PDB-5fw2: Crystal structure of SpCas9 variant EQR bound to sgRNA and TGAG P...

ID or keywords:

Entry

Database: PDB / ID: 5fw2

Title

Crystal structure of SpCas9 variant EQR bound to sgRNA and TGAG PAM target DNA

Components

CRISPR-ASSOCIATED ENDONUCLEASE CAS9/CSN1
NON-TARGET DNA STRAND
SGRNASubgenomic mRNA
TARGET DNA STRAND

Keywords

HYDROLASE/DNA/RNA / HYDROLASE-DNA-RNA COMPLEX /

CRISPR /

CAS9 /

ENDONUCLEASE / PAM /

GENOME EDITING / RNP / PROTEIN-RNA 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 (bacteria)
SYNTHETIC CONSTRUCT (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.676 Å

Authors

Anders, C. / Bargsten, K. / Jinek, M.

Citation

Journal: Mol.Cell / Year: 2016
Title: Structural Plasticity of Pam Recognition by Engineered Variants of the RNA-Guided Endonuclease Cas9.
Authors: Anders, C. / Bargsten, K. / Jinek, M.

History

Deposition	Feb 11, 2016	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 15, 2016	Provider: repository / Type: Initial release
Revision 2.0	Oct 23, 2019	Group: Atomic model / Data collection / Other / Category: atom_site / pdbx_database_status Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_database_status.status_code_sf
Revision 2.1	Jan 10, 2024	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 / struct_site 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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5fw2.cif.gz	953.2 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fw/5fw2 ftp://data.pdbj.org/pub/pdb/validation_reports/fw/5fw2	HTTPS FTP

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Related structure data

Related structure data	5fw1C 5fw3C 4un3S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6k4q-d 6k57-d 6k4p-d 5fw3-d 5b2t-d 5b2s-d 5fq5-d 4un5-d 5b2r-d 6k3z-d 6k4u-d 5fw1-d 4un3-d 6k4s-d 6ai6-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: SGRNA

B: CRISPR-ASSOCIATED ENDONUCLEASE CAS9/CSN1

C: TARGET DNA STRAND

D: NON-TARGET DNA STRAND

hetero molecules

198 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)	177.740, 68.240, 188.220
Angle α, β, γ (deg.)	90.00, 110.95, 90.00
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 STRAND Mass: 8543.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#4: DNA chain	NON-TARGET DNA STRAND Mass: 3734.479 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)

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RNA chain / Protein , 2 types, 2 molecules AB

#1: RNA chain	SGRNA / Subgenomic mRNA Mass: 26788.984 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#2: Protein	CRISPR-ASSOCIATED ENDONUCLEASE CAS9/CSN1 / CAS9 EQR VARIANT / SPCAS9 Mass: 158916.062 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOCOCCUS PYOGENES (bacteria) / Strain: M1 / Plasmid: PEC-K-MBP / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA 2 References: UniProt: Q99ZW2, Hydrolases; Acting on ester bonds

#1: RNA chain

SGRNA /

Subgenomic mRNA

Mass: 26788.984 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)

#2: Protein

CRISPR-ASSOCIATED ENDONUCLEASE CAS9/CSN1 / CAS9 EQR VARIANT / SPCAS9

Mass: 158916.062 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

STREPTOCOCCUS PYOGENES (bacteria) / Strain: M1 / Plasmid: PEC-K-MBP / Production host:

ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA 2
References: UniProt: Q99ZW2,

Hydrolases; Acting on ester bonds

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Non-polymers , 3 types, 216 molecules

#5: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: K
#7: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H₂O

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Details

Sequence details	THE N-TERMINAL GAAS SEQUENCE IS DERIVED FROM THE EXPRESSION VECTOR. THE D10A AND H840A MUTATIONS ...THE N-TERMINAL GAAS SEQUENCE IS DERIVED FROM THE EXPRESSION VECTOR. THE D10A AND H840A MUTATIONS WERE ENGINEERED TO PRODUCE A CATALYTICALLY INACTIVE PROTEIN. THE D1135E, R1335Q, T1337R MUTATIONS ARE SPECIFIC FOR THE EWR ENGINEERED VARIANT OF THE PROTEIN.

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.57 Å³/Da / Density % sol: 52 % / Description: NONE
Crystal grow	pH: 8.5 / Details: 0.1 M TRIS PH 8.5 0.3M KSCN 15% (W/V) PEG 3400

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
Detector	Type: DECTRIS PILATUS / Detector: PIXEL / Date: Aug 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: 2.68→48.25 Å / Num. obs: 59682 / % possible obs: 99.3 % / Observed criterion σ(I): 2.2 / Redundancy: 7 % / B_iso Wilson estimate: 44.21 Å² / R_merge(I) obs: 0.12 / Net I/σ(I): 13.2
Reflection shell	Resolution: 2.68→2.75 Å / Redundancy: 6.5 % / R_merge(I) obs: 0.77 / Mean I/σ(I) obs: 2.2 / % possible all: 91.7

