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- PDB-5ng6: Crystal structure of FnCas12a bound to a crRNA -

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Basic information

Entry
Database: PDB / ID: 5ng6
TitleCrystal structure of FnCas12a bound to a crRNA
Components
  • CRISPR-associated endonuclease Cpf1
  • crRNA
KeywordsHYDROLASE / CRISPR / Cas / Cpf1 / Cas12a / nuclease / genome editing / R-loop / crRNA / RuvC
Function / homology
Function and homology information


Bacillus subtilis ribonuclease / : / deoxyribonuclease I / deoxyribonuclease I activity / defense response to virus / lyase activity / DNA binding / RNA binding
Similarity search - Function
CRISPR-associated endonuclease Cas12a / Cas12a, REC1 domain / Cas12a, RuvC nuclease domain / Cas12a, nuclease domain / Alpha helical recognition lobe domain / Nuclease domain / RuvC nuclease domain
Similarity search - Domain/homology
RNA / RNA (> 10) / CRISPR-associated endonuclease Cas12a
Similarity search - Component
Biological speciesFrancisella tularensis subsp. novicida (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.342 Å
AuthorsSwarts, D.C. / van der Oost, J. / Jinek, M.
CitationJournal: Mol. Cell / Year: 2017
Title: Structural Basis for Guide RNA Processing and Seed-Dependent DNA Targeting by CRISPR-Cas12a.
Authors: Swarts, D.C. / van der Oost, J. / Jinek, M.
History
DepositionMar 16, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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 / 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_database_status.process_site / _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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CRISPR-associated endonuclease Cpf1
B: crRNA
C: CRISPR-associated endonuclease Cpf1
D: crRNA
E: CRISPR-associated endonuclease Cpf1
F: crRNA
G: CRISPR-associated endonuclease Cpf1
H: crRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)664,17116
Polymers663,9778
Non-polymers1948
Water81145
1
A: CRISPR-associated endonuclease Cpf1
B: crRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,0434
Polymers165,9942
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5820 Å2
ΔGint-59 kcal/mol
Surface area62310 Å2
MethodPISA
2
C: CRISPR-associated endonuclease Cpf1
D: crRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,0434
Polymers165,9942
Non-polymers492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5900 Å2
ΔGint-57 kcal/mol
Surface area62360 Å2
MethodPISA
3
E: CRISPR-associated endonuclease Cpf1
F: crRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,0434
Polymers165,9942
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5760 Å2
ΔGint-59 kcal/mol
Surface area62380 Å2
MethodPISA
4
G: CRISPR-associated endonuclease Cpf1
H: crRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,0434
Polymers165,9942
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5870 Å2
ΔGint-61 kcal/mol
Surface area61820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)214.684, 277.061, 135.636
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
CRISPR-associated endonuclease Cpf1 / FnCpf1


Mass: 152282.188 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: SNA sequence at the N-terminus is derived from expression vector.
Source: (gene. exp.) Francisella tularensis subsp. novicida (strain U112) (bacteria)
Strain: U112 / Gene: cpf1, FTN_1397 / Plasmid: pML-1B / Details (production host): His6-TEV N-terminal fusion / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2
References: UniProt: A0Q7Q2, Hydrolases; Acting on ester bonds
#2: RNA chain
crRNA


Mass: 13712.073 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.08 Å3/Da / Density % sol: 60.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 50 mM HEPES-NaOH, pH 6.5, 20% (w/v) Polyethylene glycol 3,400, 1.5% (w/v) Tryptone

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00768 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Aug 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00768 Å / Relative weight: 1
ReflectionResolution: 3.34→169.7 Å / Num. obs: 225590 / % possible obs: 99.7 % / Observed criterion σ(I): 1.73 / Redundancy: 7 % / CC1/2: 0.997 / Rsym value: 0.195 / Net I/σ(I): 10.9
Reflection shellResolution: 3.34→3.54 Å / Redundancy: 7 % / Mean I/σ(I) obs: 1.73 / Num. unique obs: 33814 / CC1/2: 0.595 / Rsym value: 1.1179 / % possible all: 98.1

