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- PDB-5b2o: Crystal structure of Francisella novicida Cas9 in complex with sg... -

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Basic information

Entry
Database: PDB / ID: 5b2o
TitleCrystal structure of Francisella novicida Cas9 in complex with sgRNA and target DNA (TGG PAM)
Components
  • CRISPR-associated endonuclease Cas9
  • DNA (5'-D(*TP*GP*GP*TP*AP*TP*CP*GP*G)-3')
  • Guide RNA
  • Target DNA
KeywordsHYDROLASE/RNA/DNA / CRISPR-Cas9 / genome engineering / HYDROLASE-RNA-DNA complex
Function / homology
Function and homology information


endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / DNA binding / RNA binding / metal ion binding
Similarity search - Function
CRISPR system subtype II-B RNA-guided endonuclease Cas9/Csx12 / : / CRISPR-associated endonuclease Cas9 alpha-helical lobe / Cas9-type HNH domain / Cas9-type HNH domain profile.
Similarity search - Domain/homology
ACETATE ION / DNA / DNA (> 10) / RNA / RNA (> 10) / CRISPR-associated endonuclease Cas9
Similarity search - Component
Biological speciesFrancisella tularensis subsp. novicida U112 (bacteria)
synthetic construct (others)
Francisella tularensis subsp. novicida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsHirano, H. / Nishimasu, H. / Nakane, T. / Ishitani, R. / Nureki, O.
CitationJournal: Cell / Year: 2016
Title: Structure and Engineering of Francisella novicida Cas9
Authors: Hirano, H. / Gootenberg, J.S. / Horii, T. / Abudayyeh, O.O. / Kimura, M. / Hsu, P.D. / Nakane, T. / Ishitani, R. / Hatada, I. / Zhang, F. / Nishimasu, H. / Nureki, O.
History
DepositionFeb 1, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2016Group: Database references
Revision 1.2Oct 4, 2017Group: Advisory / Data collection / Derived calculations
Category: diffrn_detector / diffrn_source ...diffrn_detector / diffrn_source / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms
Item: _diffrn_detector.detector / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type
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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_value_order / _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_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CRISPR-associated endonuclease Cas9
B: Guide RNA
C: Target DNA
D: DNA (5'-D(*TP*GP*GP*TP*AP*TP*CP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)235,51053
Polymers233,0554
Non-polymers2,45549
Water18,5731031
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32480 Å2
ΔGint-326 kcal/mol
Surface area77420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.922, 159.105, 96.808
Angle α, β, γ (deg.)90.000, 107.040, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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DNA chain , 2 types, 2 molecules CD

#3: DNA chain Target DNA


Mass: 8993.800 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemical synthesis
Source: (synth.) Francisella tularensis subsp. novicida (bacteria)
#4: DNA chain DNA (5'-D(*TP*GP*GP*TP*AP*TP*CP*GP*G)-3')


Mass: 2786.833 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Francisella tularensis subsp. novicida (bacteria)

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Protein / RNA chain , 2 types, 2 molecules AB

#1: Protein CRISPR-associated endonuclease Cas9


Mass: 190995.422 Da / Num. of mol.: 1 / Mutation: N995A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis subsp. novicida U112 (bacteria)
Strain: U112 / Gene: cas9, FTN_0757 / Plasmid: pE-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Rosetta2
References: UniProt: A0Q5Y3, Hydrolases; Acting on ester bonds
#2: RNA chain Guide RNA /


Mass: 30278.863 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: in vitro transcription / Source: (synth.) synthetic construct (others)

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Non-polymers , 7 types, 1080 molecules

#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#8: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Ca
#9: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C2H6O2
#10: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1031 / 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: 2.59 Å3/Da / Density % sol: 52.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 9-11% PEG 3350, 0.2 M calcium acetate, 0.1 M sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→46.28 Å / Num. obs: 249301 / % possible obs: 96.3 % / Redundancy: 7.2 % / Net I/σ(I): 14.2

