mar 23, 2016	Provider: repository / Type: Initial release
Revision 1.1	Apr 6, 2016	Group: Database references
Revision 1.2	Oct 4, 2017	Group: Data collection / Database references / Derived calculations Category: citation / diffrn_detector ...citation / diffrn_detector / diffrn_source / pdbx_struct_oper_list Item: _citation.journal_id_CSD / _diffrn_detector.detector ..._citation.journal_id_CSD / _diffrn_detector.detector / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3	Nov 8, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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.ptnr2_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5b2s.cif.gz	691.5 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	5b2s_validation.pdf.gz	495.7 KB	Display	wwPDB validaton report
Full document	5b2s_full_validation.pdf.gz	509.1 KB	Display
Data in XML	5b2s_validation.xml.gz	53.1 KB	Display
Data in CIF	5b2s_validation.cif.gz	77.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/b2/5b2s ftp://data.pdbj.org/pub/pdb/validation_reports/b2/5b2s	HTTPS FTP

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Related structure data

Related structure data	5b2rC 5b2tC 4un3S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5b2r-d 5fq5-d 5fw2-d 6k4q-d 4un5-d 6k57-d 6k4p-d 5fw1-d 5b2t-d 6k3z-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
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PDB pages

PDBj /

wwPDB /

NCBI

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Deposited unit

A: Guide RNA

B: CRISPR-associated endonuclease Cas9

C: Target DNA

D: Non-target DNA, DNA (5'-D(*TP*GP*AP*GP*AP*TP*TP*G)-3')

hetero molecules

197 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	178.016, 67.822, 187.567
Angle α, β, γ (deg.)	90.000, 111.120, 90.000
Int Tables number	5
Space group name H-M	C121

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DNA chain , 2 types, 2 molecules CD

#3: DNA chain	Target DNA Mass: 8454.472 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemical synthesis / Source: (synth.) Streptococcus pyogenes (bacteria)
#4: DNA chain	Non-target DNA, DNA (5'-D(TPGPAPGPAPTPTPG)-3') Mass: 2481.652 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Streptococcus pyogenes (bacteria)

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RNA chain / Protein , 2 types, 2 molecules AB

#1: RNA chain	Guide RNA Mass: 26209.588 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: in vitro transcription / Source: (synth.) Streptococcus pyogenes (bacteria)
#2: Protein	CRISPR-associated endonuclease Cas9 / SpyCas9 Mass: 159005.094 Da / Num. of mol.: 1 / Mutation: D10A, C80L, C574E, H840A, D1135E, R1335Q, T1337R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pyogenes serotype M1 (bacteria) Strain: serotype M1 / Gene: cas9, csn1, SPy_1046 / Production host: Escherichia coli (E. coli) References: UniProt: Q99ZW2, Hydrolases; Acting on ester bonds

#1: RNA chain

Guide RNA

Mass: 26209.588 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: in vitro transcription / Source: (synth.)

Streptococcus pyogenes (bacteria)

#2: Protein

CRISPR-associated endonuclease Cas9 / SpyCas9

Mass: 159005.094 Da / Num. of mol.: 1 / Mutation: D10A, C80L, C574E, H840A, D1135E, R1335Q, T1337R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Streptococcus pyogenes serotype M1 (bacteria)
Strain: serotype M1 / Gene: cas9, csn1, SPy_1046 / Production host:

Escherichia coli (E. coli)
References: UniProt: Q99ZW2, Hydrolases; Acting on ester bonds

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Non-polymers , 5 types, 562 molecules

#5: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: K
#6: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#7: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₆O₂
#8: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₃O₂
#9: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 543 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.69 Å³/Da / Density % sol: 54.32 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 15-17% PEG 3350, 0.4 M KSCN, 0.1 M Tris-acetate

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 22, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.2→48.005 Å / Num. obs: 103809 / % possible obs: 97.8 % / Redundancy: 2.9 % / Net I/σ(I): 8
Reflection shell	Resolution: 2.2→2.24 Å

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Processing

Software

Name	Version	Classification
Aimless		data scaling
PHENIX	1.10_2155: ???	refinement
PDB_EXTRACT	3.2	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4UN3

4un3

Resolution: 2.2→48.005 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.18

	R_factor	Num. reflection	% reflection
R_free	0.2309	5165	4.98 %
R_work	0.2071	-	-
obs	0.2083	103651	97.39 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso max: 195.84 Å² / B_iso mean: 57.086 Å² / B_iso min: 21.79 Å²

