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- PDB-5fq5: Crystal structure of Cas9-sgRNA-DNA complex solved by native SAD ... -

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Basic information

Entry
Database: PDB / ID: 5fq5
TitleCrystal structure of Cas9-sgRNA-DNA complex solved by native SAD phasing
Components
  • (TARGET DNA STRAND ...) x 2
  • CRISPR-ASSOCIATED ENDONUCLEASE CAS9/CSN1
  • NON-TARGET DNA STRAND
  • SGRNA
KeywordsHYDROLASE/DNA / HYDROLASE-DNA COMPLEX / CRISPR / CAS9 / GENOME EDITING / PROTEIN-RNA COMPLEX
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 / Cas9 RuvC domain / CRISPR-associated endonuclease Cas9 / HNH endonuclease / Cas9-type HNH domain ...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 / Cas9 RuvC domain / 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 (bacteria)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.136 Å
AuthorsOlieric, V. / Weinert, T. / Finke, A. / Anders, C. / Jinek, M. / Wang, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2016
Title: Data-Collection Strategy for Challenging Native Sad Phasing.
Authors: Olieric, V. / Weinert, T. / Finke, A.D. / Anders, C. / Li, D. / Olieric, N. / Borca, C.N. / Steinmetz, M.O. / Caffrey, M. / Jinek, M. / Wang, M.
History
DepositionDec 7, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 2.0Oct 23, 2019Group: Atomic model / Data collection / Other / Category: atom_site / pdbx_database_status
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_database_status.status_code_sf
Revision 2.1May 8, 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_site
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.ptnr1_symmetry / _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.ptnr3_symmetry / _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.ptnr1_symmetry / _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.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SGRNA
B: CRISPR-ASSOCIATED ENDONUCLEASE CAS9/CSN1
C: TARGET DNA STRAND PROXIMAL FRAGMENT
D: NON-TARGET DNA STRAND
E: TARGET DNA STRAND DISTAL FRAGMENT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,47120
Polymers197,9145
Non-polymers55715
Water19,9611108
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22520 Å2
ΔGint-181.2 kcal/mol
Surface area74720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.740, 67.570, 188.190
Angle α, β, γ (deg.)90.00, 111.31, 90.00
Int Tables number5
Space group name H-MC121

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Components

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TARGET DNA STRAND ... , 2 types, 2 molecules CE

#3: DNA chain TARGET DNA STRAND PROXIMAL FRAGMENT


Mass: 3295.203 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#5: DNA chain TARGET DNA STRAND DISTAL FRAGMENT


Mass: 5215.419 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)

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RNA chain / Protein / DNA chain , 3 types, 3 molecules ABD

#1: RNA chain SGRNA


Mass: 27118.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#2: Protein CRISPR-ASSOCIATED ENDONUCLEASE CAS9/CSN1 / SPYCAS9


Mass: 158875.031 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOCOCCUS PYOGENES (bacteria) / Gene: CAS9, CSN1, SPY_1046 / Plasmid: PEC-K-MBP / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2
References: UniProt: Q99ZW2, Hydrolases; Acting on ester bonds
#4: DNA chain NON-TARGET DNA STRAND


Mass: 3410.229 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)

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Non-polymers , 3 types, 1123 molecules

#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: K
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1108 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsD10A, H840A POINT MUTATIONS WERE INTRODUCED TO GENERATE CATALYTICALLY INACTIVE ENZYME N-TERMINAL ...D10A, H840A POINT MUTATIONS WERE INTRODUCED TO GENERATE CATALYTICALLY INACTIVE ENZYME N-TERMINAL GAAS SEQUENCE IS DERIVED FROM THE EPXRESSION VECTOR

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.1 %
Description: ACTUAL RMEAS FOR HIGHEST RESOLUTION SHELL IS 1.729
Crystal growpH: 8.5
Details: 0.1 M TRIS-ACETATE PH 8.5, 0.3 M KSCN, 15% PEG (W/V) 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 2.066
DetectorType: DECTRIS PILATUS / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.066 Å / Relative weight: 1
ReflectionResolution: 2.14→50 Å / Num. obs: 113763 / % possible obs: 96.7 % / Observed criterion σ(I): 0.76 / Redundancy: 148.1 % / Biso Wilson estimate: 40.89 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 28.61
Reflection shellResolution: 2.14→2.19 Å / Redundancy: 8.3 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 0.76 / % possible all: 65

