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- PDB-2omm: GNNQQNY peptide corresponding to residues 7-13 of yeast prion sup35 -

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Basic information

Entry
Database: PDB / ID: 2omm
TitleGNNQQNY peptide corresponding to residues 7-13 of yeast prion sup35
ComponentsGNNQQNY peptide corresponding to residues 7-13 of yeast prion sup35
KeywordsPROTEIN FIBRIL / steric zipper / glutamine zipper / polar 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 / cytoplasmic stress granule / regulation of translation / ribosome binding ...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 / cytoplasmic stress granule / regulation of translation / ribosome binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / translation / GTPase activity / mRNA binding / GTP binding / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Eukaryotic peptide chain release factor GTP-binding subunit / : / GTP-eEF1A C-terminal domain-like / : / 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 ...Eukaryotic peptide chain release factor GTP-binding subunit / : / GTP-eEF1A C-terminal domain-like / : / 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 / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSawaya, M.R. / Nelson, R. / Eisenberg, D.
CitationJournal: Nature / Year: 2007
Title: Atomic structures of amyloid cross-beta spines reveal varied steric zippers.
Authors: Sawaya, M.R. / Sambashivan, S. / Nelson, R. / Ivanova, M.I. / Sievers, S.A. / Apostol, M.I. / Thompson, M.J. / Balbirnie, M. / Wiltzius, J.J. / McFarlane, H.T. / Madsen, A.O. / Riekel, C. / Eisenberg, D.
History
DepositionJan 22, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GNNQQNY peptide corresponding to residues 7-13 of yeast prion sup35


Theoretical massNumber of molelcules
Total (without water)8371
Polymers8371
Non-polymers00
Water543
1
A: GNNQQNY peptide corresponding to residues 7-13 of yeast prion sup35

A: GNNQQNY peptide corresponding to residues 7-13 of yeast prion sup35

A: GNNQQNY peptide corresponding to residues 7-13 of yeast prion sup35

A: GNNQQNY peptide corresponding to residues 7-13 of yeast prion sup35


Theoretical massNumber of molelcules
Total (without water)3,3474
Polymers3,3474
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation3_645-x+1,y-1/2,-z+1/21
crystal symmetry operation3_655-x+1,y+1/2,-z+1/21
Unit cell
Length a, b, c (Å)23.324, 4.934, 37.548
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsOne sheet of the steric zipper can be generated by repeated application of the crystallographic unit cell translation along the b axis. The second sheet of the steric zipper can be generated by application of the crystallographic operator -X+1,-1/2+Y,1/2-Z, and repeated unit cell translations of this strand along the b axis.

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Components

#1: Protein/peptide GNNQQNY peptide corresponding to residues 7-13 of yeast prion sup35


Mass: 836.807 Da / Num. of mol.: 1 / Fragment: residues 7-13 / Source method: obtained synthetically / References: UniProt: P05453*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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

Crystal growTemperature: 298 K / Method: evaporation, recrystallization
Details: peptide was dissolved at 10 mg/mL in water, quickly filtered, and left to sit at room temperature, EVAPORATION, RECRYSTALLIZATION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.9466
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 16, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9466 Å / Relative weight: 1
ReflectionResolution: 2→19.81 Å / Num. obs: 380 / % possible obs: 96.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 2.446 Å2 / Rmerge(I) obs: 0.248 / Net I/σ(I): 4.61
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique all% possible all
2-2.20.4172.72619098.9
2.2-2.50.3913.32679794.2
2.5-30.3013.81936998.6
30.138.130710197.1

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1yjp

1yjp


Resolution: 2→19.81 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.885 / SU B: 5.08 / SU ML: 0.141 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.382 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.252 18 4.8 %RANDOM
Rwork0.241 ---
obs0.242 372 94.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.533 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2--0.19 Å20 Å2
3----0.24 Å2
Refinement stepCycle: LAST / Resolution: 2→19.81 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms59 0 0 3 62
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02159
X-RAY DIFFRACTIONr_bond_other_d0.0010.0234
X-RAY DIFFRACTIONr_angle_refined_deg1.5441.85779
X-RAY DIFFRACTIONr_angle_other_deg0.635383
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.41856
X-RAY DIFFRACTIONr_dihedral_angle_2_deg56.11528.3336
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.183158
X-RAY DIFFRACTIONr_chiral_restr0.1040.26
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0274
X-RAY DIFFRACTIONr_gen_planes_other0.0020.0210
X-RAY DIFFRACTIONr_nbd_refined0.1230.23
X-RAY DIFFRACTIONr_nbd_other0.180.224
X-RAY DIFFRACTIONr_nbtor_refined0.180.223
X-RAY DIFFRACTIONr_nbtor_other0.0850.227
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1530.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1590.213
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0760.24
X-RAY DIFFRACTIONr_mcbond_it2.691245
X-RAY DIFFRACTIONr_mcbond_other0.873214
X-RAY DIFFRACTIONr_mcangle_it3.309352
X-RAY DIFFRACTIONr_scbond_it2.295234
X-RAY DIFFRACTIONr_scangle_it2.561327
LS refinement shellResolution: 2→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.088 1 -
Rwork0.22 18 -
obs-19 95 %

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