[English] 日本語
Yorodumi
- PDB-3m7n: archaeoglobus fulgidus exosome with RNA bound to the active site -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3m7n
Titlearchaeoglobus fulgidus exosome with RNA bound to the active site
Components
  • (Probable exosome complex exonuclease ...) x 2
  • 5'-R(*C*UP*CP*CP*CP*C)-3'
  • Putative uncharacterized protein AF_0206
KeywordsHYDROLASE/RNA / exosome / RNA / Exonuclease / Hydrolase / Nuclease / HYDROLASE-RNA complex
Function / homology
Function and homology information


exosome (RNase complex) / RNA catabolic process / RNA processing / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-RNA exonuclease activity / RNA binding / zinc ion binding / cytoplasm
Similarity search - Function
Exosome complex component Csl4, archaea / Exosome complex component Rrp41 / Exosome complex component Rrp42, archaea / Exosome complex component CSL4, C-terminal / Exosome complex component, N-terminal domain / Exosome complex component Csl4 / Exosome component EXOSC1/CSL4 / Exosome complex exonuclease RRP4 N-terminal region / GHMP Kinase, N-terminal domain / Exoribonuclease, phosphorolytic domain 2 ...Exosome complex component Csl4, archaea / Exosome complex component Rrp41 / Exosome complex component Rrp42, archaea / Exosome complex component CSL4, C-terminal / Exosome complex component, N-terminal domain / Exosome complex component Csl4 / Exosome component EXOSC1/CSL4 / Exosome complex exonuclease RRP4 N-terminal region / GHMP Kinase, N-terminal domain / Exoribonuclease, phosphorolytic domain 2 / 3' exoribonuclease family, domain 2 / Ubiquitin Ligase Nedd4; Chain: W; - #10 / Exoribonuclease, phosphorolytic domain 1 / PNPase/RNase PH domain superfamily / Exoribonuclease, PH domain 2 superfamily / 3' exoribonuclease family, domain 1 / Ubiquitin Ligase Nedd4; Chain: W; / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Ribosomal Protein S5; domain 2 / Ribosomal protein S1-like RNA-binding domain / S1 domain / Single Sheet / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Ribosomal protein S5 domain 2-type fold / Nucleic acid-binding, OB-fold / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
RNA / Exosome complex component Rrp42 / Exosome complex component Rrp41 / Exosome complex component Csl4
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsHartung, S. / Hopfner, K.-P.
CitationJournal: Nucleic Acids Res. / Year: 2010
Title: Quantitative analysis of processive RNA degradation by the archaeal RNA exosome
Authors: Hartung, S. / Niederberger, T. / Hartung, M. / Tresch, A. / Hopfner, K.-P.
History
DepositionMar 16, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_seq_id / _struct_conn.ptnr1_label_asym_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 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative uncharacterized protein AF_0206
B: Putative uncharacterized protein AF_0206
C: Putative uncharacterized protein AF_0206
D: Probable exosome complex exonuclease 1
E: Probable exosome complex exonuclease 1
F: Probable exosome complex exonuclease 1
G: Probable exosome complex exonuclease 2
H: Probable exosome complex exonuclease 2
I: Probable exosome complex exonuclease 2
X: 5'-R(*C*UP*CP*CP*CP*C)-3'
Y: 5'-R(*C*UP*CP*CP*CP*C)-3'
Z: 5'-R(*C*UP*CP*CP*CP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,04815
Polymers236,85212
Non-polymers1963
Water12,899716
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31580 Å2
ΔGint-147 kcal/mol
Surface area81720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.268, 138.268, 262.273
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

-
Components

-
Probable exosome complex exonuclease ... , 2 types, 6 molecules DEFGHI

#2: Protein Probable exosome complex exonuclease 1 / exosome RNA binding protein Rrp41


Mass: 28860.266 Da / Num. of mol.: 3 / Mutation: R65E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: AF_0493 / Plasmid: pET-21 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3
References: UniProt: O29757, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters
#3: Protein Probable exosome complex exonuclease 2 / exosome RNA binding protein Rrp42


Mass: 28677.609 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: AF_0494 / Plasmid: pET-21 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3
References: UniProt: O29756, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters

-
Protein / RNA chain , 2 types, 6 molecules ABCXYZ

#1: Protein Putative uncharacterized protein AF_0206 / exosome RNA binding protein Csl4


