PDB-4qyz: Crystal structure of a CRISPR RNA-guided surveillance complex, Ca...

ID or keywords:

Entry

Database: PDB / ID: 4qyz

Title

Crystal structure of a CRISPR RNA-guided surveillance complex, Cascade, bound to a ssDNA target

Components

(CRISPR system Cascade subunit ...) x 5
DNA (33-MER)
RNA (55-MER)

Keywords

IMMUNE SYSTEM/DNA/RNA / CRISPR-Associated / Bacterial Immunity /

Cas3 /

IMMUNE SYSTEM-DNA-RNA complex

Function / homology

Function and homology information

CRISPR-cas system / DNA/RNA hybrid binding / maintenance of CRISPR repeat elements /

RNA processing / RNA endonuclease activity / defense response to virus /

Hydrolases; Acting on ester bonds /

nucleic acid binding / protein-containing complex /

DNA binding ...
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Enterobacteria phage lambda (virus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 3.0303 Å

Authors

Mulepati, S. / Bailey, S.

Citation

Journal: Science / Year: 2014
Title: Structural biology. Crystal structure of a CRISPR RNA-guided surveillance complex bound to a ssDNA target.
Authors: Mulepati, S. / Heroux, A. / Bailey, S.

History

Deposition	Jul 26, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 3, 2014	Provider: repository / Type: Initial release
Revision 1.1	Oct 1, 2014	Group: Database references

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4qyz.cif.gz	1.3 MB	Display	PDBx/mmCIF format
PDB format	pdb4qyz.ent.gz	1.1 MB	Display	PDB format
PDBx/mmJSON format	4qyz.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qy/4qyz ftp://data.pdbj.org/pub/pdb/validation_reports/qy/4qyz	HTTPS FTP

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Related structure data

Similar structure data	4tvx-2 5h9e-d 5u07-d 4u7u-3 5u0a-d 5t5m-1 5cd4-2 4u7u-2 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	#181 - Jan 2015 Cascade and CRISPR similarity (23) #253 - Jan 2021 Expressome similarity (2) #121 - Jan 2010 70S Ribosomes similarity (1) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1) #130 - Oct 2010 Riboswitches similarity (1) #157 - Jan 2013 Transfer-Messenger RNA similarity (1) #67 - Jul 2005 TATA-Binding Protein similarity (1) #229 - Jan 2019 Fluorescent RNA Aptamers similarity (1) #168 - Dec 2013 DNA Helicase similarity (1) #87 - Mar 2007 Zinc Fingers similarity (2) #91 - Jul 2007 Thymine Dimers similarity (1) #260 - Aug 2021 Ribonuclease P similarity (1) #255 - Mar 2021 Cisplatin and DNA similarity (1) #249 - Sep 2020 SARS-CoV-2 RNA-dependent RNA Polymerase similarity (1) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #227 - Nov 2018 Telomerase similarity (2) #122 - Feb 2010 Enhanceosome similarity (1) #15 - Mar 2001 Transfer RNA similarity (1) #84 - Dec 2006 Transposase similarity (1) #48 - Dec 2003 Catabolite Activator Protein similarity (1) #10 - Oct 2000 Ribosome similarity (1) #210 - Jun 2017 Adenine Riboswitch in Action similarity (1) #150 - Jun 2012 Sliding Clamps similarity (1) #135 - Mar 2011 Integrase similarity (1) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (1) #180 - Dec 2014 TAL Effectors similarity (1) #65 - May 2005 Self-splicing RNA 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) #98 - Feb 2008 Small Interfering RNA similarity (1) #73 - Jan 2006 Topoisomerase similarity (1) #40 - Apr 2003 RNA Polymerase similarity (1) #139 - Jul 2011 DNA Methyltransferase similarity (1) #155 - Nov 2012 Vitamin D Receptor similarity (1) #3 - Mar 2000 DNA Polymerase similarity (1) #161 - May 2013 Ricin similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1) #81 - Sep 2006 Elongation Factors similarity (1) #119 - Nov 2009 Designed DNA Crystal similarity (1) #266 - Feb 2022 Oligosaccharyltransferase similarity (1) #125 - May 2010 Parvoviruses similarity (1) #131 - Nov 2010 Inteins similarity (1) #230 - Feb 2019 Initiation Factor eIF4E similarity (1) #160 - Apr 2013 Actinomycin similarity (1) #190 - Oct 2015 Two-component Systems similarity (1) #23 - Nov 2001 DNA similarity (1) #7 - Jul 2000 Nucleosome similarity (1) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (1) #8 - Aug 2000 Restriction Enzymes similarity (1) #257 - May 2021 Fetal Hemoglobin similarity (1) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (1) #143 - Nov 2011 Toll-like Receptors similarity (1) #31 - Jul 2002 p53 Tumor Suppressor similarity (1) #106 - Oct 2008 Poly(A) Polymerase similarity (1) #33 - Sep 2002 HIV Reverse Transcriptase similarity (1) #104 - Aug 2008 Selenocysteine Synthase similarity (1) #39 - Mar 2003 lac Repressor similarity (1) #92 - Aug 2007 Anabolic Steroids similarity (1) #45 - Sep 2003 Estrogen Receptor similarity (1) #55 - Jul 2004 DNA Ligase similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (2)