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ID6
Resolution: 3.342→49.239 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.13 / Phase error: 26.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2584 10907 4.84 %
Rwork0.2386 --
obs0.2397 225492 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.342→49.239 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms41732 2028 8 45 43813
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01244860
X-RAY DIFFRACTIONf_angle_d0.68760636
X-RAY DIFFRACTIONf_dihedral_angle_d18.79627058
X-RAY DIFFRACTIONf_chiral_restr0.0466572
X-RAY DIFFRACTIONf_plane_restr0.0047418
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3419-3.37990.39233320.38686544X-RAY DIFFRACTION91
3.3799-3.41970.35673680.34887200X-RAY DIFFRACTION100
3.4197-3.46140.34523660.32757166X-RAY DIFFRACTION100
3.4614-3.50520.3653610.32777124X-RAY DIFFRACTION100
3.5052-3.55130.34053710.30587172X-RAY DIFFRACTION100
3.5513-3.59990.31643560.30267179X-RAY DIFFRACTION100
3.5999-3.65130.30853900.30017239X-RAY DIFFRACTION100
3.6513-3.70580.30633490.29167068X-RAY DIFFRACTION100
3.7058-3.76370.30563680.28637268X-RAY DIFFRACTION100
3.7637-3.82540.29054030.28377057X-RAY DIFFRACTION100
3.8254-3.89130.32313360.27937268X-RAY DIFFRACTION100
3.8913-3.9620.28084060.27037144X-RAY DIFFRACTION100
3.962-4.03820.27773290.26747206X-RAY DIFFRACTION100
4.0382-4.12060.24183570.25177171X-RAY DIFFRACTION100
4.1206-4.21020.23713780.23377145X-RAY DIFFRACTION100
4.2102-4.3080.24873590.23337187X-RAY DIFFRACTION100
4.308-4.41570.24183660.22227182X-RAY DIFFRACTION100
4.4157-4.5350.23453540.22067197X-RAY DIFFRACTION100
4.535-4.66840.24183550.22477222X-RAY DIFFRACTION100
4.6684-4.81890.23913660.21457172X-RAY DIFFRACTION100
4.8189-4.9910.24073830.21067144X-RAY DIFFRACTION100
4.991-5.19060.23923480.21257148X-RAY DIFFRACTION100
5.1906-5.42660.25863850.22457195X-RAY DIFFRACTION100
5.4266-5.71230.23453210.22737195X-RAY DIFFRACTION100
5.7123-6.06960.22133940.2327170X-RAY DIFFRACTION100
6.0696-6.53720.25623760.22757166X-RAY DIFFRACTION100
6.5372-7.19330.23793590.21777171X-RAY DIFFRACTION100
7.1933-8.230.22873350.19637203X-RAY DIFFRACTION100
8.23-10.3530.19723590.16457196X-RAY DIFFRACTION100
10.353-49.24390.23573770.21297086X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.0104-0.1781-0.34231.12310.3010.5125-0.05680.0823-0.23440.07830.00430.00230.1450.0379-00.693-0.0545-0.0310.5984-0.01810.613719.8592-251.425840.9057
21.76480.48760.30160.6937-0.31.66050.11940.41660.1497-0.1524-0.2029-0.6092-0.21430.270600.6643-0.00550.04350.73190.0670.662128.4795-231.812222.3482
31.95-0.7793-2.28341.2451.52973.15180.1580.58410.1353-0.323-0.0416-0.1778-0.2584-0.3016-0.00240.7040.0039-0.00450.94920.03850.594929.0238-240.0992-1.0702
40.1975-0.1645-0.29990.12780.25840.76640.01390.06730.3961-0.1630.19340.0751-0.4670.21640.00010.6602-0.04730.05440.56610.00130.710628.9902-221.355438.0712
50.02350.03890.01970.1232-0.03180.08540.11370.2226-1.74460.1848-0.0438-0.20441.90390.22250.0010.9633-0.04510.03940.45370.08880.999319.2341-242.792345.8889
60.15090.3199-0.44322.7403-0.4491.05780.0783-0.04580.18350.34470.08430.4898-0.2242-0.206200.82860.06110.14420.91290.07470.7988-32.2505-230.2395-22.8756
70.4659-0.03280.50770.5731-0.20470.76280.1084-0.33850.62210.3010.22510.5909-0.3609-0.18420.00020.84470.01160.14650.69960.00470.9005-26.3972-200.6257-34.4136
80.59420.2255-0.28691.0291-0.35020.843-0.0164-0.002-0.07040.15890.10250.11390.0367-0.12330.00010.72260.0134-0.00130.7537-0.05640.7274-20.7271-241.8384-27.382
91.4949-0.33860.40810.48010.51271.0043-0.14280.3281-0.1505-0.28030.1184-0.0492-0.04340.3274-00.79380.07150.01510.8636-0.00330.7503-5.7143-256.468-33.7271
102.84420.6192-1.34121.1229-0.35461.5268-0.0820.1024-0.1078-0.2762-0.0037-0.26340.19250.5783-0.00190.74860.0762-0.08351.12230.02810.752217.7175-249.1092-35.4124