Mass: 19625.604 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: AF_0206 / Plasmid: pET-28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 / References: UniProt: O30033
#4: RNA chain 5'-R(*C*UP*CP*CP*CP*C)-3'


Mass: 1787.117 Da / Num. of mol.: 3 / Source method: obtained synthetically

-
Non-polymers , 2 types, 719 molecules

#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 716 / 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: 2.65 Å3/Da / Density % sol: 53.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1 M Na Acetate, pH 4.6, 30% MPD, 100mM NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 6, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 94454 / Num. obs: 94417 / % possible obs: 94.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Biso Wilson estimate: 42.22 Å2
Reflection shellResolution: 2.4→2.5 Å / % possible all: 86.4

-
Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
PHENIX(phenix.refine: 1.4_129)refinement
XDSdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BA1

2ba1


Resolution: 2.4→48.057 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.83 / SU ML: 0.41 / σ(F): 1.96 / σ(I): 2 / Phase error: 24.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2556 5026 5.05 %RANDOM
Rwork0.1971 94428 --
all0.27 99465 --
obs0.2 89224 99.68 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.018 Å2 / ksol: 0.341 e/Å3
Displacement parametersBiso max: 153.88 Å2 / Biso mean: 49.712 Å2 / Biso min: 17.11 Å2
Baniso -1Baniso -2Baniso -3
1-2.483 Å20 Å2-0 Å2
2--2.483 Å20 Å2
3----4.966 Å2
Refine analyzeLuzzati coordinate error obs: 0.41 Å
Refinement stepCycle: LAST / Resolution: 2.4→48.057 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15866 274 3 716 16859
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00816376
X-RAY DIFFRACTIONf_angle_d1.12922120
X-RAY DIFFRACTIONf_dihedral_angle_d18.8646361
X-RAY DIFFRACTIONf_chiral_restr0.0692541
X-RAY DIFFRACTIONf_plane_restr0.0042862
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4002-2.42750.27471620.22962976X-RAY DIFFRACTION95
2.4275-2.45610.28551880.22453054X-RAY DIFFRACTION100
2.4561-2.4860.28081700.21413071X-RAY DIFFRACTION100
2.486-2.51750.29091810.21673139X-RAY DIFFRACTION100
2.5175-2.55060.31271610.2173107X-RAY DIFFRACTION100
2.5506-2.58550.28731650.21323095X-RAY DIFFRACTION100
2.5855-2.62250.27741670.20823129X-RAY DIFFRACTION100
2.6225-2.66160.27391650.20563128X-RAY DIFFRACTION100
2.6616-2.70320.28891610.20573106X-RAY DIFFRACTION100
2.7032-2.74750.30991660.2143100X-RAY DIFFRACTION100
2.7475-2.79490.3231600.22143153X-RAY DIFFRACTION100
2.7949-2.84570.32171620.22293113X-RAY DIFFRACTION100
2.8457-2.90040.29191720.21813114X-RAY DIFFRACTION100
2.9004-2.95960.28481670.21123148X-RAY DIFFRACTION100
2.9596-3.0240.29341970.2093093X-RAY DIFFRACTION100
3.024-3.09430.28871870.20683111X-RAY DIFFRACTION100
3.0943-3.17170.26331680.19543116X-RAY DIFFRACTION100
3.1717-3.25740.26651650.18773157X-RAY DIFFRACTION100
3.2574-3.35320.26011410.19863158X-RAY DIFFRACTION100
3.3532-3.46140.25831590.19093176X-RAY DIFFRACTION100
3.4614-3.58510.22211750.18533133X-RAY DIFFRACTION100
3.5851-3.72860.22641550.17473158X-RAY DIFFRACTION100
3.7286-3.89820.23351560.17123189X-RAY DIFFRACTION100
3.8982-4.10360.2221630.17373162X-RAY DIFFRACTION100
4.1036-4.36060.191550.15493206X-RAY DIFFRACTION100
4.3606-4.6970.21071780.1533185X-RAY DIFFRACTION100
4.697-5.16920.19311900.16283195X-RAY DIFFRACTION100
5.1692-5.9160.26171750.1843231X-RAY DIFFRACTION100
5.916-7.44910.27641560.20093292X-RAY DIFFRACTION100
7.4491-48.06710.21781590.20443433X-RAY DIFFRACTION98

+
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