[English] 日本語
Yorodumi
- PDB-5fw3: Crystal structure of SpCas9 variant VRER bound to sgRNA and TGCG ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5fw3
TitleCrystal structure of SpCas9 variant VRER bound to sgRNA and TGCG PAM target DNA
Components
  • CRISPR-ASSOCIATED ENDONUCLEASE CAS9/CSN1
  • NON-TARGET DNA STRAND
  • SGRNASubgenomic mRNA
  • TARGET DNA STRAND
KeywordsHYDROLASE/DNA/RNA / HYDROLASE-DNA-RNA COMPLEX / CRISPR / CAS9 / ENDONUCLEASE / PAM / 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 / 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 (bacteria)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsAnders, C. / Bargsten, K. / Jinek, M.
CitationJournal: Mol.Cell / Year: 2016
Title: Structural Plasticity of Pam Recognition by Engineered Variants of the RNA-Guided Endonuclease Cas9.
Authors: Anders, C. / Bargsten, K. / Jinek, M.
History
DepositionFeb 11, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 15, 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 2.1Jan 10, 2024Group: 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_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.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.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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)198,51917
Polymers198,0404
Non-polymers47913
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22470 Å2
ΔGint-173.4 kcal/mol
Surface area74860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.520, 67.800, 187.700
Angle α, β, γ (deg.)90.00, 111.15, 90.00
Int Tables number5
Space group name H-MC121

-
Components

-
DNA chain , 2 types, 2 molecules CD

#3: DNA chain TARGET DNA STRAND


Mass: 8553.552 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#4: DNA chain NON-TARGET DNA STRAND


Mass: 3710.454 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)

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

#1: RNA chain SGRNA / Subgenomic mRNA


Mass: 26788.984 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#2: Protein CRISPR-ASSOCIATED ENDONUCLEASE CAS9/CSN1 / CAS9 VRER VARIANT / SPCAS9


Mass: 158987.203 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

-
Non-polymers , 3 types, 165 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 39.098 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: K
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence detailsTHE N-TERMINAL GAAS SEQUENCE IS DERIVED FROM THE EXPRESSION VECTOR. THE D10A AND H840A MUTATIONS ...THE N-TERMINAL GAAS SEQUENCE IS DERIVED FROM THE EXPRESSION VECTOR. THE D10A AND H840A MUTATIONS HAVE BEEN ENGINEERED TO INACTIVATE THE ENZYME. THE G1218R, D1135V, R1335E, T1337R MUTATIONS ARE SPECIFIC FOR THE VRER SPYCAS9 VARIANT.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52 % / Description: NONE
Crystal growpH: 8.5 / Details: 0.1 M TRIS PH 8.5 0.3M KSCN 15% (W/V) PEG 3400

