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- PDB-5eo3: Crystal Structure of Pelota C terminal domain from human -

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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 / nuclear-transcribed mRNA catabolic process, non-stop decay / ribosome disassembly / nonfunctional rRNA decay / PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA / rescue of stalled cytosolic ribosome / cytosolic ribosome ...stalled ribosome sensor activity / Dom34-Hbs1 complex / RNA surveillance / nuclear-transcribed mRNA catabolic process, no-go decay / nuclear-transcribed mRNA catabolic process, non-stop decay / ribosome disassembly / nonfunctional rRNA decay / PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA / rescue of stalled cytosolic ribosome / cytosolic ribosome / regulation of translation / ribosome binding / cell division / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Translation release factor pelota / Pelota/DOM34, N-terminal domain / : / Pelota N-terminal domain / eRF1 domain 2 / eRF1 domain 2 / eRF1 domain 1/Pelota-like / eRF1 domain 3 / eRF1, domain 2 superfamily / eRF1 domain 3 ...Translation release factor pelota / Pelota/DOM34, N-terminal domain / : / Pelota N-terminal domain / eRF1 domain 2 / eRF1 domain 2 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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 (eV)
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

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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

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Experimental details

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Experiment

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

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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

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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

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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 %

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