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.136→47.906 Å / SU ML: 0.32 / σ(F): 1.33 / Phase error: 24.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2248 3834 1.8 %
Rwork0.1909 --
obs0.1915 113763 96.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.136→47.906 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10774 2466 15 1108 14363
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01113802
X-RAY DIFFRACTIONf_angle_d0.65719038
X-RAY DIFFRACTIONf_dihedral_angle_d15.218079
X-RAY DIFFRACTIONf_chiral_restr0.0412172
X-RAY DIFFRACTIONf_plane_restr0.0032007
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.136-2.16310.476740.44664538X-RAY DIFFRACTION54
2.1631-2.19150.5131020.40016220X-RAY DIFFRACTION76
2.1915-2.22160.411400.34927700X-RAY DIFFRACTION93
2.2216-2.25330.32291430.29957881X-RAY DIFFRACTION96
2.2533-2.28690.29661430.26597958X-RAY DIFFRACTION97
2.2869-2.32270.29821440.24798094X-RAY DIFFRACTION98
2.3227-2.36080.34651460.23678105X-RAY DIFFRACTION99
2.3608-2.40150.29311480.23088225X-RAY DIFFRACTION100
2.4015-2.44510.2741480.23068258X-RAY DIFFRACTION100
2.4451-2.49220.25261470.22498245X-RAY DIFFRACTION100
2.4922-2.5430.2431450.22418208X-RAY DIFFRACTION100
2.543-2.59830.25881460.21588252X-RAY DIFFRACTION100
2.5983-2.65880.23731490.21338158X-RAY DIFFRACTION100
2.6588-2.72520.24491460.2068310X-RAY DIFFRACTION100
2.7252-2.79890.27781480.2118204X-RAY DIFFRACTION100
2.7989-2.88130.29031450.20648194X-RAY DIFFRACTION100
2.8813-2.97420.23491460.21278281X-RAY DIFFRACTION100
2.9742-3.08050.27471460.2168254X-RAY DIFFRACTION100
3.0805-3.20380.25031450.20788216X-RAY DIFFRACTION100
3.2038-3.34960.25981420.1878185X-RAY DIFFRACTION100
3.3496-3.52620.18441480.18228260X-RAY DIFFRACTION100
3.5262-3.7470.19591490.16878257X-RAY DIFFRACTION100
3.747-4.03620.20051470.15618161X-RAY DIFFRACTION100
4.0362-4.44210.15621480.14768258X-RAY DIFFRACTION100
4.4421-5.08430.17651510.14418228X-RAY DIFFRACTION100
5.0843-6.40320.19931500.16778250X-RAY DIFFRACTION100
6.4032-47.91850.1851480.16978222X-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)
12.1075-1.76-1.13212.54961.12332.5987-0.07270.2234-0.17810.2383-0.11470.26190.2054-0.26540.14150.4708-0.03250.02440.4602-0.06410.437-12.17236.449273.2178
20.6648-0.11620.07470.53810.08550.7873-0.0045-0.00580.06650.11520.1013-0.06440.26020.2063-0.04210.2592-0.0082-0.02430.2894-0.02080.28026.8183.477434.3972
30.58970.420.74391.13651.04571.28230.47120.8095-0.2025-1.151-0.19210.58640.7486-0.2161-0.23071.22310.3178-0.17871.2289-0.20560.693122.4154-17.39781.4951
40.51610.36770.1790.3324-0.04670.86390.00340.11250.1028-0.03410.0610.04990.03520.0838-0.07630.2924-0.0245-0.02710.2963-0.0020.298-1.24518.631329.2243
50.0249-0.0408-0.03670.05210.05580.05960.06730.42651.4471-0.3087-0.0949-0.2554-1.92720.8512-0.03271.0392-0.18830.07080.65860.25791.1737-39.206617.235229.1605
