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- PDB-6ai6: Crystal structure of SpCas9-NG -

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Basic information

Entry
Database: PDB / ID: 6ai6
TitleCrystal structure of SpCas9-NG
Components
  • CRISPR-associated endonuclease Cas9/Csn1
  • DNA (28-MER)
  • DNA (8-MER)
  • RNA (81-MER)
KeywordsHYDROLASE/RNA/DNA / nuclease / HYDROLASE-RNA-DNA complex / HYDROLASE
Function / homology
Function and homology information


maintenance of CRISPR repeat elements / 3'-5' exonuclease activity / DNA endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / DNA binding / RNA binding / metal ion binding
Similarity search - Function
CRISPR-associated endonuclease Cas9, PAM-interacting domain / CRISPR-associated endonuclease Cas9, bridge helix / CRISPR-associated endonuclease Cas9, REC lobe / REC lobe of CRISPR-associated endonuclease Cas9 / Bridge helix of CRISPR-associated endonuclease Cas9 / PAM-interacting domain of CRISPR-associated endonuclease Cas9 / CRISPR-associated endonuclease Cas9 / HNH endonuclease / Cas9-type HNH domain / Cas9-type HNH domain profile. ...CRISPR-associated endonuclease Cas9, PAM-interacting domain / CRISPR-associated endonuclease Cas9, bridge helix / CRISPR-associated endonuclease Cas9, REC lobe / REC lobe of CRISPR-associated endonuclease Cas9 / Bridge helix of CRISPR-associated endonuclease Cas9 / PAM-interacting domain of CRISPR-associated endonuclease Cas9 / CRISPR-associated endonuclease Cas9 / HNH endonuclease / Cas9-type HNH domain / Cas9-type HNH domain profile. / HNH nuclease / Ribonuclease H superfamily
Similarity search - Domain/homology
: / DNA / DNA (> 10) / RNA / RNA (> 10) / CRISPR-associated endonuclease Cas9/Csn1
Similarity search - Component
Biological speciesStreptococcus pyogenes serotype M1 (bacteria)
Streptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsNishimasu, H. / Hirano, S. / Ishitani, R. / Nureki, O.
CitationJournal: Science / Year: 2018
Title: Engineered CRISPR-Cas9 nuclease with expanded targeting space
Authors: Nishimasu, H. / Shi, X. / Ishiguro, S. / Gao, L. / Hirano, S. / Okazaki, S. / Noda, T. / Abudayyeh, O.O. / Gootenberg, J.S. / Mori, H. / Oura, S. / Holmes, B. / Tanaka, M. / Seki, M. / ...Authors: Nishimasu, H. / Shi, X. / Ishiguro, S. / Gao, L. / Hirano, S. / Okazaki, S. / Noda, T. / Abudayyeh, O.O. / Gootenberg, J.S. / Mori, H. / Oura, S. / Holmes, B. / Tanaka, M. / Seki, M. / Hirano, H. / Aburatani, H. / Ishitani, R. / Ikawa, M. / Yachie, N. / Zhang, F. / Nureki, O.
History
DepositionAug 21, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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.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/Csn1
B: RNA (81-MER)
C: DNA (28-MER)
D: DNA (8-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,02220
Polymers196,3724
Non-polymers65016
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22880 Å2
ΔGint-176 kcal/mol
Surface area72490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.377, 68.568, 187.968
Angle α, β, γ (deg.)90.00, 111.51, 90.00
Int Tables number5
Space group name H-MC121

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Components

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DNA chain , 2 types, 2 molecules CD

#3: DNA chain DNA (28-MER)


Mass: 8463.485 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Streptococcus pyogenes (bacteria)
#4: DNA chain DNA (8-MER)


Mass: 2472.638 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Streptococcus pyogenes (bacteria)

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Protein / RNA chain , 2 types, 2 molecules AB

#1: Protein CRISPR-associated endonuclease Cas9/Csn1 / SpCas9 / SpyCas9


Mass: 159226.516 Da / Num. of mol.: 1
Mutation: N863A, L1111R, D1135V, G1218R, E1219F, A1322R, R1355V, T1357R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes serotype M1 (bacteria)
Gene: cas9, csn1, SPy_1046 / Production host: Escherichia coli (E. coli)
References: UniProt: Q99ZW2, Hydrolases; Acting on ester bonds
#2: RNA chain RNA (81-MER)