PDB pages

PDBj /

wwPDB /

NCBI

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Deposited unit

A: CRISPR system Cascade subunit CasA

B: CRISPR system Cascade subunit CasB

C: CRISPR system Cascade subunit CasB

D: CRISPR system Cascade subunit CasC

E: CRISPR system Cascade subunit CasC

F: CRISPR system Cascade subunit CasC

G: CRISPR system Cascade subunit CasC

H: CRISPR system Cascade subunit CasC

I: CRISPR system Cascade subunit CasC

J: CRISPR system Cascade subunit CasD

K: CRISPR system Cascade subunit CasE

L: RNA (55-MER)

M: DNA (33-MER)

hetero molecules

413 kDa, 13 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)	223.869, 223.869, 290.651
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	152
Space group name H-M	P3₁21

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	2

/ NCS ensembles :

ID
1
2

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CRISPR system Cascade subunit ... , 5 types, 11 molecules ABCDEFGHIJK

#1: Protein	CRISPR system Cascade subunit CasA / CRISPR type I-E/Ecoli-associated protein CasA/Cse1 / CRISPR-associated protein CasA/Cse1 Mass: 55964.957 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: casA, cse1, ygcL, b2760, JW2730 / Production host: Escherichia coli (E. coli) / References: UniProt: Q46901
#2: Protein	CRISPR system Cascade subunit CasB Mass: 18728.525 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: casB, cse2, ygcK, b2759, JW2729 / Production host: Escherichia coli (E. coli) / References: UniProt: P76632
#3: Protein	CRISPR system Cascade subunit CasC Mass: 40071.402 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: casC, cas4, cse4, ygcJ, b2758, JW2728 / Production host: Escherichia coli (E. coli) / References: UniProt: Q46899
#4: Protein	CRISPR system Cascade subunit CasD Mass: 25239.803 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: casD, cas5, ygcI, b2757, JW5844 / Production host: Escherichia coli (E. coli) / References: UniProt: Q46898
#5: Protein	CRISPR system Cascade subunit CasE / CasE endoRNase / crRNA endonuclease Mass: 22324.002 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: casE, cas6e, ygcH, b2756, JW2726 / Production host: Escherichia coli (E. coli) References: UniProt: Q46897, Hydrolases; Acting on ester bonds

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RNA chain / DNA chain / Non-polymers , 3 types, 3 molecules LM

#6: RNA chain	RNA (55-MER) Mass: 19734.770 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: crRNA / Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#7: DNA chain	DNA (33-MER) Mass: 12185.856 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence is from lambda phage / Source: (synth.) Enterobacteria phage lambda (virus)
#8: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 5.09 Å³/Da / Density % sol: 75.82 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion / pH: 5 Details: 0.1 M sodium cacodylate, 0.1 M calcium acetate, 10% PEG 8,000, pH 5.0, VAPOR DIFFUSION, temperature 298K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.2131 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 20, 2014
Radiation	Monochromator: Liquid nitrogen-cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.2131 Å / Relative weight: 1
Reflection	Resolution: 3.03→39.473 Å / Num. all: 16404 / Num. obs: 163355 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3.7
Reflection shell	Resolution: 3.03→3.05 Å / % possible all: 96.4

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Processing

Software

Name	Version	Classification
Blu-Ice		data collection
SOLVE		phasing
PHENIX	(phenix.refine: 1.9_1692)	refinement
XDS		data reduction
Aimless		data scaling