110.05890.0043-0.02230.0508-0.03180.0258-0.47690.48430.0526-0.2797-0.14080.14730.43210.0846-0.00021.024-0.13480.08660.8849-0.05350.7222-26.8016-265.0651-34.6808
120.2677-0.00450.08940.1058-0.11390.1327-0.0430.2196-0.60470.26150.02950.32310.5756-0.290300.9815-0.07570.08820.7632-0.06890.9185-20.0599-267.2001-32.5712
130.04910.010.00610.06090.00940.01060.0122-0.17840.9459-0.37080.0798-0.3412-1.37060.324600.92710.0446-0.00720.90440.10380.9977-29.2484-244.1233-25.3963
140.12760.1033-0.05460.6171-0.02520.72730.0018-0.0979-0.2362-0.0202-0.0137-0.01630.41150.1393-0.0020.91240.1183-0.00230.89250.02560.9419-22.8045-181.47427.3664
152.4862-0.0465-0.07931.5275-0.53640.45710.08120.10580.24610.058-0.0118-0.1424-0.26190.14930.00010.6069-0.0292-0.02680.6849-0.02340.5945-5.8563-155.4176.8193
164.0763-0.62691.05240.4782-0.00891.6447-0.1213-0.2087-0.45760.14960.0479-0.12590.12890.4226-0.00120.68390.03160.05350.78660.03660.748615.5428-164.843713.4184
170.63170.0901-0.17830.1239-0.16970.22190.1285-0.00320.2154-0.0343-0.0391-0.074-0.4612-0.0957-0.00010.644-0.0091-0.01590.6119-0.09160.7293-18.6611-148.600712.8353
180.2444-0.0225-0.29250.04380.19491.0434-0.6145-0.5738-1.56590.49780.28540.0321.82210.1939-0.0010.8161-0.16210.13570.9509-0.01741.221-26.5123-171.50575.2112
191.24440.04670.23961.15240.15060.4986-0.0933-0.30410.5118-0.12210.087-0.1099-0.24360.07870.00040.82290.00840.10760.7192-0.13930.827222.2229-161.3448-63.2562
200.3804-0.41830.64671.66790.20392.4076-0.0634-0.4854-0.15290.22970.0499-0.22710.15970.2705-00.7103-0.0469-0.00610.83250.00050.673527.7753-185.9431-46.6174
210.74910.50281.38091.21781.43523.24510.023-0.6039-0.04360.33030.1746-0.31280.04240.148100.88330.02360.00281.2734-0.1070.842131.2835-174.5943-22.7747
220.02130.03330.0380.04830.05870.06740.3832-0.2787-0.10860.32040.1756-0.0019-0.47720.4879-0.00040.5429-0.03670.00060.8337-0.04890.77634.6288-190.7049-64.3523
230.0049-0.00920.01030.01310.00090.039-0.0596-0.3221-0.1523-0.50210.7865-0.18620.3475-0.01670.00090.73910.07310.03570.7081-0.08350.918837.8701-189.8729-56.4708
240.00360.01750.0260.05420.0180.27240.1655-0.2899-0.0637-0.33350.1056-0.61410.1120.264200.75210.02840.04910.6942-0.08260.768130.3844-194.5718-58.0938
250.01240.00570.01490.0388-0.03060.05060.4390.01371.5247-0.09260.347-0.0908-1.0191-0.09640.00271.1222-0.13920.02530.56880.08591.071822.5913-171.5168-67.1301
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 934 )
2X-RAY DIFFRACTION2chain 'A' and (resid 935 through 1036 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1037 through 1299 )
4X-RAY DIFFRACTION4chain 'B' and (resid -18 through 1 )
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 6 )
6X-RAY DIFFRACTION6chain 'C' and (resid 0 through 206 )
7X-RAY DIFFRACTION7chain 'C' and (resid 207 through 286 )
8X-RAY DIFFRACTION8chain 'C' and (resid 287 through 934 )
9X-RAY DIFFRACTION9chain 'C' and (resid 935 through 1036 )
10X-RAY DIFFRACTION10chain 'C' and (resid 1037 through 1299 )
11X-RAY DIFFRACTION11chain 'D' and (resid -18 through -14 )
12X-RAY DIFFRACTION12chain 'D' and (resid -13 through 1 )
13X-RAY DIFFRACTION13chain 'D' and (resid 2 through 6 )
14X-RAY DIFFRACTION14chain 'E' and (resid 0 through 863 )
15X-RAY DIFFRACTION15chain 'E' and (resid 864 through 970 )
16X-RAY DIFFRACTION16chain 'E' and (resid 971 through 1299 )
17X-RAY DIFFRACTION17chain 'F' and (resid -18 through 1 )
18X-RAY DIFFRACTION18chain 'F' and (resid 2 through 6 )
19X-RAY DIFFRACTION19chain 'G' and (resid 0 through 863 )
20X-RAY DIFFRACTION20chain 'G' and (resid 864 through 999 )
21X-RAY DIFFRACTION21chain 'G' and (resid 1000 through 1299 )
22X-RAY DIFFRACTION22chain 'H' and (resid -18 through -14 )
23X-RAY DIFFRACTION23chain 'H' and (resid -13 through -9 )
24X-RAY DIFFRACTION24chain 'H' and (resid -8 through 1 )
25X-RAY DIFFRACTION25chain 'H' and (resid 2 through 6 )

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