[English] 日本語
Yorodumi
- PDB-4q8h: Structure of the Saccharomyces cerevisiae PAN2 pseudoubiquitin-hy... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4q8h
TitleStructure of the Saccharomyces cerevisiae PAN2 pseudoubiquitin-hydrolase-RNase module
ComponentsPAB-dependent poly(A)-specific ribonuclease subunit PAN2
KeywordsHYDROLASE / Ubiquitin carboxyl-terminal hydrolase-like domain / UCH / RNase / PAN3
Function / homology
Function and homology information


PAN complex / poly(A)-specific ribonuclease / poly(A)-specific ribonuclease activity / nuclear-transcribed mRNA poly(A) tail shortening / postreplication repair / P-body / mRNA processing / nucleic acid binding / metal ion binding / cytoplasm
Similarity search - Function
PAN2, UCH domain / PAN2-PAN3 deadenylation complex catalytic subunit PAN2 / : / Ubiquitin carboxyl-terminal hydrolase / PAN2 N-terminal / Exonuclease / Exonuclease, RNase T/DNA polymerase III / EXOIII / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. ...PAN2, UCH domain / PAN2-PAN3 deadenylation complex catalytic subunit PAN2 / : / Ubiquitin carboxyl-terminal hydrolase / PAN2 N-terminal / Exonuclease / Exonuclease, RNase T/DNA polymerase III / EXOIII / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / Quinoprotein alcohol dehydrogenase-like superfamily / Cysteine proteinases / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / WD40/YVTN repeat-like-containing domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
PAN2-PAN3 deadenylation complex catalytic subunit PAN2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsSchaefer, I.B. / Conti, E.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2014
Title: The structure of the Pan2-Pan3 core complex reveals cross-talk between deadenylase and pseudokinase.
Authors: Schafer, I.B. / Rode, M. / Bonneau, F. / Schussler, S. / Conti, E.
History
DepositionApr 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 4, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2014Group: Database references
Revision 1.2Jul 16, 2014Group: Database references
Revision 1.3Sep 20, 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 / 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_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _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.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PAB-dependent poly(A)-specific ribonuclease subunit PAN2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,0463
Polymers75,9971
Non-polymers492
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.712, 115.505, 257.449
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-716-

CYS

-
Components

#1: Protein PAB-dependent poly(A)-specific ribonuclease subunit PAN2 / PAB1P-dependent poly(A)-nuclease / PAN deadenylation complex catalytic subunit 2


Mass: 75997.008 Da / Num. of mol.: 1 / Fragment: UNP residues 460-1115
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PAN2, YGL094C / Plasmid: pFL / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P53010, poly(A)-specific ribonuclease
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.49 Å3/Da / Density % sol: 72.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 100 mM sodium acetate, pH 5.5, 10% v/v PEG200, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.93908 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 30, 2013
RadiationMonochromator: channel cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93908 Å / Relative weight: 1
ReflectionResolution: 3.1→48.013 Å / Num. all: 25287 / Num. obs: 25287 / % possible obs: 100 % / Observed criterion σ(F): -3.7 / Observed criterion σ(I): -3.7 / Redundancy: 5.3 % / Biso Wilson estimate: 92 Å2 / Rmerge(I) obs: 0.133 / Net I/σ(I): 9.6
Reflection shellResolution: 3.1→3.32 Å / Redundancy: 5.4 % / Rmerge(I) obs: 2.488 / Mean I/σ(I) obs: 0.7 / Num. unique all: 4503 / % possible all: 100

-
Processing

Software
NameVersionClassification
AutoSolphasing
PHENIX(phenix.refine: dev_1647)refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1WLJ AND 4Q8G

1wlj

4q8g


Resolution: 3.1→48.013 Å / SU ML: 0.53 / σ(F): 1.34 / Phase error: 31.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2753 1268 5.02 %RANDOM
Rwork0.2387 ---
obs0.2406 25241 99.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.1→48.013 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4902 0 2 0 4904
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045013
X-RAY DIFFRACTIONf_angle_d0.8726803
X-RAY DIFFRACTIONf_dihedral_angle_d12.3291802
X-RAY DIFFRACTIONf_chiral_restr0.035772
X-RAY DIFFRACTIONf_plane_restr0.003877
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.22410.44831300.40382599X-RAY DIFFRACTION99
3.2241-3.37080.38571340.34352630X-RAY DIFFRACTION100
3.3708-3.54850.31271230.30272651X-RAY DIFFRACTION100
3.5485-3.77070.32751390.2912621X-RAY DIFFRACTION100
3.7707-4.06170.28831430.24942639X-RAY DIFFRACTION100
4.0617-4.47020.25051540.21612649X-RAY DIFFRACTION100
4.4702-5.11640.24881520.19732672X-RAY DIFFRACTION100
5.1164-6.44370.28011490.24642695X-RAY DIFFRACTION100
6.4437-48.01850.24421440.20972817X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.2656-2.2911-2.0862.35553.29055.359-0.3197-1.3513-0.05361.70360.8584-0.069-0.10110.1022-0.34541.57740.1529-0.03721.4140.12960.840223.995554.006554.8437
25.10790.52490.38667.03980.20357.6444-0.2675-0.47420.11870.11510.20040.4306-0.3619-0.51450.11240.610.002-0.0110.70730.0240.508816.940267.397637.2028
32.96580.16110.45023.74090.15164.35530.03350.6864-0.2449-0.46910.0328-0.1239-0.0220.4092-0.06290.51420.1365-0.00910.9905-0.0060.482425.69357.468325.8206
43.02480.42860.20854.39172.37925.0410.0496-0.10310.09090.4523-0.36340.8313-0.2678-0.69610.22470.83620.07790.11410.5526-0.10980.77111.76986.112955.7775
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 459 through 499 )
2X-RAY DIFFRACTION2chain 'A' and (resid 500 through 618 )
3X-RAY DIFFRACTION3chain 'A' and (resid 619 through 881 )
4X-RAY DIFFRACTION4chain 'A' and (resid 882 through 1111 )

+
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