[English] 日本語
Yorodumi
- PDB-5b2s: Crystal structure of the Streptococcus pyogenes Cas9 EQR variant ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5b2s
TitleCrystal structure of the Streptococcus pyogenes Cas9 EQR variant in complex with sgRNA and target DNA (TGAG PAM)
Components
  • CRISPR-associated endonuclease Cas9
  • Guide RNA
  • Non-target DNA, DNA (5'-D(*TP*GP*AP*GP*AP*TP*TP*G)-3')
  • Target DNA
KeywordsHYDROLASE/RNA/DNA / CRISPR-Cas9 / genome engineering / HYDROLASE-RNA-DNA 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 / 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
ACETATE ION / : / 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: 2.2 Å
AuthorsHirano, S. / Nishimasu, H. / Ishitani, R. / Nureki, O.
CitationJournal: Mol.Cell / Year: 2016
Title: Structural Basis for the Altered PAM Specificities of Engineered CRISPR-Cas9
Authors: Hirano, S. / Nishimasu, H. / Ishitani, R. / Nureki, O.
History
DepositionFeb 2, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2016Group: Database references
Revision 1.2Oct 4, 2017Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_detector ...citation / diffrn_detector / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_detector.detector ..._citation.journal_id_CSD / _diffrn_detector.detector / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 8, 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
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.ptnr2_symmetry / _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_conn.ptnr2_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)196,96123
Polymers196,1514
Non-polymers81019
Water9,782543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23360 Å2
ΔGint-168 kcal/mol
Surface area72740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.016, 67.822, 187.567
Angle α, β, γ (deg.)90.000, 111.120, 90.000
Int Tables number5
Space group name H-MC121

-
Components

-
DNA chain , 2 types, 2 molecules CD

#3: DNA chain Target DNA


Mass: 8454.472 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemical synthesis / Source: (synth.) Streptococcus pyogenes (bacteria)
#4: DNA chain Non-target DNA, DNA (5'-D(*TP*GP*AP*GP*AP*TP*TP*G)-3')


Mass: 2481.652 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Streptococcus pyogenes (bacteria)

-
RNA chain / Protein , 2 types, 2 molecules AB

#1: RNA chain Guide RNA /


Mass: 26209.588 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: in vitro transcription / Source: (synth.) Streptococcus pyogenes (bacteria)
#2: Protein CRISPR-associated endonuclease Cas9 / SpyCas9


Mass: 159005.094 Da / Num. of mol.: 1 / Mutation: D10A, C80L, C574E, H840A, D1135E, R1335Q, T1337R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes serotype M1 (bacteria)
Strain: serotype M1 / Gene: cas9, csn1, SPy_1046 / Production host: Escherichia coli (E. coli)
References: UniProt: Q99ZW2, Hydrolases; Acting on ester bonds

-
Non-polymers , 5 types, 562 molecules

#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 11 / 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 / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 543 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 15-17% PEG 3350, 0.4 M KSCN, 0.1 M Tris-acetate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→48.005 Å / Num. obs: 103809 / % possible obs: 97.8 % / Redundancy: 2.9 % / Net I/σ(I): 8
Reflection shellResolution: 2.2→2.24 Å

