PDB-5b2t: Crystal structure of the Streptococcus pyogenes Cas9 VRER variant...

ID or keywords:

Entry

Database: PDB / ID: 5b2t

Title

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

Components

CRISPR-associated endonuclease Cas9
Guide RNA
Non-target DNA, DNA (5'-D(*TP*GP*CP*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.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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5b2t.cif.gz	690.2 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	5b2t_validation.pdf.gz	495.1 KB	Display	wwPDB validaton report
Full document	5b2t_full_validation.pdf.gz	507.7 KB	Display
Data in XML	5b2t_validation.xml.gz	54.1 KB	Display
Data in CIF	5b2t_validation.cif.gz	79 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/b2/5b2t ftp://data.pdbj.org/pub/pdb/validation_reports/b2/5b2t	HTTPS FTP

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Related structure data

Related structure data	5b2rC 5b2sC 4un3S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5fw3-d 6k57-d 5fw2-d 6k4q-d 4un3-d 5fq5-d 6k4u-d 5b2r-d 6k4p-d 4un4-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*CP*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)	176.967, 69.448, 188.199
Angle α, β, γ (deg.)	90.000, 109.670, 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: 8479.484 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(TPGPCPGPAPTPTPG)-3') Mass: 2457.627 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: 159076.234 Da / Num. of mol.: 1 Mutation: D10A, C80L, C574E, H840A, D1135V, G1218R, R1335E, 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: 159076.234 Da / Num. of mol.: 1
Mutation: D10A, C80L, C574E, H840A, D1135V, G1218R, R1335E, 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, 627 molecules

#5: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 10 / 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.: 5 / 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.: 608 / 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: 2.77 Å³/Da / Density % sol: 55.67 %
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→49.011 Å / Num. obs: 103625 / % possible obs: 94.7 % / Redundancy: 2.4 % / Net I/σ(I): 11.2
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→49.011 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.77

	R_factor	Num. reflection	% reflection
R_free	0.2233	5152	4.97 %
R_work	0.204	-	-
obs	0.205	103608	94.47 %

Solvent computation

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

Displacement parameters

B_iso max: 143.15 Å² / B_iso mean: 56.6207 Å² / B_iso min: 22.04 Å²

Refinement step

Cycle: final / Resolution: 2.2→49.011 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10499	2464	37	608	13608
B_iso mean	-	-	51.6	44.07	-
Num. residues	-	-	-	-	1443

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	13464
X-RAY DIFFRACTION	f_angle_d	0.434	18721
X-RAY DIFFRACTION	f_chiral_restr	0.034	2179
X-RAY DIFFRACTION	f_plane_restr	0.002	1972
X-RAY DIFFRACTION	f_dihedral_angle_d	15.821	7826

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	0.3485	181	0.2989	3332	3513	96
2.225-2.2512	0.2902	170	0.2912	3287	3457	95
2.2512-2.2786	0.3356	164	0.2854	3292	3456	95
2.2786-2.3075	0.3011	169	0.2753	3298	3467	95
2.3075-2.3378	0.2844	185	0.2638	3223	3408	95
2.3378-2.3699	0.2467	154	0.253	3275	3429	94
2.3699-2.4037	0.2633	200	0.2578	3210	3410	94
2.4037-2.4396	0.2663	167	0.2576	3194	3361	92
2.4396-2.4777	0.2993	150	0.2545	2901	3051	85
2.4777-2.5183	0.287	183	0.2605	3106	3289	91
2.5183-2.5618	0.268	178	0.2425	3347	3525	97
2.5618-2.6084	0.2576	165	0.243	3314	3479	97
2.6084-2.6585	0.2783	183	0.2412	3361	3544	97
2.6585-2.7128	0.2786	167	0.234	3379	3546	97
2.7128-2.7718	0.2805	185	0.2363	3298	3483	96
2.7718-2.8362	0.2366	161	0.2268	3287	3448	96
2.8362-2.9072	0.279	181	0.2341	3354	3535	96
2.9072-2.9857	0.2484	167	0.2363	3284	3451	95
2.9857-3.0736	0.2647	169	0.2317	3254	3423	94
3.0736-3.1728	0.2138	128	0.2292	3223	3351	91
3.1728-3.2862	0.2321	164	0.2146	3053	3217	88
3.2862-3.4177	0.2381	177	0.2017	3386	3563	98
3.4177-3.5732	0.2275	180	0.1947	3356	3536	97
3.5732-3.7615	0.1977	178	0.1869	3397	3575	97
3.7615-3.9971	0.2023	174	0.1739	3366	3540	96
3.9971-4.3055	0.1817	166	0.1714	3349	3515	95
4.3055-4.7385	0.177	177	0.159	3091	3268	89
4.7385-5.4234	0.1588	180	0.1659	3405	3585	97
5.4234-6.83	0.1962	175	0.1829	3445	3620	97
6.83-49.0234	0.1952	174	0.1748	3389	3563	93

