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- PDB-4un4: Crystal structure of Cas9 bound to PAM-containing DNA target with... -

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Basic information

Entry
Database: PDB / ID: 4un4
TitleCrystal structure of Cas9 bound to PAM-containing DNA target with mismatches at positions 1-2
Components
  • (TARGET DNA STRAND ...) x 2
  • CRISPR-ASSOCIATED ENDONUCLEASE CAS9/CSN1
  • NON-TARGET DNA STRAND
  • SGRNA
KeywordsHYDROLASE/DNA/RNA / HYDROLASE-DNA-RNA COMPLEX / GENOME EDITING / RNP / 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 / MOLECULAR REPLACEMENT / Resolution: 2.371 Å
AuthorsAnders, C. / Niewoehner, O. / Duerst, A. / Jinek, M.
CitationJournal: Nature / Year: 2014
Title: Structural Basis of Pam-Dependent Target DNA Recognition by the Cas9 Endonuclease
Authors: Anders, C. / Niewoehner, O. / Duerst, A. / Jinek, M.
History
DepositionMay 25, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2014Group: Database references
Revision 1.2Oct 1, 2014Group: Database references
Revision 1.3Jan 10, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_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 / _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)197,77913
Polymers197,5855
Non-polymers1948
Water12,376687
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19930 Å2
ΔGint-230.1 kcal/mol
Surface area74620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.780, 66.816, 186.834
Angle α, β, γ (deg.)90.00, 111.39, 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: 3286.189 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: 26788.984 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#2: Protein CRISPR-ASSOCIATED ENDONUCLEASE CAS9/CSN1


Mass: 158875.031 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOCOCCUS PYOGENES (bacteria) / Strain: M1 / Plasmid: PEC-K-MBP / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA 2
References: UniProt: Q99ZW2, Hydrolases; Acting on ester bonds
#4: DNA chain NON-TARGET DNA STRAND


Mass: 3419.243 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)

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Non-polymers , 2 types, 695 molecules

#6: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 687 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsN-TERMINAL GAAS SEQUENCE IS DERIVED FROM EXPRESSION PLASMID. H840A MUTATION WAS INTRODUCED TO ...N-TERMINAL GAAS SEQUENCE IS DERIVED FROM EXPRESSION PLASMID. H840A MUTATION WAS INTRODUCED TO INACTIVATE THE HNH DOMAIN. D10A MUTATION WAS INTRODUCED TO INACTIVATE THE RUVC DOMAIN.