Mass: 26209.588 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Streptococcus pyogenes (bacteria)

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Non-polymers , 4 types, 52 molecules

#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: K
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.71 Å3/Da / Density % sol: 54.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: Tris-acetate, pH 8.0, KSCN, PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→48.17 Å / Num. obs: 58235 / % possible obs: 100 % / Redundancy: 3.5 % / CC1/2: 0.992 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.063 / Net I/σ(I): 9.5
Reflection shellResolution: 2.7→2.77 Å / Rmerge(I) obs: 1.202 / Num. unique obs: 4509 / CC1/2: 0.553 / Rpim(I) all: 0.778

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UN3
Resolution: 2.7→48.166 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.96
RfactorNum. reflection% reflection
Rfree0.2435 2891 4.98 %
Rwork0.218 --
obs0.2193 58087 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.7→48.166 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10535 2464 25 36 13060
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00213496
X-RAY DIFFRACTIONf_angle_d0.45218765
X-RAY DIFFRACTIONf_dihedral_angle_d16.4447846
X-RAY DIFFRACTIONf_chiral_restr0.0352178
X-RAY DIFFRACTIONf_plane_restr0.0031979
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.74430.36651220.33462636X-RAY DIFFRACTION100
2.7443-2.79160.37361260.32832598X-RAY DIFFRACTION99
2.7916-2.84230.3781490.32542585X-RAY DIFFRACTION99
2.8423-2.8970.4071280.35142623X-RAY DIFFRACTION100
2.897-2.95610.39811340.33592600X-RAY DIFFRACTION100
2.9561-3.02040.33051430.30812592X-RAY DIFFRACTION100
3.0204-3.09060.29931150.29122661X-RAY DIFFRACTION100
3.0906-3.16790.32591180.27562626X-RAY DIFFRACTION99
3.1679-3.25360.30041540.2572568X-RAY DIFFRACTION99
3.2536-3.34930.25641450.25192577X-RAY DIFFRACTION99
3.3493-3.45740.27911440.25282612X-RAY DIFFRACTION99
3.4574-3.58090.27071390.23382622X-RAY DIFFRACTION100
3.5809-3.72420.26181510.21812591X-RAY DIFFRACTION100
3.7242-3.89360.24331360.19692625X-RAY DIFFRACTION100
3.8936-4.09880.20741460.19732639X-RAY DIFFRACTION100
4.0988-4.35550.20291330.18662645X-RAY DIFFRACTION100
4.3555-4.69150.20311520.17542626X-RAY DIFFRACTION100
4.6915-5.16310.20821280.17132654X-RAY DIFFRACTION100
5.1631-5.90910.19521450.18532676X-RAY DIFFRACTION100
5.9091-7.44040.21381470.20532677X-RAY DIFFRACTION100
7.4404-48.17410.21381360.18792763X-RAY DIFFRACTION100
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)
10.4226-0.07780.20730.3215-0.09471.4206-0.01850.1066-0.04060.1055-0.0199-0.10790.10210.46260.02640.4429-0.06450.02080.5083-0.04350.445312.15785.410447.3659
22.73551.3511-0.14543.0535-1.16964.1118-0.0627-0.1846-0.04490.94320.1105-0.3091-0.8778-0.0907-0.03940.78530.103-0.08540.3374-0.03570.6464-3.475520.390977.929
32.6861-1.2171.40731.3937-0.59412.40950.25350.1555-0.6110.1855-0.0575-0.28910.81350.3606-0.18680.9134-0.0298-0.04720.6814-0.11150.8843-8.5633-15.355263.06
41.57660.2449-0.42870.6835-0.13021.8222-0.0485-0.0337-0.24910.1660.082-0.01850.4886-0.3246-0.02210.609-0.18970.02750.589-0.06440.551-28.3622-12.228944.1364