Refinement

Method to determine structure:

SAD / Resolution: 3.0303→39.473 Å / SU ML: 0.48 / σ(F): 1.33 / Phase error: 27.49 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2672	7915	5.05 %
R_work	0.2235	-	-
obs	0.2257	156727	96.2 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3.0303→39.473 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	24694	1848	1	0	26543

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.012	27209
X-RAY DIFFRACTION	f_angle_d	1.524	37157
X-RAY DIFFRACTION	f_dihedral_angle_d	20.092	10295
X-RAY DIFFRACTION	f_chiral_restr	0.061	4183
X-RAY DIFFRACTION	f_plane_restr	0.007	4511

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 (%)
3.0303-3.0647	0.3618	260	0.322	4580	X-RAY DIFFRACTION	90
3.0647-3.1008	0.3483	284	0.3098	5005	X-RAY DIFFRACTION	99
3.1008-3.1386	0.3589	254	0.2962	5085	X-RAY DIFFRACTION	99
3.1386-3.1783	0.3313	275	0.2872	5059	X-RAY DIFFRACTION	99
3.1783-3.2201	0.3532	252	0.3045	5094	X-RAY DIFFRACTION	99
3.2201-3.2642	0.3878	271	0.3245	5090	X-RAY DIFFRACTION	99
3.2642-3.3108	0.3642	262	0.3119	5092	X-RAY DIFFRACTION	99
3.3108-3.3602	0.365	266	0.3038	5114	X-RAY DIFFRACTION	100
3.3602-3.4127	0.5165	250	0.4267	4415	X-RAY DIFFRACTION	87
3.4127-3.4686	0.562	220	0.4857	4027	X-RAY DIFFRACTION	78
3.4686-3.5283	0.3402	286	0.2923	5061	X-RAY DIFFRACTION	99
3.5283-3.5925	0.2841	285	0.2441	5074	X-RAY DIFFRACTION	99
3.5925-3.6615	0.4992	225	0.4183	4153	X-RAY DIFFRACTION	81
3.6615-3.7362	0.4766	230	0.4096	4330	X-RAY DIFFRACTION	84
3.7362-3.8174	0.299	252	0.2592	5109	X-RAY DIFFRACTION	100
3.8174-3.9061	0.5621	235	0.4475	4441	X-RAY DIFFRACTION	86
3.9061-4.0037	0.3164	243	0.2545	4599	X-RAY DIFFRACTION	90
4.0037-4.1118	0.2201	265	0.1787	5103	X-RAY DIFFRACTION	99
4.1118-4.2327	0.2171	283	0.1684	5110	X-RAY DIFFRACTION	99
4.2327-4.3691	0.1932	284	0.1554	5132	X-RAY DIFFRACTION	100
4.3691-4.5251	0.1861	250	0.1505	5136	X-RAY DIFFRACTION	99
4.5251-4.706	0.1694	252	0.1392	5145	X-RAY DIFFRACTION	100
4.706-4.9198	0.1674	312	0.1376	5115	X-RAY DIFFRACTION	100
4.9198-5.1786	0.1872	261	0.1504	5190	X-RAY DIFFRACTION	100
5.1786-5.5023	0.2128	288	0.1628	5170	X-RAY DIFFRACTION	100
5.5023-5.9258	0.2327	278	0.173	5207	X-RAY DIFFRACTION	100
5.9258-6.5198	0.2122	233	0.1751	5229	X-RAY DIFFRACTION	100
6.5198-7.4577	0.2167	273	0.175	5274	X-RAY DIFFRACTION	100
7.4577-9.3751	0.1756	293	0.152	5250	X-RAY DIFFRACTION	100
9.3751-39.4766	0.2051	293	0.1959	5423	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	2.6274	-1.1801	0.7039	1.3112	-0.5187	0.9163	0.0357	0.2946	-0.0551	-0.0375	-0.1258	-0.2366	-0.0513	0.1594	0.0845	0.8255	0.2639	0.0473	0.7254	0.0135	0.5134	44.5465	126.0091	10.2749
