[English] 日本語
Yorodumi
- PDB-4qts: Crystal structure of Csm3-Csm4 subcomplex in the type III-A CRISP... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4qts
TitleCrystal structure of Csm3-Csm4 subcomplex in the type III-A CRISPR-Cas interference complex
Components
  • CRISPR type III-associated RAMP protein Csm3
  • CRISPR type III-associated RAMP protein Csm4
KeywordsRNA BINDING PROTEIN / CRISPR-associated protein / ferredoxin-like fold / Type III-A CRISPR-Cas system
Function / homology
Function and homology information


endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / RNA binding / metal ion binding
Similarity search - Function
Csm4, C-terminal / CRISPR Csm4 C-terminal domain / CRISPR-associated RAMP Csm3 / CRISPR type III-associated RAMP protein Csm4 / : / CRISPR type III-associated protein / RAMP superfamily
Similarity search - Domain/homology
CRISPR system Cms protein Csm4 / CRISPR system Cms endoribonuclease Csm3
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii DSM 2661 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.105 Å
AuthorsNumata, T. / Inanaga, H. / Osawa, T.
CitationJournal: J.Mol.Biol. / Year: 2015
Title: Crystal structure of the Csm3-Csm4 subcomplex in the type III-A CRISPR-Cas interference complex.
Authors: Numata, T. / Inanaga, H. / Sato, C. / Osawa, T.
History
DepositionJul 9, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CRISPR type III-associated RAMP protein Csm4
B: CRISPR type III-associated RAMP protein Csm4
C: CRISPR type III-associated RAMP protein Csm3
D: CRISPR type III-associated RAMP protein Csm3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,7316
Polymers148,6014
Non-polymers1312
Water00
1
A: CRISPR type III-associated RAMP protein Csm4
C: CRISPR type III-associated RAMP protein Csm3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,3663
Polymers74,3002
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-4 kcal/mol
Surface area25880 Å2
MethodPISA
2
B: CRISPR type III-associated RAMP protein Csm4
D: CRISPR type III-associated RAMP protein Csm3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,3663
Polymers74,3002
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-4 kcal/mol
Surface area25770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.653, 96.319, 194.797
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein CRISPR type III-associated RAMP protein Csm4 / CRISPR type III-A/Mtube-associated RAMP protein Csm4


Mass: 43922.531 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii DSM 2661 (archaea)
Gene: csm4, MJ1668 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIL / References: UniProt: Q59062
#2: Protein CRISPR type III-associated RAMP protein Csm3 / CRISPR type III-A/Mtube-associated RAMP protein Csm3


Mass: 30377.734 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii DSM 2661 (archaea)
Gene: csm3, MJ1669 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIL / References: UniProt: Q59063
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 50mM HEPES-Na (pH 6.8), 200mM potassium chrolide, 30% v/v Pentaerythritol propoxylate (5/4 PO/OH), VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 11, 2012
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator, liquid nitrogen cooling
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 25906 / % possible obs: 99.2 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 15.1
Reflection shellResolution: 3.1→3.29 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.557 / Mean I/σ(I) obs: 2.7 / Num. unique all: 30283 / % possible all: 99.4

-
Processing

Software
NameVersionClassification
XDSdata scaling
SHARPphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 3.105→43.46 Å / SU ML: 0.46 / σ(F): 1.37 / Phase error: 30.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2882 1296 5 %RANDOM
Rwork0.2251 ---
obs0.2282 25882 99.32 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.105→43.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8020 0 2 0 8022
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038154
X-RAY DIFFRACTIONf_angle_d0.70410896
X-RAY DIFFRACTIONf_dihedral_angle_d13.1123185
X-RAY DIFFRACTIONf_chiral_restr0.0291196
X-RAY DIFFRACTIONf_plane_restr0.0031359
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.1047-3.2290.34261400.299266499
3.229-3.37590.33291430.28542707100
3.3759-3.55380.31751430.27392728100
3.5538-3.77630.3191430.25292701100
3.7763-4.06770.32591430.2362732100
4.0677-4.47660.31371440.21782720100
4.4766-5.12350.24971460.18932776100
5.1235-6.45170.27351470.23092795100
6.4517-43.46430.271470.2092278795

+
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