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4UN3

4un3

Resolution: 2.676→48.251 Å / SU ML: 0.34 / σ(F): 1.11 / Phase error: 25.28 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.231	5799	5 %
R_work	0.205	-	-
obs	0.2064	59668	99.36 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.676→48.251 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10764	2526	12	204	13506

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.012	13837
X-RAY DIFFRACTION	f_angle_d	0.658	19105
X-RAY DIFFRACTION	f_dihedral_angle_d	16.408	8091
X-RAY DIFFRACTION	f_chiral_restr	0.04	2182
X-RAY DIFFRACTION	f_plane_restr	0.003	2004

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.6762-2.7066	0.4192	160	0.3605	3082	X-RAY DIFFRACTION	82
2.7066-2.7384	0.3579	196	0.3027	3688	X-RAY DIFFRACTION	100
2.7384-2.7718	0.3523	185	0.2862	3675	X-RAY DIFFRACTION	100
2.7718-2.8069	0.2639	196	0.2642	3680	X-RAY DIFFRACTION	100
2.8069-2.8438	0.2948	188	0.2597	3698	X-RAY DIFFRACTION	100
2.8438-2.8828	0.2956	201	0.2607	3724	X-RAY DIFFRACTION	100
2.8828-2.9239	0.2947	197	0.2723	3599	X-RAY DIFFRACTION	100
2.9239-2.9676	0.3027	202	0.2756	3792	X-RAY DIFFRACTION	100
2.9676-3.014	0.2884	199	0.2709	3598	X-RAY DIFFRACTION	100
3.014-3.0634	0.2802	194	0.2743	3735	X-RAY DIFFRACTION	100
3.0634-3.1162	0.3016	181	0.2587	3656	X-RAY DIFFRACTION	100
3.1162-3.1728	0.3008	200	0.2603	3701	X-RAY DIFFRACTION	100
3.1728-3.2338	0.2407	198	0.2345	3674	X-RAY DIFFRACTION	100
3.2338-3.2998	0.2325	192	0.2166	3699	X-RAY DIFFRACTION	100
3.2998-3.3716	0.2503	193	0.2165	3650	X-RAY DIFFRACTION	100
3.3716-3.45	0.2521	195	0.2168	3706	X-RAY DIFFRACTION	100
3.45-3.5362	0.2379	195	0.2136	3714	X-RAY DIFFRACTION	100
3.5362-3.6318	0.246	203	0.2121	3684	X-RAY DIFFRACTION	100
3.6318-3.7386	0.2448	184	0.1949	3611	X-RAY DIFFRACTION	100
3.7386-3.8593	0.1602	203	0.1879	3756	X-RAY DIFFRACTION	100
3.8593-3.9971	0.2373	190	0.1774	3722	X-RAY DIFFRACTION	100
3.9971-4.1571	0.2062	194	0.1763	3650	X-RAY DIFFRACTION	100
4.1571-4.3462	0.2081	193	0.1761	3686	X-RAY DIFFRACTION	100
4.3462-4.5751	0.1795	199	0.1698	3707	X-RAY DIFFRACTION	100
4.5751-4.8615	0.1954	195	0.1564	3685	X-RAY DIFFRACTION	100
4.8615-5.2365	0.1761	196	0.1582	3706	X-RAY DIFFRACTION	100
5.2365-5.7627	0.2138	188	0.1651	3626	X-RAY DIFFRACTION	100
5.7627-6.5947	0.2265	195	0.1853	3716	X-RAY DIFFRACTION	100
6.5947-8.3018	0.1841	197	0.1786	3683	X-RAY DIFFRACTION	100
8.3018-48.2587	0.2025	190	0.1903	3687	X-RAY DIFFRACTION	99

