PDB-5b43: Crystal structure of Acidaminococcus sp. Cpf1 in complex with crR...

ID or keywords:

Entry

Database: PDB / ID: 5b43

Title

Crystal structure of Acidaminococcus sp. Cpf1 in complex with crRNA and target DNA

Components

CRISPR-associated endonuclease Cpf1
DNA (34-MER)
DNA (5'-D(*CP*AP*GP*TP*CP*CP*TP*TP*TP*A)-3')
RNA (43-MER)

Keywords

HYDROLASE/RNA/DNA /

nuclease / HYDROLASE-RNA-DNA complex

Function / homology

Function and homology information

Bacillus subtilis ribonuclease /

Bacillus subtilis ribonuclease activity /

deoxyribonuclease I /

deoxyribonuclease I activity / defense response to virus /

lyase activity /

DNA binding /

Biological species

Acidaminococcus sp. BV3L6 (bacteria)

Acidaminococcus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.8 Å

Authors

Yamano, T. / Nishimasu, H. / Hirano, H. / Nakane, T. / Ishitani, R. / Nureki, O.

Citation

Journal: Cell / Year: 2016
Title: Crystal Structure of Cpf1 in Complex with Guide RNA and Target DNA
Authors: Yamano, T. / Nishimasu, H. / Zetsche, B. / Hirano, H. / Slaymaker, I.M. / Li, Y. / Fedorova, I. / Nakane, T. / Makarova, K.S. / Koonin, E.V. / Ishitani, R. / Zhang, F. / Nureki, O.

History

Deposition	Mar 30, 2016	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	May 4, 2016	Provider: repository / Type: Initial release
Revision 1.1	May 18, 2016	Group: Database references
Revision 1.2	Oct 4, 2017	Group: Data collection / Derived calculations / Category: diffrn_detector / pdbx_struct_oper_list Item: _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3	Mar 20, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5b43.cif.gz	619.2 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/b4/5b43 ftp://data.pdbj.org/pub/pdb/validation_reports/b4/5b43	HTTPS FTP

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Related structure data

Similar structure data	5xh7-d 5xh6-d 6ehm-d 6i1l-1 6gtg-d 5xuz-2 6gtf-d 6xny-d 4pj3-d 7kho-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

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Deposited unit

A: CRISPR-associated endonuclease Cpf1

B: RNA (43-MER)

C: DNA (34-MER)

D: DNA (5'-D(*CP*AP*GP*TP*CP*CP*TP*TP*TP*A)-3')

hetero molecules

179 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)	81.515, 136.732, 196.909
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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DNA chain , 2 types, 2 molecules CD

#3: DNA chain	DNA (34-MER) / Target DNA Mass: 10443.726 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Acidaminococcus (bacteria)
#4: DNA chain	DNA (5'-D(CPAPGPTPCPCPTPTPTPA)-3') Mass: 2994.979 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Acidaminococcus (bacteria)

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Protein / RNA chain , 2 types, 2 molecules AB

#1: Protein	CRISPR-associated endonuclease Cpf1 / AsCpf1 Mass: 151701.219 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acidaminococcus sp. BV3L6 (bacteria) / Strain: BV3L6 / Gene: cpf1 / Production host: Escherichia coli (E. coli) References: UniProt: U2UMQ6, Hydrolases; Acting on ester bonds
#2: RNA chain	RNA (43-MER) / crRNA Mass: 13756.139 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Acidaminococcus (bacteria)

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Non-polymers , 3 types, 29 molecules

#5: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₆O₂
#6: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 25 / 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: 3.07 Å³/Da / Density % sol: 59.9 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: PEG3350, sodium acetate, 1,6-hexanediol

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 22, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.8→196.91 Å / Num. obs: 54319 / % possible obs: 99 % / Redundancy: 4.4 % / Net I/σ(I): 8.6
Reflection shell	Resolution: 2.8→2.88 Å

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Processing

Software

Name	Version	Classification
PHENIX	(1.10_2155: ???)	refinement
Aimless		data scaling
PDB_EXTRACT	3.2	data extraction
Coot		model building
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.8→56.155 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 27.01 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2571	2656	4.9 %
R_work	0.2203	-	-
obs	0.2221	54241	98.61 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.8→56.155 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10157	1657	13	25	11852

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	12250
X-RAY DIFFRACTION	f_angle_d	0.447	16956
X-RAY DIFFRACTION	f_dihedral_angle_d	16.086	7097
X-RAY DIFFRACTION	f_chiral_restr	0.036	1929
X-RAY DIFFRACTION	f_plane_restr	0.003	1896

