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- PDB-1yjp: Structure of GNNQQNY from yeast prion Sup35 -

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Basic information

Entry
Database: PDB / ID: 1yjp
TitleStructure of GNNQQNY from yeast prion Sup35
ComponentsEukaryotic peptide chain release factor GTP-binding subunit
KeywordsPROTEIN BINDING / beta sheet / steric zipper / glutamine zipper / asparagine zipper
Function / homology
Function and homology information


Eukaryotic Translation Termination / translation release factor complex / translation release factor activity / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / translational termination / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / cytoplasmic stress granule / translation ...Eukaryotic Translation Termination / translation release factor complex / translation release factor activity / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / translational termination / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / cytoplasmic stress granule / translation / mRNA binding / GTPase activity / GTP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Eukaryotic peptide chain release factor GTP-binding subunit / Translation elongation factor EFTu/EF1A, C-terminal / Elongation factor Tu C-terminal domain / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain ...Eukaryotic peptide chain release factor GTP-binding subunit / Translation elongation factor EFTu/EF1A, C-terminal / Elongation factor Tu C-terminal domain / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Translation protein, beta-barrel domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Eukaryotic peptide chain release factor GTP-binding subunit
Similarity search - Component
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsNelson, R. / Sawaya, M.R. / Balbirnie, M. / Madsen, A.O. / Riekel, C. / Grothe, R. / Eisenberg, D.
Citation
Journal: Nature / Year: 2005
Title: Structure of the cross-beta spine of amyloid-like fibrils.
Authors: Nelson, R. / Sawaya, M.R. / Balbirnie, M. / Madsen, A.O. / Riekel, C. / Grothe, R. / Eisenberg, D.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1997
Title: Refinement of Macromolecular Structures by the Maximum-Likelihood Method
Authors: Murshudov, G.N. / Vagin, A.A. / Dodson, E.J.
History
DepositionJan 15, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). The second beta strand of the beta sandwich is generated as described in remark 350. Beta sheets are generated from unit cell translations along the unit cell b dimension: x,y+1,z.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Eukaryotic peptide chain release factor GTP-binding subunit


Theoretical massNumber of molelcules
Total (without water)8371
Polymers8371
Non-polymers00
Water1267
1
A: Eukaryotic peptide chain release factor GTP-binding subunit

A: Eukaryotic peptide chain release factor GTP-binding subunit


Theoretical massNumber of molelcules
Total (without water)1,6742
Polymers1,6742
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y+1/2,-z1
Unit cell
Length a, b, c (Å)21.937, 4.866, 23.477
Angle α, β, γ (deg.)90.00, 107.08, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide Eukaryotic peptide chain release factor GTP-binding subunit / ERF2 / Translation release factor 3 / ERF3 / ERF-3 / Omnipotent suppressor protein 2 / G1 to S ...ERF2 / Translation release factor 3 / ERF3 / ERF-3 / Omnipotent suppressor protein 2 / G1 to S phase transition protein 1


Mass: 836.807 Da / Num. of mol.: 1 / Fragment: prion determining domain of Sup35 / Source method: obtained synthetically
Details: This sequence is from the prion determining domain of Saccharomyces cerevisiae Sup35
References: UniProt: P05453
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 1.43 Å3/Da / Density % sol: 14.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: water, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.975 / Wavelength: 0.975 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 12, 2004 / Details: Ellipsoidal Mirror
RadiationMonochromator: channel-cut Si-111 monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 1.8→80 Å / Num. all: 509 / Num. obs: 509 / % possible obs: 89.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 45.6 Å2 / Rmerge(I) obs: 0.204 / Χ2: 1.057 / Net I/σ(I): 3.75
Reflection shellResolution: 1.8→1.94 Å / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 1.5 / Num. unique all: 85 / Χ2: 1.092 / % possible all: 84.2

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Processing

Software
NameClassificationNB
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.8→22.44 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.19014 20 RANDOM
Rwork0.18086 --
all0.18139 474 -
obs0.18139 474 -
Refinement stepCycle: LAST / Resolution: 1.8→22.44 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms59 0 0 7 66
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_angle_refined_deg1.228
X-RAY DIFFRACTIONr_bond_refined_d0.014

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