PDB-4c8y: Cas6 (TTHA0078) substrate mimic complex

ID or keywords:

Entry

Database: PDB / ID: 4c8y

Title

Cas6 (TTHA0078) substrate mimic complex

Components

CAS6A
R1 REPEAT RNA SUBSTRATE MIMIC

Keywords

RNA BINDING PROTEIN/RNA / RNA BINDING PROTEIN-RNA COMPLEX / CRISPR CAS PROTEIN RNA / PROCESSING RIBONUCLEASE

Function / homology

Function and homology information

endonuclease activity / defense response to virus
Similarity search - Function

Biological species

THERMUS THERMOPHILUS (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Jinek, M. / Niewoehner, O. / Doudna, J.A.

Citation

Journal: Nucleic Acids Res. / Year: 2014
Title: Evolution of Crispr RNA Recognition and Processing by Cas6 Endonucleases.
Authors: Niewoehner, O. / Jinek, M. / Doudna, J.A.

History

Deposition	Oct 2, 2013	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 6, 2013	Provider: repository / Type: Initial release
Revision 1.1	Nov 20, 2013	Group: Atomic model
Revision 1.2	Feb 12, 2014	Group: Database references
Revision 1.3	May 1, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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	4c8y.cif.gz	301.3 KB	Display	PDBx/mmCIF format
PDB format	pdb4c8y.ent.gz	248.4 KB	Display	PDB format
PDBx/mmJSON format	4c8y.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4c8y_validation.pdf.gz	474 KB	Display	wwPDB validaton report
Full document	4c8y_full_validation.pdf.gz	480.9 KB	Display
Data in XML	4c8y_validation.xml.gz	23.9 KB	Display
Data in CIF	4c8y_validation.cif.gz	35.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/c8/4c8y ftp://data.pdbj.org/pub/pdb/validation_reports/c8/4c8y	HTTPS FTP