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 (%)
2.8-2.8509	0.3392	151	0.3373	2649	X-RAY DIFFRACTION	98
2.8509-2.9058	0.3337	116	0.3139	2734	X-RAY DIFFRACTION	99
2.9058-2.9651	0.396	149	0.3157	2646	X-RAY DIFFRACTION	99
2.9651-3.0295	0.3249	126	0.3039	2691	X-RAY DIFFRACTION	99
3.0295-3.1	0.3057	138	0.288	2655	X-RAY DIFFRACTION	98
3.1-3.1775	0.3184	151	0.2743	2660	X-RAY DIFFRACTION	98
3.1775-3.2634	0.2827	131	0.2625	2651	X-RAY DIFFRACTION	97
3.2634-3.3594	0.2838	141	0.2527	2689	X-RAY DIFFRACTION	100
3.3594-3.4679	0.2982	139	0.2508	2725	X-RAY DIFFRACTION	99
3.4679-3.5918	0.2933	142	0.2491	2729	X-RAY DIFFRACTION	100
3.5918-3.7356	0.2863	136	0.242	2718	X-RAY DIFFRACTION	99
3.7356-3.9055	0.2426	135	0.2229	2720	X-RAY DIFFRACTION	99
3.9055-4.1114	0.2266	142	0.2008	2711	X-RAY DIFFRACTION	99
4.1114-4.3689	0.2282	152	0.1869	2721	X-RAY DIFFRACTION	99
4.3689-4.706	0.203	125	0.1828	2682	X-RAY DIFFRACTION	97
4.706-5.1793	0.219	152	0.1795	2740	X-RAY DIFFRACTION	99
5.1793-5.9281	0.2164	143	0.1895	2785	X-RAY DIFFRACTION	99
5.9281-7.466	0.2436	127	0.2182	2832	X-RAY DIFFRACTION	99
7.466-56.1664	0.2485	160	0.1819	2847	X-RAY DIFFRACTION	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	0.4673	-0.256	0.7565	0.2059	-0.4979	3.0628	-0.2505	0.0615	0.2895	0.1572	0.034	-0.033	-0.9046	0.1202	0.1483	0.6281	-0.064	-0.0721	0.3704	0.0531	0.5263	32.4313	4.3683	-9.5416
2	0.4995	-0.6012	0.7487	0.8232	-0.7806	2.3502	0.0221	0.3886	0.0695	0.0455	-0.2384	-0.0859	-0.0999	0.7931	0.153	0.348	-0.0634	-0.0016	0.6164	0.1778	0.4518	36.3972	-5.5227	-43.4603
3	2.1046	0.0648	0.0201	1.9674	-2.6617	4.0597	0.1847	-0.3014	-0.3819	-0.2115	-0.0536	0.1497	0.4116	0.0953	-0.1435	0.4811	0.0647	-0.0655	0.2898	-0.0206	0.4639	31.1812	-39.2482	-15.6655
4	0.0331	0.0258	-0.0888	0.0962	-0.007	0.2581	-0.3001	-0.2088	-0.0337	0.2987	-0.5533	-0.6676	0.101	1.6751	0.4036	0.556	-0.2252	-0.2595	1.8745	0.9294	0.7048	56.0702	-3.0914	-37.7511
5	6.9533	-0.9887	-3.3377	1.6689	-0.1003	2.7159	-0.2564	0.7627	-0.1121	-0.2878	-0.5091	-0.516	-0.2582	0.7619	0.3667	0.4771	-0.0193	0.0392	1.7299	0.4481	0.6484	60.0782	-10.2632	-39.2794
6	-0.2462	-0.1093	0.8032	0.6524	-0.1291	3.1831	0.0601	0.163	0.1376	0.0532	-0.0786	-0.1652	-0.8423	0.7439	0.0258	0.4816	-0.1066	-0.0895	0.6813	0.2045	0.4635	38.2836	-1.9513	-21.6946
7	8.8153	-3.9255	-1.0424	2.6526	-2.1428	7.8138	0.4623	0.3736	-0.3029	0.1815	-0.7031	0.5178	-0.6606	0.1745	0.1282	0.6136	0.0375	-0.014	0.551	0.0414	0.3714	33.6205	-12.7823	11.1015
8	6.5978	1.3953	-1.2332	5.6139	2.2929	1.9131	-0.3562	-0.5809	-0.1172	-0.2671	-0.5995	-0.7202	-0.698	1.4335	0.9132	0.5675	0.0532	0.0236	0.9105	0.2074	0.5848	37.4604	-11.3678	3.145
9	0.3036	0.3028	1.6597	0.2153	0.1718	5.0379	-0.0208	0.137	0.154	0.1734	0.0338	0.082	-0.6865	0.3262	0.0422	0.5598	-0.055	-0.0804	0.5741	0.1232	0.4543	30.5154	4.7337	-28.0359
10	3.6345	3.27	3.691	3.5072	2.5294	5.04	0.4224	-0.0553	2.4077	0.5792	-1.0373	-0.1784	-2.6629	1.4908	0.502	2.1621	-0.1675	-0.1388	0.7173	0.133	1.7135	23.7524	33.0729	-48.1624
11	2.8879	0.7589	-1.3683	3.2747	1.6775	3.9997	-0.336	0.7661	1.1641	-0.701	-0.4239	0.3334	-1.1407	-0.0794	-0.3104	1.5618	-0.316	-0.5196	0.4561	0.5724	0.9829	23.2251	25.0076	-50.0547

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 577 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 578 through 1024 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 1025 through 1307 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid -19 through -15 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid -14 through -5 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid -4 through 15 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 16 through 20 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid -19 through -15 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid -14 through 5 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 6 through 10 )
11	X-RAY DIFFRACTION	11	chain 'D' and (resid -10 through -1 )

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-DNA chain , 2 types, 2 molecules CD

-Protein / RNA chain , 2 types, 2 molecules AB

-Non-polymers , 3 types, 29 molecules

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Assembly

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Components

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DNA chain , 2 types, 2 molecules CD

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Protein / RNA chain , 2 types, 2 molecules AB

-
Non-polymers , 3 types, 29 molecules

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

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About Yorodumi

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News

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Aug 12, 2020. Covid-19 info

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Mar 5, 2020. Novel coronavirus structure data

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Jul 12, 2017. Major update of PDB

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