[English] 日本語
Yorodumi
- PDB-5eo3: Crystal Structure of Pelota C terminal domain from human -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5eo3
TitleCrystal Structure of Pelota C terminal domain from human
ComponentsProtein pelota homolog
KeywordsCELL CYCLE / Pelota c terminal domain
Function / homology
Function and homology information


stalled ribosome sensor activity / Dom34-Hbs1 complex / RNA surveillance / nuclear-transcribed mRNA catabolic process, no-go decay / mesenchymal to epithelial transition / nuclear-transcribed mRNA catabolic process, non-stop decay / nonfunctional rRNA decay / endoderm development / positive regulation of BMP signaling pathway / ribosome disassembly ...stalled ribosome sensor activity / Dom34-Hbs1 complex / RNA surveillance / nuclear-transcribed mRNA catabolic process, no-go decay / mesenchymal to epithelial transition / nuclear-transcribed mRNA catabolic process, non-stop decay / nonfunctional rRNA decay / endoderm development / positive regulation of BMP signaling pathway / ribosome disassembly / inner cell mass cell proliferation / stem cell population maintenance / chromosome organization / cytosolic ribosome / rescue of stalled ribosome / ribosome binding / regulation of translation / cell cycle / cell division / metal ion binding / cytoplasm
Similarity search - Function
Translation release factor pelota / Pelota/DOM34, N-terminal domain / eRF1 domain 2 / eRF1 domain 2 / eRF1 domain 1 / eRF1 domain 1/Pelota-like / eRF1 domain 3 / eRF1, domain 2 superfamily / eRF1 domain 3 / eRF1_1 ...Translation release factor pelota / Pelota/DOM34, N-terminal domain / eRF1 domain 2 / eRF1 domain 2 / eRF1 domain 1 / eRF1 domain 1/Pelota-like / eRF1 domain 3 / eRF1, domain 2 superfamily / eRF1 domain 3 / eRF1_1 / Ribosomal protein L30/S12 / 60s Ribosomal Protein L30; Chain: A; / 50S ribosomal protein L30e-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Protein pelota homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.6 Å
AuthorsZhang, L. / Cai, Q. / Lin, T.
CitationJournal: to be published
Title: Purification, crystallization and crystallographic analysis of the Pelota C terminal domian from human
Authors: Zhang, L. / Cai, Q. / Lin, T.
History
DepositionNov 10, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 20, 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_struct_oper_list / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein pelota homolog
B: Protein pelota homolog


Theoretical massNumber of molelcules
Total (without water)27,0342
Polymers27,0342
Non-polymers00
Water81145
1
A: Protein pelota homolog


Theoretical massNumber of molelcules
Total (without water)13,5171
Polymers13,5171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein pelota homolog


Theoretical massNumber of molelcules
Total (without water)13,5171
Polymers13,5171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area940 Å2
ΔGint-7 kcal/mol
Surface area11000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.822, 78.822, 197.456
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-404-

HOH

21B-406-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: _ / Auth seq-ID: 272 - 371 / Label seq-ID: 8 - 107

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

#1: Protein Protein pelota homolog


Mass: 13517.014 Da / Num. of mol.: 2 / Fragment: Pelota C terminal domain, residues 265-385
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Pelota / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9BRX2, Hydrolases; Acting on ester bonds
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 3.27 Å3/Da / Density % sol: 62.44 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 20mM Tris HCl pH 7.5, 200mM NaCl, 5mM DTT

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 13, 2013 / Details: mirrors
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 11850 / % possible obs: 99.4 % / Redundancy: 8.6 % / Net I/σ(I): 10.6

-
Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
RefinementResolution: 2.6→50 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.905 / SU B: 8.232 / SU ML: 0.183 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.333 / ESU R Free: 0.268 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2669 565 4.8 %RANDOM
Rwork0.2158 ---
obs0.2183 11286 99.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 144.81 Å2 / Biso mean: 53.346 Å2 / Biso min: 18.16 Å2
Baniso -1Baniso -2Baniso -3
1-0.83 Å20.41 Å20 Å2
2--0.83 Å20 Å2
3----2.69 Å2
Refinement stepCycle: final / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1583 0 0 45 1628
Biso mean---44.67 -
Num. residues----201
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0191606
X-RAY DIFFRACTIONr_bond_other_d0.0060.021572
X-RAY DIFFRACTIONr_angle_refined_deg1.7221.972165
X-RAY DIFFRACTIONr_angle_other_deg1.27233602
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3445197
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.50623.63677
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.97115285
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.3061514
X-RAY DIFFRACTIONr_chiral_restr0.0940.2250
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021795
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02365
X-RAY DIFFRACTIONr_mcbond_it4.7194.924800
X-RAY DIFFRACTIONr_mcbond_other4.7074.92799
X-RAY DIFFRACTIONr_mcangle_it6.8357.342993
Refine LS restraints NCS

Ens-ID: 1 / Number: 5418 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.18 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.596→2.664 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 35 -
Rwork0.246 778 -
all-813 -
obs--93.88 %

+
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://pdbjlvh1.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