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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: 2.68 Å3/Da / Density % sol: 54.1 % / Description: NONE
Crystal growpH: 8.5
Details: 0.1 M TRIS-ACETATE, PH 8.5, 0.3 M KSCN, 15% (W/V) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: May 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.37→47.49 Å / Num. obs: 160249 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 16.5
Reflection shellResolution: 2.37→2.46 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 2.2 / % possible all: 91.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4UN3
Resolution: 2.371→47.493 Å / SU ML: 0.36 / σ(F): 1.3 / Phase error: 27.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2481 8029 5 %
Rwork0.2169 --
obs0.2185 160249 98.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.371→47.493 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10716 2503 8 687 13914
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01313721
X-RAY DIFFRACTIONf_angle_d0.69419015
X-RAY DIFFRACTIONf_dihedral_angle_d15.8845549
X-RAY DIFFRACTIONf_chiral_restr0.0452169
X-RAY DIFFRACTIONf_plane_restr0.0021994
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3709-2.39790.40681880.34193607X-RAY DIFFRACTION70
2.3979-2.42610.34812640.30965039X-RAY DIFFRACTION99
2.4261-2.45570.35322680.3125039X-RAY DIFFRACTION99
2.4557-2.48680.34522740.3095152X-RAY DIFFRACTION99
2.4868-2.51950.34222680.30565083X-RAY DIFFRACTION99
2.5195-2.5540.33212720.31195140X-RAY DIFFRACTION100
2.554-2.59050.36242820.31025070X-RAY DIFFRACTION100
2.5905-2.62910.36652750.29355180X-RAY DIFFRACTION100
2.6291-2.67020.31172650.28195120X-RAY DIFFRACTION100
2.6702-2.7140.34322690.28725156X-RAY DIFFRACTION100
2.714-2.76080.36382360.28625084X-RAY DIFFRACTION100
2.7608-2.8110.31272810.26685164X-RAY DIFFRACTION100
2.811-2.8650.30963020.27445126X-RAY DIFFRACTION100
2.865-2.92350.31562610.26995169X-RAY DIFFRACTION100
2.9235-2.98710.30752720.26815074X-RAY DIFFRACTION100
2.9871-3.05660.27172700.26025234X-RAY DIFFRACTION100
3.0566-3.1330.31522840.26045016X-RAY DIFFRACTION100
3.133-3.21770.30782450.24175151X-RAY DIFFRACTION100
3.2177-3.31230.25442950.23045171X-RAY DIFFRACTION100
3.3123-3.41920.25632550.22225139X-RAY DIFFRACTION100
3.4192-3.54140.24592790.21265156X-RAY DIFFRACTION100
3.5414-3.68310.22462660.19325106X-RAY DIFFRACTION100
3.6831-3.85070.19152670.18945137X-RAY DIFFRACTION100
3.8507-4.05360.20222830.18075118X-RAY DIFFRACTION100
4.0536-4.30740.17892670.17295156X-RAY DIFFRACTION100
4.3074-4.63970.19732640.16915108X-RAY DIFFRACTION100
4.6397-5.10610.20492740.16295143X-RAY DIFFRACTION100
5.1061-5.84390.23372650.17585120X-RAY DIFFRACTION100
5.8439-7.35820.20812720.1915150X-RAY DIFFRACTION100
7.3582-47.50260.17962660.16725112X-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)
10.0211-0.00110.04760.0325-0.02890.11630.02250.09120.03670.0052-0.01010.00260.03310.08640.0977-0.0217-0.07520.00560.14910.00420.056218.292256.9954378.7395
20.02250.017-0.00010.019-0.01260.0122-0.06450.0223-0.01120.0395-0.00970.028-0.05450.000100.25330.01840.02650.2468-0.00970.1174245.51848.4515411.7959
30.1256-0.07730.03180.0707-0.07950.30090.0232-0.02960.02370.04790.0066-0.013-0.04390.14130.07730.0507-0.0149-0.02460.0574-0.00560.1145227.478361.6085408.1712
40.0544-0.00450.03030.08180.06540.1152-0.0089-0.0803-0.03270.1180.0519-0.01770.11920.03510.05620.114-0.03890.01820.04290.01330.1061200.79239.974411.6218
50.14990.0563-0.02380.14060.07290.0473-0.05520.1056-0.04220.08230.03110.05960.2327-0.08050.10230.1138-0.22050.04530.0508-0.01890.1055190.974636.2348381.8885
60.06790.0008-0.00760.0056-0.00420.05350.06220.01930.03880.016-0.00870.00570.0690.03330.02230.1328-0.00150.01960.1487-0.04330.0908222.749552.4379390.0209
70.001-0.0016-0.00060.00220.00110.00080.01450.00660.0148-0.00330.01170.00120.00070.000900.66660.0578-0.040.6156-0.11650.4669240.533430.5952349.8992
80.04130.0083-0.03790.0260.0410.15160.02710.03610.0613-0.05120.09030.02950.06270.07660.02130.1409-0.012-0.01780.16930.01940.1778218.484859.3358377.2643
90.00260.00030.00140.00090.00090.00070.0219-0.0069-0.02930.00610.01410.0103-0.00380.004600.4086-0.0224-0.00840.36710.10390.5036182.304466.4652378.1507
100.00290.00180.00010.0012-0.00070.00050.0176-0.00810.01340.00040.0158-0.0037-0.01550.0072-00.4931-0.0180.02480.45410.03760.4681176.957762.3073386.0416
110.0039-0.0022-0.00240.00270.00010.0021-0.03060.01490.0110.0059-0.0134-0.04650.0232-0.025-00.2933-0.0109-0.02640.2632-0.04830.2896210.455634.6143374.5199
120.00280.0016-0.00190.0051-0.00260.00210.00760.0233-0.03380.0050.03290.00190.0080.00670.00050.2818-0.04640.0120.221-0.13180.2881207.195935.0919371.6181
130.0015-0.0021-0.00110.0064-0.00020.00070.0108-0.0179-0.010.0022-0.01820.03440.03810.0079-00.2308-0.04770.040.2289-0.0070.2184215.635357.3055405.0316
1400.00030.00060.00310.00060.0001-0.0079-0.00440.0318-0.0253-0.00760.01130.0411-0.002400.2379-0.04120.03930.23240.07490.2339204.249153.659427.4364
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN B AND (RESID 4 THROUGH 163 )
2X-RAY DIFFRACTION2CHAIN B AND (RESID 164 THROUGH 283 )
3X-RAY DIFFRACTION3CHAIN B AND (RESID 284 THROUGH 711 )
4X-RAY DIFFRACTION4CHAIN B AND (RESID 712 THROUGH 1040 )
5X-RAY DIFFRACTION5CHAIN B AND (RESID 1041 THROUGH 1364 )
6X-RAY DIFFRACTION6CHAIN A AND (RESID 0 THROUGH 32 )
7X-RAY DIFFRACTION7CHAIN A AND (RESID 33 THROUGH 40 )
8X-RAY DIFFRACTION8CHAIN A AND (RESID 41 THROUGH 68 )
9X-RAY DIFFRACTION9CHAIN A AND (RESID 69 THROUGH 76 )
10X-RAY DIFFRACTION10CHAIN A AND (RESID 77 THROUGH 81 )
11X-RAY DIFFRACTION11CHAIN C AND (RESID 1 THROUGH 11 )
12X-RAY DIFFRACTION12CHAIN D AND (RESID 3 THROUGH 12 )
13X-RAY DIFFRACTION13CHAIN E AND (RESID 12 THROUGH 21 )
14X-RAY DIFFRACTION14CHAIN E AND (RESID 22 THROUGH 28 )

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