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Related structure data

Related structure data	4c8zC 4c97C 4c98C 4c9dC C: citing same article (ref.)
Similar structure data	4c8z-d 4ht3-d 6l4b-2 1l2g-2 3mgu-d 4o3z-d 1a5b-d 4rzg-d 5yu4-1 4kzj-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
Related items in Molecule of the Month	#121 - Jan 2010 70S Ribosomes similarity (1) #130 - Oct 2010 Riboswitches similarity (1) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1) #157 - Jan 2013 Transfer-Messenger RNA similarity (1) #181 - Jan 2015 Cascade and CRISPR similarity (1) #229 - Jan 2019 Fluorescent RNA Aptamers similarity (1) #253 - Jan 2021 Expressome similarity (1) #260 - Aug 2021 Ribonuclease P similarity (1) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (1) #15 - Mar 2001 Transfer RNA similarity (1) #249 - Sep 2020 SARS-CoV-2 RNA-dependent RNA Polymerase similarity (1) #10 - Oct 2000 Ribosome similarity (1) #210 - Jun 2017 Adenine Riboswitch in Action similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #105 - Sep 2008 Ribonuclease A similarity (1) #226 - Oct 2018 Aminoglycoside Antibiotics and Resistance similarity (1) #245 - May 2020 Spliceosomes similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #65 - May 2005 Self-splicing RNA similarity (1) #98 - Feb 2008 Small Interfering RNA similarity (1) #104 - Aug 2008 Selenocysteine Synthase similarity (1) #106 - Oct 2008 Poly(A) Polymerase similarity (1) #143 - Nov 2011 Toll-like Receptors similarity (1) #161 - May 2013 Ricin similarity (1) #227 - Nov 2018 Telomerase similarity (1) #230 - Feb 2019 Initiation Factor eIF4E similarity (1) #266 - Feb 2022 Oligosaccharyltransferase similarity (1) #81 - Sep 2006 Elongation Factors similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#121 - Jan 2010
70S Ribosomes
similarity (1)
#130 - Oct 2010
Riboswitches
similarity (1)
#16 - Apr 2001
Aminoacyl-tRNA Synthetases
similarity (1)
#157 - Jan 2013
Transfer-Messenger RNA
similarity (1)
#181 - Jan 2015
Cascade and CRISPR
similarity (1)
#229 - Jan 2019
Fluorescent RNA Aptamers
similarity (1)
#253 - Jan 2021
Expressome
similarity (1)
#260 - Aug 2021
Ribonuclease P
similarity (1)
#146 - Feb 2012
Aminoglycoside Antibiotics
similarity (1)
#15 - Mar 2001
Transfer RNA
similarity (1)
#249 - Sep 2020
SARS-CoV-2 RNA-dependent RNA Polymerase
similarity (1)
#10 - Oct 2000
Ribosome
similarity (1)
#210 - Jun 2017
Adenine Riboswitch in Action
similarity (1)
#87 - Mar 2007
Zinc Fingers
similarity (1)
#105 - Sep 2008
Ribonuclease A
similarity (1)
#226 - Oct 2018
Aminoglycoside Antibiotics and Resistance
similarity (1)
#245 - May 2020
Spliceosomes
similarity (1)
#262 - Oct 2021
Fifty Years of Open Access to PDB Structures
similarity (1)
#65 - May 2005
Self-splicing RNA
similarity (1)
#98 - Feb 2008
Small Interfering RNA
similarity (1)
#104 - Aug 2008
Selenocysteine Synthase
similarity (1)
#106 - Oct 2008
Poly(A) Polymerase
similarity (1)
#143 - Nov 2011
Toll-like Receptors
similarity (1)
#161 - May 2013
Ricin
similarity (1)
#227 - Nov 2018
Telomerase
similarity (1)
#230 - Feb 2019
Initiation Factor eIF4E
similarity (1)
#266 - Feb 2022
Oligosaccharyltransferase
similarity (1)
#81 - Sep 2006
Elongation Factors
similarity (1)
#89 - May 2007
Aconitase and Iron Regulatory Protein 1
similarity (1)
#241 - Jan 2020
Twenty Years of Molecules
similarity (1)

Deposited unit

A: CAS6A

B: CAS6A

C: R1 REPEAT RNA SUBSTRATE MIMIC

hetero molecules

58.5 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	43.070, 83.300, 73.440
Angle α, β, γ (deg.)	90.00, 101.41, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	CAS6A Mass: 26580.473 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / Plasmid: PEC-K-MBP / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA 2 / References: UniProt: Q5SM65
#2: RNA chain	R1 REPEAT RNA SUBSTRATE MIMIC Mass: 5160.160 Da / Num. of mol.: 1 / Fragment: REPEAT STEM-LOOP / Source method: obtained synthetically / Details: R1 REPEAT RNA SUBSTRATE MIMIC
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 380 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	N-TERMINAL GSSLD TAG DERIVED FROM EXPRESSION PLASMID

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.2 Å³/Da / Density % sol: 44 % / Description: NONE
Crystal grow	pH: 6.5 Details: 0.1 M BIS-TRIS PROPANE (PH 6.5), 18% (W/V) PEG 335, 0.3M SODIUM SULFATE

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.999951
Detector	Type: ADSC CCD / Detector: CCD / Date: Dec 20, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.999951 Å / Relative weight: 1
Reflection	Resolution: 1.8→72 Å / Num. obs: 46544 / % possible obs: 98.8 % / Observed criterion σ(I): 1.9 / Redundancy: 3.7 % / R_merge(I) obs: 0.06 / Net I/σ(I): 15.5
Reflection shell	Resolution: 1.8→1.9 Å / Redundancy: 3.6 % / R_merge(I) obs: 0.7 / Mean I/σ(I) obs: 1.9 / % possible all: 97.8

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE: 1.8.2_1309)	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: TTCAS6B STRUCTURE