51.093-0.6721-2.06730.47760.73137.4321-0.38060.0851-0.0120.26590.35770.09711.1129-0.67380.04780.6469-0.15550.12990.6578-0.12520.5572-5.29676.268359.347
61.84860.25030.6263.13030.58643.60760.13520.39160.0385-0.17590.0781-0.50590.91030.6227-0.20710.54330.04250.06850.8215-0.10240.458316.4024-1.637117.5035
71.8883-0.7132-0.33292.55450.25344.24941.31381.577-0.0622-1.243-0.29490.160.97830.517-1.07731.82760.474-0.05981.6359-0.17940.767622.5479-17.94682.2729
82.53270.0480.71950.8672-0.14361.7620.10180.13470.0932-0.1083-0.14190.12140.06360.07940.04470.3101-0.08170.00330.3507-0.01780.269-2.94419.392329.8222
90.5995-0.29721.4560.1694-0.78934.2101-0.63730.87781.276-0.42880.1317-0.725-1.38741.62410.53031.6384-0.39390.73841.44510.30752.2275-35.144218.297732.6891
103.7505-0.14650.08432.60031.52631.14330.5878-2.17991.3115-0.3287-0.0087-1.1162-0.79991.2787-0.60951.36530.24710.12711.859-0.41131.0983-40.174811.942439.6068
115.19991.0165-2.31199.19181.16281.91740.19310.7471-1.4218-0.31620.4163-0.9619-0.0744-0.2707-0.56411.386-0.55720.05761.4466-0.48691.2706-16.123-20.729418.2963
125.6612-0.8411-1.39782.7467-2.3352.990.2960.1146-0.69150.0739-0.85010.52880.58920.32720.54440.46750.01910.0530.9161-0.19770.671-2.4957-9.841831.0091
138.0733-1.7482-0.50661.9488-2.95446.12320.232-0.43530.29080.22470.288-0.14410.443-1.2729-0.53180.58230.02480.10060.6235-0.02790.37075.99474.068149.306
141.9518-1.30511.10677.389-1.40254.05340.0813-0.84390.1496-0.83410.5290.06580.21060.2567-0.61040.7912-0.34070.22170.7788-0.17890.5249-8.013510.337960.5748
156.113-1.4746-0.4638.46264.1149.1683-0.67620.5603-0.08210.77630.93461.4221.2223-0.9712-0.21610.8665-0.15110.04740.88890.13750.6404-13.0416-1.104374.9685
162.0936-1.4881-1.51693.41723.41683.4174-1.1052-0.41250.60811.07270.80380.5714-0.4451-1.6170.26860.87760.25340.20951.03580.1141.0032-19.36968.987384.0703
172.419-1.27591.54235.02470.08153.46230.36281.0322-1.5226-1.51270.0966-0.65540.67070.3665-0.4941.0116-0.28280.19591.0672-0.48971.033-11.5692-14.842220.0432
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 560 )
2X-RAY DIFFRACTION2chain 'A' and (resid 561 through 730 )
3X-RAY DIFFRACTION3chain 'A' and (resid 731 through 889 )
4X-RAY DIFFRACTION4chain 'A' and (resid 890 through 1366 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 20 )
6X-RAY DIFFRACTION6chain 'B' and (resid 21 through 30 )
7X-RAY DIFFRACTION7chain 'B' and (resid 31 through 40 )
8X-RAY DIFFRACTION8chain 'B' and (resid 41 through 70 )
9X-RAY DIFFRACTION9chain 'B' and (resid 71 through 75 )
10X-RAY DIFFRACTION10chain 'B' and (resid 76 through 81 )
11X-RAY DIFFRACTION11chain 'C' and (resid 1 through 5 )
12X-RAY DIFFRACTION12chain 'C' and (resid 6 through 10 )
13X-RAY DIFFRACTION13chain 'C' and (resid 11 through 15 )
14X-RAY DIFFRACTION14chain 'C' and (resid 16 through 20 )
15X-RAY DIFFRACTION15chain 'C' and (resid 21 through 25 )
16X-RAY DIFFRACTION16chain 'C' and (resid 26 through 28 )
17X-RAY DIFFRACTION17chain 'D' and (resid 5 through 12 )

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