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.10_2155: ???refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.7→46.278 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.53
RfactorNum. reflection% reflection
Rfree0.2073 12436 4.99 %
Rwork0.1844 --
obs0.1856 249252 96.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 153.69 Å2 / Biso mean: 47.6372 Å2 / Biso min: 15.79 Å2
Refinement stepCycle: final / Resolution: 1.7→46.278 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11677 2771 124 1031 15603
Biso mean--46.7 40.63 -
Num. residues----1588
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115203
X-RAY DIFFRACTIONf_angle_d1.14421120
X-RAY DIFFRACTIONf_chiral_restr0.0632413
X-RAY DIFFRACTIONf_plane_restr0.0072237
X-RAY DIFFRACTIONf_dihedral_angle_d17.0098849
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.71930.34624270.33117874830196
1.7193-1.73960.32254200.3137886830696
1.7396-1.76080.32844030.30137857826096
1.7608-1.78310.31093980.29287844824296
1.7831-1.80650.29214090.287786819595
1.8065-1.83130.29653830.26947356773990
1.8313-1.85740.2624040.25037737814195
1.8574-1.88520.27844180.24137934835297
1.8852-1.91460.24884110.22887939835097
1.9146-1.9460.24184260.21577940836697
1.946-1.97960.2314190.20947925834497
1.9796-2.01560.23114180.1997968838697
2.0156-2.05430.2284190.20297973839297
2.0543-2.09630.21774270.19467913834097
2.0963-2.14180.22084210.19217863828497
2.1418-2.19170.21743990.18367527792692
2.1917-2.24650.20543960.18047729812594
2.2465-2.30720.19794200.17328046846698
2.3072-2.37510.20214260.17517992841898
2.3751-2.45170.24190.17448063848298
2.4517-2.53940.20374230.17488034845798
2.5394-2.6410.22674250.18088029845498
2.641-2.76120.23034090.18927917832697
2.7612-2.90680.21053950.18187498789391
2.9068-3.08890.19394220.17548127854999
3.0889-3.32730.18524250.17258126855199
3.3273-3.6620.19664180.1698078849698
3.662-4.19160.20454020.16037664806693
4.1916-5.27980.16554340.15268173860799
5.2798-46.29520.18374200.18498018843896
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)
11.2876-0.2231.15440.5778-0.03643.9167-0.0138-0.24950.17020.13780.0895-0.05-0.0954-0.05630.02120.1526-0.02060.01760.1577-0.06810.18483.94042.389825.3208
21.74642.2547-0.77151.98-1.0124-0.2008-0.11750.2548-1.101-0.23380.0401-0.01550.4081-0.08710.05990.6375-0.09160.02180.3849-0.11921.1368-16.208-33.74990.333
31.5606-0.40171.42190.4212-0.19271.98660.07590.36050.06140.0361-0.0544-0.0870.20250.5586-0.02310.19780.00640.04380.2982-0.01780.201727.0794-8.415322.802
40.92070.26830.2883.39291.15420.5522-0.0908-0.0419-0.33840.63020.21570.26060.52730.1063-0.10250.5710.01960.06210.3169-0.00310.385223.0859-31.480828.1705
51.4099-0.6771-0.18021.75120.74591.2595-0.0886-0.219-0.20860.25770.13590.10440.38250.0101-0.04750.43950.01090.00110.33450.02320.214418.2519-20.002438.5917
62.3775-1.6240.32852.311-1.60442.94850.1560.1039-0.2985-0.4731-0.19710.01650.86330.49870.01651.1927-0.1339-0.05820.92280.24450.80717.9294-30.835665.2117
72.7868-0.0554-0.19943.2639-0.26192.6224-0.1168-0.926-0.40820.44240.0583-0.01280.4551-0.43850.03470.3952-0.0563-0.0160.62710.02760.21139.5147-8.994956.0143
81.3432-0.46860.73090.6988-0.26671.1555-0.1137-0.22020.14470.04260.04430.1128-0.2222-0.22840.05270.23-0.00610.05170.1821-0.03320.2652-22.638713.721512.8068
91.11920.1618-0.05872.42290.50482.2155-0.004-0.3330.28790.7065-0.00840.2499-0.2878-0.0265-0.00890.39880.03350.05540.2224-0.07130.3248-16.394515.9130.156