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	0.716	-0.5364	-0.4816	4.604	2.4912	6.4557	-0.1977	0.2266	-0.4429	0.8623	0.2303	0.1679	0.9235	-0.2959	-0.0277	0.6891	0.0036	0.0335	0.4972	-0.0408	0.5159	-10.9053	4.5152	72.1057
2	1.2436	0.0804	-0.4628	0.593	0.2288	2.0083	0.053	-0.0204	0.0901	0.1605	0.0065	-0.0381	0.4166	0.0314	-0.0346	0.3298	-0.0692	0.0036	0.289	-0.0371	0.3347	8.7036	3.447	31.6962
3	1.8641	-2.7907	-0.189	4.2038	0.1215	9.8402	0.4971	0.1567	0.0903	-0.9586	0.5162	-0.1625	0.8079	-0.2262	-0.9838	1.1386	0.1355	-0.0153	1.1035	-0.1034	0.5507	23.9617	-15.7218	-2.3915
4	3.9228	-0.4668	-0.258	3.9216	-0.4406	1.6968	0.0195	-0.1723	-0.0966	0.0669	0.6099	-0.1376	0.5216	0.1013	-0.6033	1.2251	0.0709	-0.0107	0.8334	-0.1557	0.6023	21.6273	-19.4279	6.062
5	1.5983	0.15	0.1709	0.2707	-0.257	0.5362	0.08	0.0153	0.1203	0.0187	-0.0306	0.1177	0.0464	-0.0378	-0.0543	0.2865	-0.0915	-0.0049	0.3017	-0.0367	0.3122	-3.113	9.7784	29.8308
6	1.3678	1.1933	-0.7279	1.935	-0.7141	1.6478	0.2857	-0.3986	0.3424	0.3166	-0.6917	-0.6744	-0.9712	0.4762	0.3908	0.989	-0.3322	0.0882	0.7963	0.1428	1.0848	-37.6929	15.2448	36.9723
7	0.4523	-0.1057	-0.0501	0.2731	-0.0553	0.6903	-0.0101	-0.1342	-0.0303	0.2004	-0.0059	-0.1221	0.0325	0.2349	0.0117	0.4207	-0.0645	-0.0649	0.3477	-0.0116	0.3649	11.3379	6.7289	51.0973
8	1.1856	0.7976	0.8514	1.8951	0.4518	1.2861	-0.1527	-0.0729	0.0325	0.4523	0.2176	-0.2024	-0.2402	-0.0028	-0.0492	0.579	0.0703	0.0394	0.3684	-0.0727	0.389	-11.0484	19.1865	69.2408
9	2.539	-2.1499	0.669	2.4627	-0.4835	1.1263	-0.1504	-0.3054	0.2168	0.3518	0.2399	-0.6125	0.2554	0.0743	-0.0982	0.6357	-0.0027	-0.0514	0.4735	-0.0775	0.6538	-11.7351	-12.7135	66.993
10	1.2264	0.0334	-0.4414	0.5772	-0.0485	0.8758	-0.122	-0.0227	-0.2414	0.081	0.132	0.0718	0.2844	-0.0809	-0.0041	0.3897	-0.1398	0.015	0.3288	-0.0242	0.3756	-28.908	-13.7186	39.7372
11	1.1857	0.8591	-0.2834	3.4076	0.2785	1.5767	0.133	0.3049	-0.728	-0.1918	-0.04	-0.0361	0.4753	0.0209	-0.0713	0.4947	-0.0705	-0.0079	0.4435	-0.1169	0.5724	-8.8025	-15.4646	24.8411
12	0.8438	-0.4612	-1.1901	1.0526	0.3057	2.0314	-0.201	-0.2637	-0.0675	0.4072	0.2504	0.2406	0.5747	0.0339	0.0068	0.6485	-0.0689	0.0412	0.5396	0.0204	0.3884	-6.8463	4.9579	65.268
13	2.1978	-0.8038	0.9555	2.6871	-1.5252	1.0514	0.2641	0.6768	-0.729	-0.7063	-0.0283	-0.7541	0.6363	-0.0728	-0.2205	0.6309	-0.161	0.1436	0.4325	-0.249	0.7006	-11.0607	-15.3377	20.3046

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 35 )	A	31 - 35
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 36 through 40 )	A	36 - 40
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 41 through 70 )	A	41 - 70
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 71 through 81 )	A	71 - 81
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 3 through 625 )	B	3 - 625
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 626 through 750 )	B	626 - 750
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 751 through 953 )	B	751 - 953
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 954 through 1366 )	B	954 - 1366
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 1 through 10 )	C	1 - 10
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 11 through 28 )	C	11 - 28
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 5 through 12 )	D	5 - 12

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