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Aug 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→47.98 Å / Num. obs: 57691 / % possible obs: 99.9 % / Observed criterion σ(I): 1.9 / Redundancy: 7 % / Biso Wilson estimate: 48.68 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 13.2
Reflection shellResolution: 2.7→2.77 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 1.9 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UN3
Resolution: 2.7→47.983 Å / SU ML: 0.37 / σ(F): 1.25 / Phase error: 27.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2419 5612 5 %
Rwork0.2144 --
obs0.2159 57665 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→47.983 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10824 2525 13 152 13514
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00813877
X-RAY DIFFRACTIONf_angle_d0.68219183
X-RAY DIFFRACTIONf_dihedral_angle_d17.6868133
X-RAY DIFFRACTIONf_chiral_restr0.0412192
X-RAY DIFFRACTIONf_plane_restr0.0032014
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.73070.39461830.35473489X-RAY DIFFRACTION100
2.7307-2.76280.37461890.31363539X-RAY DIFFRACTION100
2.7628-2.79650.31531880.31373577X-RAY DIFFRACTION100
2.7965-2.83190.29881880.28423505X-RAY DIFFRACTION100
2.8319-2.86920.32081950.28443602X-RAY DIFFRACTION100
2.8692-2.90850.34921810.30333510X-RAY DIFFRACTION100
2.9085-2.950.31851910.29373612X-RAY DIFFRACTION100
2.95-2.9940.30981900.29623504X-RAY DIFFRACTION100
2.994-3.04080.33591840.29513520X-RAY DIFFRACTION100
3.0408-3.09070.32481810.27663606X-RAY DIFFRACTION100
3.0907-3.14390.33161890.27823515X-RAY DIFFRACTION100
3.1439-3.20110.26981900.25953543X-RAY DIFFRACTION100
3.2011-3.26270.25691920.24263544X-RAY DIFFRACTION100
3.2627-3.32920.26091860.23553518X-RAY DIFFRACTION100
3.3292-3.40160.28981880.23693610X-RAY DIFFRACTION100
3.4016-3.48070.30081810.24353478X-RAY DIFFRACTION100
3.4807-3.56770.25191920.22583616X-RAY DIFFRACTION100
3.5677-3.66420.27591900.21453497X-RAY DIFFRACTION100
3.6642-3.77190.21361930.2073564X-RAY DIFFRACTION100
3.7719-3.89360.2021760.18843493X-RAY DIFFRACTION100
3.8936-4.03270.20981800.18673542X-RAY DIFFRACTION100
4.0327-4.19410.2371970.18543594X-RAY DIFFRACTION100
4.1941-4.38490.18491850.17963520X-RAY DIFFRACTION100
4.3849-4.61590.23551860.17853549X-RAY DIFFRACTION100
4.6159-4.90480.1941830.16543569X-RAY DIFFRACTION100
4.9048-5.28310.20811920.16773584X-RAY DIFFRACTION100
5.2831-5.81390.20611860.17183511X-RAY DIFFRACTION100
5.8139-6.65330.21111840.19083551X-RAY DIFFRACTION100
6.6533-8.37520.17981910.17993556X-RAY DIFFRACTION100
8.3752-47.99020.19481810.19333546X-RAY DIFFRACTION99
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)
11.26730.2919-0.41680.3472-0.0171.20770.03010.08060.09080.03660.0119-0.0055-0.01210.2012-0.06120.2265-0.0331-0.01260.19790.00020.2324111.127266.5513207.9633
22.3136-0.1504-1.4321.9535-0.48712.10290.2640.2437-0.28440.0473-0.49080.3698-0.6803-0.04320.17980.77030.0051-0.0010.6871-0.09970.6383138.958257.4722241.2633
31.3294-0.3119-0.22450.06770.06891.7925-0.0069-0.1707-0.09310.03530.10530.05730.13710.5991-0.07690.2334-0.0018-0.02320.37850.0160.3065126.447464.1906214.7241
41.7523-0.08320.1520.8476-0.74392.057-0.075-0.2493-0.18590.3583-0.0163-0.2303-0.31720.04450.07560.48230.0246-0.09280.2229-0.03580.3873112.615376.602257.335
50.63910.28450.52090.52130.030.7321-0.0834-0.0426-0.00910.1988-0.02410.0855-0.0041-0.25380.0650.40740.02720.08110.38110.0030.321489.73269.7524241.3465
61.5257-0.06470.1041.87470.17011.8185-0.06780.1246-0.1916-0.17760.1331-0.08790.37260.1652-0.02660.52040.0454-0.04540.4023-0.01150.4582108.508636.7626240.5618
70.89020.156-0.08640.3988-0.00350.8828-0.06580.0546-0.10890.07270.06280.00810.3685-0.2303-0.01410.4044-0.09920.03110.256-0.06380.34282.787147.0843220.9562
81.517-0.866-0.2822.42030.88782.7449-0.2230.0624-0.10590.10690.20950.04860.2925-0.5727-0.04660.5496-0.0099-0.00340.6491-0.10450.513498.691864.2669247.0207
91.06070.15030.12560.5172-0.04440.89880.1420.02180.16410.06130.1527-0.1320.27970.3282-0.24480.2558-0.01290.00020.2963-0.02540.2953118.568762.1621206.7601
100.35830.45450.1060.71150.61821.77360.19990.6709-0.1278-0.65640.11080.12490.4526-0.3436-0.31451.18510.1859-0.09831.1224-0.16980.6267132.085841.4032176.7237
111.08610.20280.40140.2957-0.15221.18130.05370.11150.032-0.0366-0.03440.0687-0.05420.06-0.01620.1814-0.0218-0.01410.2064-0.0110.2386106.80968.663204.8507
122.91591.56790.30421.95310.26011.19480.071-0.45930.7481-0.1295-0.1284-1.0271-0.96071.1461-0.021.0396-0.14740.14661.0578-0.02051.012271.923274.0792211.8276
133.07371.1056-0.4196.0171-0.7055.56890.37920.4917-0.247-0.0516-0.0847-0.0882-0.0325-0.9785-0.19580.6989-0.11750.0160.9253-0.2370.634794.412437.0028194.0278
140.8626-0.15090.18620.0110.00290.80180.0391-0.1702-0.01070.14860.07090.09910.2790.0379-0.09110.4252-0.0850.01450.34270.01970.3499103.616360.9158233.0179
153.7799-0.3153-0.60294.2453-0.09412.41820.06090.2589-0.61260.33660.109-0.86610.48510.6309-0.23160.5886-0.03470.09360.4686-0.12950.60898.95944.5507200.8576
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'B' AND (RESID 3 THROUGH 180 )
2X-RAY DIFFRACTION2CHAIN 'B' AND (RESID 181 THROUGH 300 )
3X-RAY DIFFRACTION3CHAIN 'B' AND (RESID 301 THROUGH 512 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 513 THROUGH 663 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 664 THROUGH 790 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 791 THROUGH 872 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 873 THROUGH 1365 )
8X-RAY DIFFRACTION8CHAIN 'A' AND (RESID 1 THROUGH 10 )
9X-RAY DIFFRACTION9CHAIN 'A' AND (RESID 11 THROUGH 30 )
10X-RAY DIFFRACTION10CHAIN 'A' AND (RESID 31 THROUGH 40 )
11X-RAY DIFFRACTION11CHAIN 'A' AND (RESID 41 THROUGH 70 )
12X-RAY DIFFRACTION12CHAIN 'A' AND (RESID 71 THROUGH 81 )
13X-RAY DIFFRACTION13CHAIN 'C' AND (RESID 1 THROUGH 5 )
14X-RAY DIFFRACTION14CHAIN 'C' AND (RESID 6 THROUGH 28 )
15X-RAY DIFFRACTION15CHAIN 'D' AND (RESID 2 THROUGH 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