Refinement step

Cycle: final / Resolution: 2.2→48.005 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10483	2464	34	543	13524
B_iso mean	-	-	50.24	42.24	-
Num. residues	-	-	-	-	1436

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	13460
X-RAY DIFFRACTION	f_angle_d	0.467	18706
X-RAY DIFFRACTION	f_chiral_restr	0.035	2169
X-RAY DIFFRACTION	f_plane_restr	0.003	1970
X-RAY DIFFRACTION	f_dihedral_angle_d	17.014	7832

LS refinement shell

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

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.2-2.225	0.296	184	0.2934	3294	3478	98
2.225-2.2512	0.2885	170	0.2971	3239	3409	97
2.2512-2.2787	0.3549	161	0.2865	3256	3417	97
2.2787-2.3075	0.2819	166	0.272	3266	3432	98
2.3075-2.3379	0.289	171	0.2735	3243	3414	96
2.3379-2.3699	0.327	154	0.2636	3061	3215	92
2.3699-2.4037	0.283	175	0.2724	3283	3458	98
2.4037-2.4396	0.3332	157	0.2711	3324	3481	98
2.4396-2.4777	0.3277	161	0.2648	3245	3406	98
2.4777-2.5184	0.2985	199	0.2545	3330	3529	98
2.5184-2.5618	0.2931	175	0.2483	3275	3450	98
2.5618-2.6084	0.2814	171	0.2536	3323	3494	98
2.6084-2.6585	0.2869	197	0.2461	3256	3453	98
2.6585-2.7128	0.2753	192	0.2488	3290	3482	98
2.7128-2.7718	0.2772	169	0.2402	3213	3382	98
2.7718-2.8362	0.2426	154	0.2412	3279	3433	97
2.8362-2.9072	0.2916	148	0.246	3153	3301	93
2.9072-2.9858	0.2766	173	0.2444	3345	3518	99
2.9858-3.0736	0.2588	170	0.2411	3345	3515	99
3.0736-3.1728	0.2584	163	0.2374	3298	3461	98
3.1728-3.2862	0.265	171	0.2178	3314	3485	98
3.2862-3.4177	0.2139	163	0.2076	3320	3483	99
3.4177-3.5732	0.2327	181	0.2098	3298	3479	98
3.5732-3.7615	0.2305	164	0.1877	3173	3337	93
3.7615-3.9971	0.1725	168	0.1782	3334	3502	98
3.9971-4.3055	0.2028	182	0.1652	3338	3520	99
4.3055-4.7384	0.1716	169	0.157	3375	3544	99
4.7384-5.4233	0.1958	185	0.1616	3302	3487	97
5.4233-6.8297	0.1807	162	0.184	3335	3497	96
6.8297-48.0159	0.1954	210	0.1749	3379	3589	97

Refinement TLS params.