Resolution: 1.8→71.988 Å / SU ML: 0.22 / σ(F): 1.99 / Phase error: 22.05 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2157	2347	5 %
R_work	0.1908	-	-
obs	0.192	46544	98.79 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.8→71.988 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3655	279	10	380	4324

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	4069
X-RAY DIFFRACTION	f_angle_d	1.114	5584
X-RAY DIFFRACTION	f_dihedral_angle_d	13.547	1543
X-RAY DIFFRACTION	f_chiral_restr	0.055	609
X-RAY DIFFRACTION	f_plane_restr	0.005	683

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 (%)
1.8-1.8368	0.292	123	0.3191	2479	X-RAY DIFFRACTION	95
1.8368-1.8767	0.2926	152	0.2752	2617	X-RAY DIFFRACTION	100
1.8767-1.9204	0.2738	155	0.2565	2567	X-RAY DIFFRACTION	100
1.9204-1.9684	0.2692	146	0.2431	2606	X-RAY DIFFRACTION	100
1.9684-2.0216	0.2341	130	0.2213	2610	X-RAY DIFFRACTION	100
2.0216-2.0811	0.2396	142	0.2238	2617	X-RAY DIFFRACTION	100
2.0811-2.1483	0.2384	150	0.2046	2626	X-RAY DIFFRACTION	99
2.1483-2.2251	0.2635	143	0.2036	2603	X-RAY DIFFRACTION	99
2.2251-2.3142	0.222	113	0.2005	2608	X-RAY DIFFRACTION	99
2.3142-2.4195	0.2024	126	0.19	2614	X-RAY DIFFRACTION	99
2.4195-2.5471	0.2222	148	0.1834	2587	X-RAY DIFFRACTION	99
2.5471-2.7066	0.21	155	0.1854	2592	X-RAY DIFFRACTION	99
2.7066-2.9156	0.2097	147	0.1895	2560	X-RAY DIFFRACTION	98
2.9156-3.209	0.2107	125	0.1828	2594	X-RAY DIFFRACTION	98
3.209-3.6734	0.1954	122	0.1733	2632	X-RAY DIFFRACTION	98
3.6734-4.628	0.1667	129	0.1551	2619	X-RAY DIFFRACTION	98
4.628-72.0454	0.2156	141	0.1796	2666	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	0.0689	0.0642	0.0377	0.1654	-0.0261	0.1734	-0.0407	0.1362	0.2784	-0.2994	0.0774	0.1589	-0.2412	-0.089	-0.0027	0.3022	-0.0059	0.0324	0.1533	-0.0103	0.2007	7.7817	32.1212	-0.6922
2	0.0248	-0.0191	0.0211	0.0362	-0.0056	0.0212	-0.0094	0.0381	0.3855	-0.1013	-0.0059	0.301	-0.0483	-0.1223	0.0006	0.2328	-0.0476	-0.027	0.2773	-0.0006	0.3966	-2.7418	31.1551	3.1696
3	0.1171	-0.0273	-0.1415	0.2458	0.1918	0.3035	-0.021	-0.0113	-0.0179	-0.302	-0.0148	-0.1053	-0.3233	-0.1898	-0.0037	0.2942	-0.0374	0.0229	0.2338	0.0211	0.1526	7.2629	29.8025	-5.0683
4	0.9521	-0.1332	0.41	0.2278	-0.0248	0.1937	0.0683	0.3752	-0.0658	-0.2348	0.0814	-0.0318	-0.3021	0.2707	0.113	0.3139	-0.0532	0.0805	0.28	0.0227	0.1627	14.4116	27.6099	-5.5595
5	0.474	-0.0059	-0.2107	0.0079	0.005	0.0913	-0.0112	0.2312	0.023	0.0078	0.0363	-0.1166	0.2787	-0.2255	-0.0757	0.5211	-0.1506	-0.1047	0.2576	-0.0382	0.1621	4.4613	7.6306	4.5312
6	0.9081	-0.0182	-0.2269	0.2795	0.1342	0.1459	0.0783	-0.175	0.1684	-0.0691	0.0869	0.0717	0.2714	-0.1946	0.0649	0.2342	0.0015	-0.0323	0.1873	-0.0116	0.1486	8.4325	23.986	19.8446
