[English] 日本語
Yorodumi
- PDB-4cmq: Crystal structure of Mn-bound S.pyogenes Cas9 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4cmq
TitleCrystal structure of Mn-bound S.pyogenes Cas9
ComponentsCRISPR-ASSOCIATED ENDONUCLEASE CAS9/CSN1
KeywordsHYDROLASE / DNASE / ENDONUCLEASE / RNA-GUIDED / IMMUNITY / CRRNA / GENOME EDITING
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
: / CRISPR-associated endonuclease Cas9/Csn1
Similarity search - Component
Biological speciesSTREPTOCOCCUS PYOGENES (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.09 Å
AuthorsJinek, M. / Jiang, F. / Taylor, D.W. / Sternberg, S.H. / Kaya, E. / Ma, E. / Anders, C. / Hauer, M. / Zhou, K. / Lin, S. ...Jinek, M. / Jiang, F. / Taylor, D.W. / Sternberg, S.H. / Kaya, E. / Ma, E. / Anders, C. / Hauer, M. / Zhou, K. / Lin, S. / Kaplan, M. / Iavarone, A.T. / Charpentier, E. / Nogales, E. / Doudna, J.A.
CitationJournal: Science / Year: 2014
Title: Structures of Cas9 endonucleases reveal RNA-mediated conformational activation.
Authors: Martin Jinek / Fuguo Jiang / David W Taylor / Samuel H Sternberg / Emine Kaya / Enbo Ma / Carolin Anders / Michael Hauer / Kaihong Zhou / Steven Lin / Matias Kaplan / Anthony T Iavarone / ...Authors: Martin Jinek / Fuguo Jiang / David W Taylor / Samuel H Sternberg / Emine Kaya / Enbo Ma / Carolin Anders / Michael Hauer / Kaihong Zhou / Steven Lin / Matias Kaplan / Anthony T Iavarone / Emmanuelle Charpentier / Eva Nogales / Jennifer A Doudna /
Abstract: Type II CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated) systems use an RNA-guided DNA endonuclease, Cas9, to generate double-strand breaks in invasive DNA ...Type II CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated) systems use an RNA-guided DNA endonuclease, Cas9, to generate double-strand breaks in invasive DNA during an adaptive bacterial immune response. Cas9 has been harnessed as a powerful tool for genome editing and gene regulation in many eukaryotic organisms. We report 2.6 and 2.2 angstrom resolution crystal structures of two major Cas9 enzyme subtypes, revealing the structural core shared by all Cas9 family members. The architectures of Cas9 enzymes define nucleic acid binding clefts, and single-particle electron microscopy reconstructions show that the two structural lobes harboring these clefts undergo guide RNA-induced reorientation to form a central channel where DNA substrates are bound. The observation that extensive structural rearrangements occur before target DNA duplex binding implicates guide RNA loading as a key step in Cas9 activation.
History
DepositionJan 17, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2014Group: Database references
Revision 1.2Mar 26, 2014Group: Database references
Revision 1.3Dec 20, 2023Group: 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_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_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CRISPR-ASSOCIATED ENDONUCLEASE CAS9/CSN1
B: CRISPR-ASSOCIATED ENDONUCLEASE CAS9/CSN1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)319,26321
Polymers317,9722
Non-polymers1,29119
Water0
1
A: CRISPR-ASSOCIATED ENDONUCLEASE CAS9/CSN1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,65911
Polymers158,9861
Non-polymers67310
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CRISPR-ASSOCIATED ENDONUCLEASE CAS9/CSN1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,60410
Polymers158,9861
Non-polymers6189
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)159.880, 210.120, 90.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.99971, -0.0238, 0.0032), (-0.0239, -0.99916, 0.03344), (0.0024, -0.0335, -0.99944)
Vector: -1.29052, -158.01754, 40.6985)

-
Components

#1: Protein CRISPR-ASSOCIATED ENDONUCLEASE CAS9/CSN1 / CAS9


Mass: 158986.109 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOCOCCUS PYOGENES (bacteria) / Strain: SEROTYPE 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
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
Sequence detailsM-TERMINAL GAAS IS DERIVED FROM THE EXPRESSION VECTOR