-
Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.10_2155: ???refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UN3
Resolution: 2.2→48.005 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.18
RfactorNum. reflection% reflection
Rfree0.2309 5165 4.98 %
Rwork0.2071 --
obs0.2083 103651 97.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 195.84 Å2 / Biso mean: 57.086 Å2 / Biso min: 21.79 Å2
Refinement stepCycle: final / Resolution: 2.2→48.005 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10483 2464 34 543 13524
Biso mean--50.24 42.24 -
Num. residues----1436
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00213460
X-RAY DIFFRACTIONf_angle_d0.46718706
X-RAY DIFFRACTIONf_chiral_restr0.0352169
X-RAY DIFFRACTIONf_plane_restr0.0031970
X-RAY DIFFRACTIONf_dihedral_angle_d17.0147832
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 (%)
2.2-2.2250.2961840.29343294347898
2.225-2.25120.28851700.29713239340997
2.2512-2.27870.35491610.28653256341797
2.2787-2.30750.28191660.2723266343298
2.3075-2.33790.2891710.27353243341496
2.3379-2.36990.3271540.26363061321592
2.3699-2.40370.2831750.27243283345898
2.4037-2.43960.33321570.27113324348198
2.4396-2.47770.32771610.26483245340698
2.4777-2.51840.29851990.25453330352998
2.5184-2.56180.29311750.24833275345098
2.5618-2.60840.28141710.25363323349498
2.6084-2.65850.28691970.24613256345398
2.6585-2.71280.27531920.24883290348298
2.7128-2.77180.27721690.24023213338298
2.7718-2.83620.24261540.24123279343397
2.8362-2.90720.29161480.2463153330193
2.9072-2.98580.27661730.24443345351899
2.9858-3.07360.25881700.24113345351599
3.0736-3.17280.25841630.23743298346198
3.1728-3.28620.2651710.21783314348598
3.2862-3.41770.21391630.20763320348399
3.4177-3.57320.23271810.20983298347998
3.5732-3.76150.23051640.18773173333793
3.7615-3.99710.17251680.17823334350298
3.9971-4.30550.20281820.16523338352099
4.3055-4.73840.17161690.1573375354499
4.7384-5.42330.19581850.16163302348797
5.4233-6.82970.18071620.1843335349796
6.8297-48.01590.19542100.17493379358997
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)
11.79330.42121.04065.73862.42518.38320.17150.0835-0.14830.0811-0.24590.24290.7467-0.97710.11820.4767-0.06680.06020.4568-0.08830.3939-11.40185.503371.881
21.8084-0.1737-1.06411.23850.53613.41370.0792-0.02490.01580.0880.0411-0.05140.26990.415-0.12590.222-0.0324-0.02650.3048-0.03350.28718.31592.941831.6968
360.8417-0.87576.4913-1.7657.19930.09680.72380.1858-1.38450.48720.25331.317-0.104-0.53251.14870.1842-0.10191.1261-0.19270.583822.3058-18.47451.8522
41.46810.2150.22910.3914-0.09341.23990.07390.11860.1333-0.0229-0.02620.0644-0.02750.1332-0.0570.2475-0.0455-0.01050.2747-0.00430.2861-3.35159.372429.586
50.0102-0.22730.01896.1482-0.39780.0277-0.33641.18072.9587-1.51490.4281-0.0802-2.82751.9151-0.09731.9801-0.48910.21561.04810.21231.7292-37.766719.409429.4053
66.0620.4144-2.24252.0421-0.63352.05230.6679-0.93521.47550.0254-0.1486-1.1593-1.83510.9349-0.4271.0306-0.13620.12251.1529-0.23070.9693-41.034613.71437.8937
71.4590.3469-0.34590.4507-0.07311.418-0.03810.01360.03490.01270.02770.09990.1-0.25990.00690.2431-0.04890.01480.2027-0.02840.278-24.3671.376341.1757
80.39010.56790.06390.8542-0.03090.98060.10320.1988-0.09120.1057-0.1646-0.0916-0.09080.79370.13430.2983-0.1120.02070.7478-0.00720.328525.34219.569132.7532
94.6037-2.2386-3.00963.0046-0.09615.23430.79540.9291-0.5954-0.7879-1.04210.7178-1.8546-1.41660.17721.01280.2985-0.05370.8083-0.17020.606825.6181-1.771966.9359
101.25580.1461-0.22952.02750.33322.39730.0237-0.0946-0.29380.33470.0808-0.21360.42630.9242-0.09720.29580.1108-0.07670.71750.02810.383924.2381-3.637834.087
110.420.07390.23130.6464-0.22373.0914-0.1302-0.060.00970.1490.1177-0.067-0.3669-0.12370.00780.42740.03320.01740.2694-0.04360.378-2.59820.518973.6328
121.1525-0.68590.12880.7528-0.03030.8289-0.0337-0.2206-0.0430.17040.1149-0.2020.27340.0952-0.07750.5176-0.0555-0.00180.4031-0.04780.4617-15.7723-11.464264.0821
131.33430.2512-0.29390.70170.15271.6291-0.02660.098-0.22190.1350.03550.09140.601-0.3269-0.00790.4696-0.15640.00520.2821-0.06430.3733-28.999-13.402238.5081
144.09443.20461.80277.63923.19955.1369-0.00960.5174-0.8622-0.50180.1204-0.0440.2852-0.0786-0.14910.4049-0.0106-0.01720.5072-0.13690.5065-9.0076-15.867725.1064
151.51370.1896-1.52870.2345-0.10384.10760.0539-0.26880.16660.15390.1350.16850.24420.0336-0.15410.4179-0.07850.03490.46170.02190.3336-7.33125.538665.1235
162.5173-0.03060.322.118-0.76745.15650.16221.103-0.9425-0.61080.0292-0.68180.97180.1879-0.17670.6005-0.06270.0690.6069-0.27570.6697-11.2147-15.808520.5482
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 10 )A1 - 10
2X-RAY DIFFRACTION2chain 'A' and (resid 11 through 30 )A11 - 30
3X-RAY DIFFRACTION3chain 'A' and (resid 31 through 40 )A31 - 40
4X-RAY DIFFRACTION4chain 'A' and (resid 41 through 70 )A41 - 70
5X-RAY DIFFRACTION5chain 'A' and (resid 71 through 75 )A71 - 75
6X-RAY DIFFRACTION6chain 'A' and (resid 76 through 81 )A76 - 81
7X-RAY DIFFRACTION7chain 'B' and (resid 4 through 85 )B4 - 85
8X-RAY DIFFRACTION8chain 'B' and (resid 86 through 207 )B86 - 207
9X-RAY DIFFRACTION9chain 'B' and (resid 208 through 299 )B208 - 299
10X-RAY DIFFRACTION10chain 'B' and (resid 300 through 445 )B300 - 445
11X-RAY DIFFRACTION11chain 'B' and (resid 446 through 730 )B446 - 730
12X-RAY DIFFRACTION12chain 'B' and (resid 731 through 980 )B731 - 980
13X-RAY DIFFRACTION13chain 'B' and (resid 981 through 1366 )B981 - 1366
14X-RAY DIFFRACTION14chain 'C' and (resid 1 through 10 )C1 - 10
15X-RAY DIFFRACTION15chain 'C' and (resid 11 through 28 )C11 - 28
16X-RAY DIFFRACTION16chain 'D' and (resid 5 through 12 )D5 - 12

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more