7	0.0426	-0.1057	-0.0075	0.2513	0.0271	0.0041	0.0616	0.0864	0.0819	0.077	0.0693	0.1162	0.1236	-0.245	0.0533	0.2325	-0.1476	-0.0175	0.3678	0.0563	0.2004	-0.5588	17.6805	14.8418
8	0.0324	-0.06	-0.0235	0.1374	0.036	0.0267	-0.0263	-0.1838	-0.1245	0.2872	-0.081	0.0737	0.1871	-0.1	-0.1987	0.5676	-0.5135	0.0333	0.667	0.4253	0.075	-3.5002	8.7805	18.1446
9	0.3993	-0.066	0.0442	0.2514	0.0027	0.0378	0.0885	-0.1496	0.2255	0.1179	-0.1277	-0.0426	0.1062	-0.0563	0.0018	0.2472	0.002	-0.0181	0.1764	-0.0108	0.1711	14.0766	26.3388	20.4103
10	0.9447	0.278	-0.2699	0.2178	0.0533	0.2568	0.1543	0.042	0.0065	0.1352	-0.0109	-0.0433	0.4588	-0.0515	0.2581	0.3647	-0.0594	-0.0627	0.1839	-0.0041	0.081	11.3987	12.4212	19.9924
11	0.6006	-0.3702	-0.2477	0.5661	0.049	0.2221	0.143	-0.045	-0.0548	-0.032	-0.0014	-0.0989	0.3756	-0.319	0.3162	0.3247	-0.0672	-0.0532	0.2076	0.0099	0.145	6.6671	16.3042	10.2999
12	0.1396	0.0471	-0.0211	0.3257	-0.0048	0.1626	0.1689	-0.0106	-0.2455	-0.0599	0.0133	-0.0999	-0.1178	-0.0454	0.0961	0.1065	-0.0221	0.0104	0.1862	0.0177	0.1945	33.1164	17.3904	48.0287
13	0.5783	-0.1896	0.1184	0.2937	0.1295	0.1666	0.1934	-0.075	-0.3286	0.0114	-0.0832	0.0385	0.0366	0.0029	0.187	0.1361	-0.0374	-0.0095	0.1679	0.042	0.2109	28.3128	12.2508	48.2541
14	0.4007	0.3852	0.105	0.4007	0.1447	0.2702	0.055	-0.1681	0.0523	0.1761	-0.0222	-0.2059	-0.0595	0.0043	0.0021	0.1725	-0.0299	-0.0076	0.1913	0.0264	0.1641	30.1561	20.9945	51.8523
15	0.0983	-0.0136	-0.0168	0.0166	-0.0141	0.0726	-0.0471	0.1348	-0.0431	0.0084	0.0071	0.0867	-0.0458	-0.0341	-0.0001	0.1543	-0.0101	-0.0033	0.161	-0.0077	0.1926	15.3386	17.4142	33.6864
16	0.0504	-0.1394	-0.0075	0.4726	0.0336	0.0756	0.0942	-0.2522	-0.053	-0.1135	-0.0559	0.2352	-0.0182	-0.0659	0.0003	0.1134	-0.026	0.0097	0.1672	0.0064	0.1604	10.3808	20.944	43.4753
17	0.2587	0.015	0.0074	1.105	-0.1534	0.0292	0.0566	-0.0582	0.1735	-0.0294	-0.0584	0.6926	0.1173	0.0741	-0.0753	0.1347	0.0075	0.0652	0.2038	0.0431	0.3541	3.5132	27.4719	43.5297
18	0.1264	-0.1281	-0.0591	0.3767	0.0257	0.0875	0.1228	0.33	-0.1968	-0.124	-0.1624	-0.0191	-0.0036	0.0336	-0.0072	0.2016	0.0095	-0.0336	0.1524	-0.0207	0.1938	20.2933	16.3914	28.8728
19	0.1322	0.0973	-0.0114	0.0748	-0.0209	0.0514	-0.0164	0.1702	-0.0652	-0.2203	0.0499	0.2101	-0.1328	0.0192	0.0021	0.1578	0.0258	-0.0076	0.1829	0.0071	0.1719	13.4234	29.0769	32.6307
20	0.0254	0.0332	-0.0119	0.0951	-0.0806	0.057	0.1516	-0.1135	-0.0271	-0.0495	-0.0372	0.0383	-0.0329	0.0016	0.0111	0.1291	-0.013	0.0172	0.143	0.0046	0.1615	17.6509	24.8647	42.9671
21	0.053	-0.0583	0.0233	0.0701	-0.0437	0.0865	-0.1289	-0.0761	-0.26	-0.0183	-0.2323	0.1937	0.103	-0.0957	-0.0293	0.5118	-0.1217	-0.1658	0.7979	0.2705	1.6027	-5.5088	38.6182	20.8989
22	0.0195	-0.0392	-0.0142	0.1825	0.0872	0.039	0.1012	-0.161	0.1937	-0.1227	-0.0313	0.0434	-0.1289	0.02	0.0611	0.3853	0.0751	0.0308	0.7159	0.2607	1.2785	-3.5117	31.9734	14.4852