63.14712.15320.49694.69350.87391.4520.1974-0.08450.7391-0.3610.3827-0.3473-1.08080.4463-0.36510.7148-0.22570.19250.9535-0.08230.9359-40.073114.573937.2873
70.86010.228-0.0270.2495-0.0460.59060.07660.0803-0.0270.0661-0.0438-0.0314-0.01950.1875-0.01780.2751-0.0435-0.02460.2836-0.00870.27895.48246.501737.0989
82.06520.029-0.90681.6525-0.42862.3250.4040.5271-0.2831-0.1614-0.6480.7321-0.9183-1.37950.24270.73520.2660.02370.7893-0.15530.621223.5526-3.403467.1486
90.9978-0.3688-0.27780.22610.31031.3622-0.0277-0.1139-0.09420.16820.0696-0.00370.14140.416-0.04410.25510.0002-0.03790.33610.01860.304616.775.327941.0421
100.7610.15890.15950.9271-0.47832.0236-0.0637-0.1286-0.03220.2430.0833-0.0652-0.2569-0.0362-0.02380.390.0554-0.01650.2346-0.0180.3096-3.485919.22380.7224
110.9769-0.44170.25240.5415-0.06780.648-0.036-0.148-0.07160.14790.0737-0.06970.19070.0161-0.03610.43-0.04290.00590.3154-0.01160.3788-17.8292-10.801364.0513
121.40180.4469-0.69470.6117-0.18461.4749-0.1160.0968-0.22030.03180.04520.02930.4544-0.15250.01440.3981-0.10330.00450.2459-0.0490.3521-28.4193-13.891236.3491
133.70130.69312.7215.38550.41534.6796-0.07570.7194-0.8187-0.2515-0.2553-0.19521.0343-1.54820.14730.6999-0.19850.08130.9869-0.19470.5434-12.1729-18.702822.7849
140.01470.0676-0.01580.4247-0.12410.0383-0.0788-0.1456-0.01950.1250.03890.120.0452-0.06510.0011.3683-0.15290.27940.9101-0.08291.056-6.4755-6.967234.4763
153.5671-0.9132-1.14663.9510.22561.691-0.12040.4581-0.9737-0.15630.1619-0.15840.67270.177-0.25910.5168-0.09790.00110.3915-0.18130.5751-12.1018-14.711724.019
161.32990.2926-1.0820.8423-0.61980.9856-0.0217-0.49840.11850.04480.05070.16840.17490.274-0.04660.4277-0.0424-0.00610.3998-0.01820.3421-3.65987.690357.6681
171.3033-0.0151-0.09951.31660.78762.9819-0.06290.18510.06990.068-0.03430.43070.467-0.7168-0.01610.4946-0.08550.02660.50920.05830.4322-15.18543.87980.0395
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 0 THROUGH 9 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 10 THROUGH 29 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 30 THROUGH 39 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 40 THROUGH 69 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 70 THROUGH 74 )
6X-RAY DIFFRACTION6CHAIN A AND (RESID 75 THROUGH 82 )
7X-RAY DIFFRACTION7CHAIN B AND (RESID 4 THROUGH 207 )
8X-RAY DIFFRACTION8CHAIN B AND (RESID 208 THROUGH 286 )
9X-RAY DIFFRACTION9CHAIN B AND (RESID 287 THROUGH 512 )
10X-RAY DIFFRACTION10CHAIN B AND (RESID 513 THROUGH 730 )
11X-RAY DIFFRACTION11CHAIN B AND (RESID 731 THROUGH 1030 )
12X-RAY DIFFRACTION12CHAIN B AND (RESID 1031 THROUGH 1365 )
13X-RAY DIFFRACTION13CHAIN C AND (RESID 1 THROUGH 8 )
14X-RAY DIFFRACTION14CHAIN C AND (RESID 9 THROUGH 9 )
15X-RAY DIFFRACTION15CHAIN D AND (RESID 3 THROUGH 12 )
16X-RAY DIFFRACTION16CHAIN E AND (RESID 12 THROUGH 21 )
17X-RAY DIFFRACTION17CHAIN E AND (RESID 22 THROUGH 28 )

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