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	0.6832	0.3207	-0.2777	0.3639	-0.0296	0.8623	0.0582	0.107	0.0523	0.0524	-0.0094	-0.0384	-0.0108	0.2164	-0.027	0.214	-0.0583	-0.0093	0.2244	-0.0178	0.2372	116.8436	65.7164	213.2802
2	1.0687	0.2349	0.0412	0.9014	-0.7587	1.6832	0.0991	0.2668	-0.2293	0.3276	-0.1948	0.1717	-0.2774	-0.234	0.0688	0.5808	0.0013	-0.0049	0.5856	-0.0968	0.6076	137.4806	58.7899	238.8243
3	1.1112	-0.3282	-0.2812	0.2333	-0.149	1.761	-0.047	-0.2442	-0.0751	0.0246	0.1265	0.0475	0.1195	0.6189	-0.0113	0.1689	-0.0495	-0.0344	0.2983	-0.0425	0.2723	126.1077	64.7842	215.2777
4	1.2159	0.3558	0.3635	1.4148	-0.6116	1.5201	0.0086	-0.2608	-0.0647	0.5645	0.05	-0.1308	-0.4738	-0.1949	-0.042	0.5465	0.0916	-0.035	0.2386	-0.0417	0.305	107.2689	78.2964	256.7991
5	1.2146	-0.5873	0.3668	0.6571	-0.1518	0.8524	-0.0775	-0.1057	0.0023	0.182	0.061	-0.1146	0.2129	-0.0021	-0.0029	0.3915	-0.0477	-0.0032	0.2785	-0.0415	0.3533	95.8107	47.5543	240.0558
6	0.9995	0.0875	-0.3119	0.4391	0.0649	0.8247	-0.1543	0.1654	-0.1532	0.0468	0.0565	0.0307	0.39	-0.2667	0.0521	0.3402	-0.1649	0.039	0.2662	-0.0993	0.2947	81.9847	46.3689	214.1503
7	0.2999	-0.1392	0.112	0.4163	-0.0812	1.7711	0.0367	-0.0725	0.1315	0.1212	0.1831	-0.0551	0.3799	-0.0546	-0.1529	0.2444	-0.0465	-0.0172	0.223	-0.0584	0.2595	112.7494	63.3254	220.9742
8	1.95	0.6109	1.6864	0.7671	1.1225	2.9318	0.3298	0.4485	0.0063	-0.4091	0.1378	0.117	0.2937	-0.4117	-0.3819	1.1025	0.24	-0.074	0.911	-0.0879	0.4904	132.6861	42.0378	177.4513
9	0.724	0.2993	0.2557	0.2782	0.0082	1.1787	0.0307	0.053	0.0206	-0.028	0.0033	0.085	-0.0478	0.0205	-0.0429	0.1922	-0.0453	0.0001	0.2035	-0.0131	0.2221	107.5409	69.1726	205.8033
10	1.7364	1.7334	0.8087	1.7301	0.7918	0.3818	0.1775	-0.4268	0.4357	0.0567	-0.4345	-0.6128	-0.7239	0.8865	0.2107	0.7738	-0.1739	0.0581	0.851	-0.0138	0.8887	72.735	74.451	212.8298
11	0.4005	0.7406	-0.9551	3.7663	-0.3804	3.3034	0.1593	0.2881	-0.3879	-0.027	0.1325	-0.0815	0.193	-0.5652	-0.183	0.6409	-0.3181	0.108	0.9691	-0.1934	0.5588	95.3283	37.6868	194.7606
12	2.7316	1.9516	-0.5496	2.2082	-0.771	0.3005	0.0216	0.2581	-0.6567	0.1365	0.0159	-0.33	0.3621	0.1206	-0.1035	0.2994	0.0029	-0.0736	0.3108	-0.041	0.3169	108.087	49.8957	206.7579
13	2.1577	0.4207	-0.589	0.4374	-0.5169	0.833	-0.1404	-0.2057	0.0334	0.2508	0.0548	0.1317	0.5382	0.0327	0.0661	0.3554	-0.0956	-0.0087	0.3565	0.0284	0.2491	109.6038	66.3572	231.0474
14	1.2644	0.2721	0.2601	0.146	-0.3919	2.9362	-0.0917	-0.1904	0.097	0.0136	0.1637	0.5964	0.1871	-0.5608	-0.0808	0.4958	0.0412	0.0155	0.5129	0.1324	0.4541	95.8423	62.2088	254.349
15	2.997	-0.0561	-0.3486	3.3981	0.9659	3.8233	-0.1135	0.2263	-0.7818	0.029	0.2934	-0.4924	0.588	0.4953	-0.2203	0.4799	-0.1133	0.0923	0.4013	-0.1179	0.4629	99.8492	44.898	201.6128

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'B' AND (RESID 3 THROUGH 207 )
2	X-RAY DIFFRACTION	2	CHAIN 'B' AND (RESID 208 THROUGH 315 )
3	X-RAY DIFFRACTION	3	CHAIN 'B' AND (RESID 316 THROUGH 512 )
4	X-RAY DIFFRACTION	4	CHAIN 'B' AND (RESID 513 THROUGH 730 )
5	X-RAY DIFFRACTION	5	CHAIN 'B' AND (RESID 731 THROUGH 980 )
6	X-RAY DIFFRACTION	6	CHAIN 'B' AND (RESID 981 THROUGH 1365 )
7	X-RAY DIFFRACTION	7	CHAIN 'A' AND (RESID 1 THROUGH 30 )
8	X-RAY DIFFRACTION	8	CHAIN 'A' AND (RESID 31 THROUGH 40 )
9	X-RAY DIFFRACTION	9	CHAIN 'A' AND (RESID 41 THROUGH 70 )
10	X-RAY DIFFRACTION	10	CHAIN 'A' AND (RESID 71 THROUGH 81 )
11	X-RAY DIFFRACTION	11	CHAIN 'C' AND (RESID 1 THROUGH 5 )
12	X-RAY DIFFRACTION	12	CHAIN 'C' AND (RESID 6 THROUGH 10 )
13	X-RAY DIFFRACTION	13	CHAIN 'C' AND (RESID 11 THROUGH 20 )
14	X-RAY DIFFRACTION	14	CHAIN 'C' AND (RESID 21 THROUGH 28 )
15	X-RAY DIFFRACTION	15	CHAIN 'D' AND (RESID 2 THROUGH 12 )

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