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 49 % / Description: NONE
Crystal growpH: 8.5
Details: 0.1 M TRIS 8.5, 0.3 M LITHIUM SULFATE, 15% PEG 3350 SOAKED IN MOTHER LIQUOR SUPPLEMENTED WITH 20 MM MNCL2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.09→47.53 Å / Num. obs: 56200 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 19.1
Reflection shellResolution: 3.09→3.18 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.94 / Mean I/σ(I) obs: 2.3 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8.2_1309)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4CMP
Resolution: 3.09→47.528 Å / SU ML: 0.45 / σ(F): 1.36 / Phase error: 28.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2771 1500 2.7 %
Rwork0.2493 --
obs0.25 56200 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.09→47.528 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18861 0 43 0 18904
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00419209
X-RAY DIFFRACTIONf_angle_d0.77225808
X-RAY DIFFRACTIONf_dihedral_angle_d15.0137295
X-RAY DIFFRACTIONf_chiral_restr0.0572917
X-RAY DIFFRACTIONf_plane_restr0.0043265
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0901-3.18980.37041000.3434438X-RAY DIFFRACTION89
3.1898-3.30380.37012000.31644879X-RAY DIFFRACTION100
3.3038-3.4360.35071000.28314975X-RAY DIFFRACTION100
3.436-3.59240.3271000.27665004X-RAY DIFFRACTION100
3.5924-3.78170.30712000.26474944X-RAY DIFFRACTION100
3.7817-4.01850.27911000.24974989X-RAY DIFFRACTION100
4.0185-4.32860.26841000.2315075X-RAY DIFFRACTION100
4.3286-4.76380.26532000.21384931X-RAY DIFFRACTION100
4.7638-5.45230.28121000.23295084X-RAY DIFFRACTION100
5.4523-6.8660.26352000.26585033X-RAY DIFFRACTION100
6.866-47.53370.20771000.235348X-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)
10.27890.0428-0.04350.2464-0.00980.31990.0160.178-0.1325-0.0666-0.0895-0.0876-0.1715-0.1963-0.28070.0928-0.0857-0.0383-0.19770.06480.0263-25.3079-51.707-6.2065
20.0128-0.0161-0.01560.11550.02140.00930.1291-0.0639-0.07290.01450.0537-0.0809-0.1784-0.02370.36820.2744-0.0288-0.04870.04540.13020.2179-14.2961-58.503116.3269
30.53130.1534-0.57270.3713-0.22980.7312-0.13720.2636-0.1153-0.090.12950.08610.0603-0.3784-0.05190.1427-0.0806-0.0450.38450.00260.2513-49.1291-84.4228-4.493
40.32870.0239-0.00530.2927-0.18280.38650.05290.1094-0.0394-0.0571-0.0511-0.0903-0.01090.16830.17510.24780.0761-0.00430.14090.01350.104-24.1471-40.8372-15.1179
50.3572-0.0427-0.03220.3237-0.02830.70310.11030.09950.1829-0.16950.05210.0692-0.3655-0.11150.37450.32990.18650.02680.29480.08390.0876-37.6452-24.1799-23.2053
60.2307-0.01230.18350.41530.18410.3275-0.0261-0.16510.20860.2665-0.25530.00830.0889-0.3079-0.8025-0.0401-0.03460.1671-0.08660.1610.0192-29.9152-99.488454.7149
70.14260.13620.06020.2235-0.04490.1555-0.14610.10760.0079-0.1798-0.0734-0.16820.09310.1218-0.58340.0892-0.07770.1981-0.00640.17410.2649-15.9286-104.611631.9375
80.1017-0.01360.05360.33760.01140.1968-0.1627-0.09720.0070.09370.1330.3286-0.0601-0.115-0.05930.27770.02630.04610.24750.20380.4244-46.9781-74.026744.5439
90.34650.1236-0.03850.0505-0.03770.1175-0.05890.14530.1896-0.04310.030.0899-0.0114-0.2555-0.45590.26-0.08340.2440.23670.00170.3748-49.9242-95.941761.2777
100.7077-0.02170.13230.0873-0.12270.33240.0769-0.178-0.49890.07-0.16970.08370.20890.13340.13140.3533-0.05240.01970.54580.13320.4844-7.7638-135.820461.1597
110.35040.0772-0.17470.1983-0.10050.26510.1029-0.4159-0.09220.4380.0184-0.05970.2341-0.07590.40920.1849-0.22950.21390.33620.1063-0.0673-39.4428-128.485868.6259
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 4 THROUGH 283 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 284 THROUGH 411 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 412 THROUGH 642 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 643 THROUGH 953 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 954 THROUGH 1363 )
6X-RAY DIFFRACTION6CHAIN B AND (RESID 4 THROUGH 207 )
7X-RAY DIFFRACTION7CHAIN B AND (RESID 208 THROUGH 394 )
8X-RAY DIFFRACTION8CHAIN B AND (RESID 395 THROUGH 678 )
9X-RAY DIFFRACTION9CHAIN B AND (RESID 679 THROUGH 751 )
10X-RAY DIFFRACTION10CHAIN B AND (RESID 752 THROUGH 925 )
11X-RAY DIFFRACTION11CHAIN B AND (RESID 926 THROUGH 1363 )

+
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