102.366-0.43140.69281.23550.17621.30580.2182-0.4986-0.08110.1628-0.07490.24520.3899-0.0759-0.3320.68560.0260.04040.43210.02290.452416.7346-24.455337.2973
111.5044-0.75491.15010.3008-0.36031.52230.11260.0508-0.1721-0.0526-0.00190.14970.11530.0531-0.1240.2054-0.03630.00880.1555-0.00020.245-6.7681-3.4617.8521
125.2345-1.3053-0.31755.2354-0.60253.29150.22020.80860.0321-0.8358-0.1150.4685-0.3415-0.1215-0.16620.40610.0508-0.14570.4198-0.07640.3458-34.06268.3116-15.9376
130.6758-0.57450.05180.50940.07290.76290.04510.09480.0076-0.065-0.0410.0713-0.04460.01860.00390.2137-0.0275-0.00610.15360.01660.2565-15.58446.30.0359
141.2459-0.2149-1.3480.11740.53892.69450.09380.06080.71750.0634-0.2968-0.0689-0.70610.30050.16720.384-0.1361-0.00140.33990.05060.4357.941313.46638.7559
151.3887-0.28770.35020.5193-0.63751.6343-0.13-0.03080.1544-0.02650.0216-0.042-0.1860.06370.11820.2197-0.02990.00040.2026-0.03170.26892.58217.009822.4446
163.06593.287-0.02946.2188-3.95225.7085-0.0618-0.30590.43620.6742-0.1274-0.0123-0.9194-0.57390.13670.26710.0521-0.03740.2979-0.06210.23989.68217.964330.3915
173.2125-0.98030.39660.2975-0.08850.35050.04380.56130.61-0.016-0.167-0.1918-0.07460.36880.12010.1995-0.0430.02280.41710.050.319125.59450.351615.9707
184.56994.3232-4.77594.1073-4.53085.001-0.1730.8146-0.774-1.0389-0.1635-0.72061.34110.60460.2920.43560.1320.08250.6207-0.10460.365627.3972-14.59329.2623
193.09780.1326-0.32422.8655-1.44612.4129-0.0210.32890.64080.1055-0.0717-0.3994-0.21760.3110.06380.1638-0.0449-0.00470.3750.02640.367225.3272-0.427116.3247
203.7249-1.7883-2.69153.00090.49464.3887-0.56220.39790.49670.43170.06971.0567-0.3487-1.1820.34290.34560.1705-0.02290.479-0.080.7974-27.586612.902227.8284
210.3335-0.17470.27770.7070.06291.1382-0.0964-0.4425-0.46030.50210.17570.26420.28010.0984-0.17670.52060.09890.08770.38780.12160.33810.0916-20.539429.4408
227.3021-2.6854-1.05581.1166-0.07162.0858-0.25170.16060.9080.26620.1031.3711-0.7551-1.0842-0.03130.37470.2054-0.00460.6165-0.06460.9745-28.66615.956826.8336
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 99 )A1 - 99
2X-RAY DIFFRACTION2chain 'A' and (resid 100 through 324 )A100 - 324
3X-RAY DIFFRACTION3chain 'A' and (resid 325 through 643 )A325 - 643
4X-RAY DIFFRACTION4chain 'A' and (resid 644 through 750 )A644 - 750
5X-RAY DIFFRACTION5chain 'A' and (resid 751 through 927 )A751 - 927
6X-RAY DIFFRACTION6chain 'A' and (resid 928 through 1065 )A928 - 1065
7X-RAY DIFFRACTION7chain 'A' and (resid 1066 through 1176 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 1177 through 1424 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 1425 through 1622 )A0
10X-RAY DIFFRACTION10chain 'B' and (resid 1 through 10 )B1 - 10
11X-RAY DIFFRACTION11chain 'B' and (resid 11 through 30 )B11 - 30
12X-RAY DIFFRACTION12chain 'B' and (resid 31 through 40 )B31 - 40
13X-RAY DIFFRACTION13chain 'B' and (resid 41 through 55 )B41 - 55
14X-RAY DIFFRACTION14chain 'B' and (resid 56 through 60 )B56 - 60
15X-RAY DIFFRACTION15chain 'B' and (resid 61 through 65 )B61 - 65
16X-RAY DIFFRACTION16chain 'B' and (resid 66 through 70 )B66 - 70
17X-RAY DIFFRACTION17chain 'B' and (resid 71 through 80 )B71 - 80
18X-RAY DIFFRACTION18chain 'B' and (resid 81 through 85 )B81 - 85
19X-RAY DIFFRACTION19chain 'B' and (resid 86 through 94 )B86 - 94
20X-RAY DIFFRACTION20chain 'C' and (resid 1 through 10 )C1 - 10
21X-RAY DIFFRACTION21chain 'C' and (resid 11 through 30 )C11 - 30
22X-RAY DIFFRACTION22chain 'D' and (resid 1 through 9 )D1 - 9

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