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESID 1 THROUGH 29 )
2	X-RAY DIFFRACTION	2	CHAIN A AND (RESID 30 THROUGH 49 )
3	X-RAY DIFFRACTION	3	CHAIN A AND (RESID 50 THROUGH 85 )
4	X-RAY DIFFRACTION	4	CHAIN A AND (RESID 86 THROUGH 101 )
5	X-RAY DIFFRACTION	5	CHAIN A AND (RESID 102 THROUGH 116 )
6	X-RAY DIFFRACTION	6	CHAIN A AND (RESID 117 THROUGH 139 )
7	X-RAY DIFFRACTION	7	CHAIN A AND (RESID 140 THROUGH 154 )
8	X-RAY DIFFRACTION	8	CHAIN A AND (RESID 155 THROUGH 170 )
9	X-RAY DIFFRACTION	9	CHAIN A AND (RESID 171 THROUGH 189 )
10	X-RAY DIFFRACTION	10	CHAIN A AND (RESID 190 THROUGH 204 )
11	X-RAY DIFFRACTION	11	CHAIN A AND (RESID 205 THROUGH 238 )
12	X-RAY DIFFRACTION	12	CHAIN B AND (RESID 0 THROUGH 17 )
13	X-RAY DIFFRACTION	13	CHAIN B AND (RESID 18 THROUGH 63 )
14	X-RAY DIFFRACTION	14	CHAIN B AND (RESID 64 THROUGH 116 )
15	X-RAY DIFFRACTION	15	CHAIN B AND (RESID 117 THROUGH 139 )
16	X-RAY DIFFRACTION	16	CHAIN B AND (RESID 140 THROUGH 154 )
17	X-RAY DIFFRACTION	17	CHAIN B AND (RESID 155 THROUGH 171 )
18	X-RAY DIFFRACTION	18	CHAIN B AND (RESID 172 THROUGH 189 )
19	X-RAY DIFFRACTION	19	CHAIN B AND (RESID 190 THROUGH 204 )
20	X-RAY DIFFRACTION	20	CHAIN B AND (RESID 205 THROUGH 237 )
21	X-RAY DIFFRACTION	21	CHAIN C AND (RESID 15 THROUGH 20 )
22	X-RAY DIFFRACTION	22	CHAIN C AND (RESID 21 THROUGH 30 )

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