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

ID	L11 (°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)
1	1.7933	0.4212	1.0406	5.7386	2.4251	8.3832	0.1715	0.0835	-0.1483	0.0811	-0.2459	0.2429	0.7467	-0.9771	0.1182	0.4767	-0.0668	0.0602	0.4568	-0.0883	0.3939	-11.4018	5.5033	71.881
2	1.8084	-0.1737	-1.0641	1.2385	0.5361	3.4137	0.0792	-0.0249	0.0158	0.088	0.0411	-0.0514	0.2699	0.415	-0.1259	0.222	-0.0324	-0.0265	0.3048	-0.0335	0.2871	8.3159	2.9418	31.6968
3	6	0.8417	-0.8757	6.4913	-1.765	7.1993	0.0968	0.7238	0.1858	-1.3845	0.4872	0.2533	1.317	-0.104	-0.5325	1.1487	0.1842	-0.1019	1.1261	-0.1927	0.5838	22.3058	-18.4745	1.8522
4	1.4681	0.215	0.2291	0.3914	-0.0934	1.2399	0.0739	0.1186	0.1333	-0.0229	-0.0262	0.0644	-0.0275	0.1332	-0.057	0.2475	-0.0455	-0.0105	0.2747	-0.0043	0.2861	-3.3515	9.3724	29.586
5	0.0102	-0.2273	0.0189	6.1482	-0.3978	0.0277	-0.3364	1.1807	2.9587	-1.5149	0.4281	-0.0802	-2.8275	1.9151	-0.0973	1.9801	-0.4891	0.2156	1.0481	0.2123	1.7292	-37.7667	19.4094	29.4053
6	6.062	0.4144	-2.2425	2.0421	-0.6335	2.0523	0.6679	-0.9352	1.4755	0.0254	-0.1486	-1.1593	-1.8351	0.9349	-0.427	1.0306	-0.1362	0.1225	1.1529	-0.2307	0.9693	-41.0346	13.714	37.8937
7	1.459	0.3469	-0.3459	0.4507	-0.0731	1.418	-0.0381	0.0136	0.0349	0.0127	0.0277	0.0999	0.1	-0.2599	0.0069	0.2431	-0.0489	0.0148	0.2027	-0.0284	0.278	-24.367	1.3763	41.1757
8	0.3901	0.5679	0.0639	0.8542	-0.0309	0.9806	0.1032	0.1988	-0.0912	0.1057	-0.1646	-0.0916	-0.0908	0.7937	0.1343	0.2983	-0.112	0.0207	0.7478	-0.0072	0.3285	25.3421	9.5691	32.7532
9	4.6037	-2.2386	-3.0096	3.0046	-0.0961	5.2343	0.7954	0.9291	-0.5954	-0.7879	-1.0421	0.7178	-1.8546	-1.4166	0.1772	1.0128	0.2985	-0.0537	0.8083	-0.1702	0.6068	25.6181	-1.7719	66.9359
10	1.2558	0.1461	-0.2295	2.0275	0.3332	2.3973	0.0237	-0.0946	-0.2938	0.3347	0.0808	-0.2136	0.4263	0.9242	-0.0972	0.2958	0.1108	-0.0767	0.7175	0.0281	0.3839	24.2381	-3.6378	34.087
11	0.42	0.0739	0.2313	0.6464	-0.2237	3.0914	-0.1302	-0.06	0.0097	0.149	0.1177	-0.067	-0.3669	-0.1237	0.0078	0.4274	0.0332	0.0174	0.2694	-0.0436	0.378	-2.598	20.5189	73.6328
12	1.1525	-0.6859	0.1288	0.7528	-0.0303	0.8289	-0.0337	-0.2206	-0.043	0.1704	0.1149	-0.202	0.2734	0.0952	-0.0775	0.5176	-0.0555	-0.0018	0.4031	-0.0478	0.4617	-15.7723	-11.4642	64.0821
13	1.3343	0.2512	-0.2939	0.7017	0.1527	1.6291	-0.0266	0.098	-0.2219	0.135	0.0355	0.0914	0.601	-0.3269	-0.0079	0.4696	-0.1564	0.0052	0.2821	-0.0643	0.3733	-28.999	-13.4022	38.5081
14	4.0944	3.2046	1.8027	7.6392	3.1995	5.1369	-0.0096	0.5174	-0.8622	-0.5018	0.1204	-0.044	0.2852	-0.0786	-0.1491	0.4049	-0.0106	-0.0172	0.5072	-0.1369	0.5065	-9.0076	-15.8677	25.1064
15	1.5137	0.1896	-1.5287	0.2345	-0.1038	4.1076	0.0539	-0.2688	0.1666	0.1539	0.135	0.1685	0.2442	0.0336	-0.1541	0.4179	-0.0785	0.0349	0.4617	0.0219	0.3336	-7.3312	5.5386	65.1235
16	2.5173	-0.0306	0.32	2.118	-0.7674	5.1565	0.1622	1.103	-0.9425	-0.6108	0.0292	-0.6818	0.9718	0.1879	-0.1767	0.6005	-0.0627	0.069	0.6069	-0.2757	0.6697	-11.2147	-15.8085	20.5482

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 10 )	A	1 - 10
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 11 through 30 )	A	11 - 30
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 31 through 40 )	A	31 - 40
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 41 through 70 )	A	41 - 70
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 71 through 75 )	A	71 - 75
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 76 through 81 )	A	76 - 81
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 4 through 85 )	B	4 - 85
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 86 through 207 )	B	86 - 207
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 208 through 299 )	B	208 - 299
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 300 through 445 )	B	300 - 445
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 446 through 730 )	B	446 - 730
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 731 through 980 )	B	731 - 980
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 981 through 1366 )	B	981 - 1366
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 1 through 10 )	C	1 - 10
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 11 through 28 )	C	11 - 28
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 5 through 12 )	D	5 - 12

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