2	4.0118	2.6513	-1.0376	2.8786	-1.9749	2.9896	-0.1912	-0.1274	0.3591	0.3492	0.287	0.5204	-0.8869	-0.7864	-0.1001	1.568	0.6232	-0.0077	1.0499	-0.0823	0.7776	70.4503	97.8475	90.3711
3	2.8688	-0.2078	-1.4985	4.7913	2.6815	6.314	-0.1674	0.4318	0.5329	0.1453	-0.0708	0.1159	-1.6151	-0.7752	0.2404	1.2145	0.2362	-0.1676	0.6889	0.0953	0.6773	83.5083	105.708	53.8509
4	1.8031	-0.0668	-0.2554	2.1674	0.187	0.9075	0.0184	-0.4961	0.5619	0.6773	-0.025	0.184	-0.8239	-0.1952	0.0137	1.9447	0.2946	0.0346	1.1392	-0.2446	0.6862	86.5127	93.6726	129.5121
5	1.9009	0.2824	-0.547	1.2866	-0.4356	1.965	-0.04	-0.4006	0.4921	0.5207	0.0166	-0.0678	-0.7707	0.204	0.0064	1.5193	0.1132	-0.1555	0.836	-0.1582	0.5617	105.1698	92.9134	104.612
6	1.4449	0.1889	-0.0478	0.9476	-0.1951	1.3414	-0.0619	-0.027	0.1297	0.2711	0.0133	-0.0368	-0.4003	0.3556	0.0586	1.0059	0.109	-0.1187	0.6618	-0.0045	0.3982	108.9366	80.3874	75.1988
7	1.4367	0.3175	0.5608	1.1509	0.3219	1.2786	0.0363	0.2506	-0.1661	0	-0.0464	-0.0534	0.0345	0.1591	0.03	0.8709	0.2976	-0.0183	0.5946	0.0382	0.4674	91.616	69.1329	50.3572
8	2.232	0.4609	0.7942	0.8075	-0.1214	1.4469	0.1199	0.1858	-0.3637	-0.0243	0.0836	0.1834	0.2484	0.0209	-0.2177	0.8268	0.2808	0.0043	0.5483	0.0584	0.5953	62.4683	70.3137	37.3141
9	3.8795	-0.1733	-0.223	2.2777	-0.2376	2.4292	0.0074	-0.3416	-0.0073	0.4917	0.1853	0.7043	-0.142	-0.5829	-0.2004	0.8109	0.2817	0.1321	0.72	0.2093	0.6507	41.471	89.8877	44.6938
10	3.0429	-1.8151	-0.2234	4.876	0.7544	2.282	-0.2236	-0.0496	0.4511	0.4454	0.3535	0.6452	-0.7549	-0.7602	-0.1352	0.9477	0.3964	0.1513	0.873	0.2043	0.7258	33.5274	114.1254	35.4922
11	6.4984	-0.6762	0.2103	7.8742	1.5917	5.6962	0.3212	0.9215	-0.3471	-1.9719	-0.395	0.9252	-0.0546	-1.172	0.0632	1.3136	0.1457	-0.0362	1.2698	-0.0911	1.0415	63.8171	59.0281	117.7887
12	0.3796	-0.2014	0.9365	0.0836	-0.3633	1.3103	0.0346	-0.378	-0.002	0.3206	0.0996	0.2903	-0.1371	-0.6373	-0.174	1.3389	0.1816	0.0856	0.897	-0.0109	0.8274	67.791	84.6908	80.257
13	1.1071	0.0235	0.2409	0.3667	0.4317	2.2956	-0.1569	0.0182	0.0938	0.412	0.2276	0.2459	-0.7609	0.1774	-0.0687	1.5581	0.4185	-0.0562	0.5637	0.1677	0.662	82.6664	95.4664	66.4462

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain A
2	X-RAY DIFFRACTION	2	chain B
3	X-RAY DIFFRACTION	3	chain C
4	X-RAY DIFFRACTION	4	chain D
5	X-RAY DIFFRACTION	5	chain E
6	X-RAY DIFFRACTION	6	chain F
7	X-RAY DIFFRACTION	7	chain G
8	X-RAY DIFFRACTION	8	chain H
9	X-RAY DIFFRACTION	9	chain I
10	X-RAY DIFFRACTION	10	chain J
11	X-RAY DIFFRACTION	11	chain K
12	X-RAY DIFFRACTION	12	chain L
13	X-RAY DIFFRACTION	13	chain M

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CRISPR system Cascade subunit ... , 5 types, 11 molecules ABCDEFGHIJK

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