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- PDB-1yjo: Structure of NNQQNY from yeast prion Sup35 with zinc acetate -

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Basic information

Entry
Database: PDB / ID: 1yjo
TitleStructure of NNQQNY from yeast prion Sup35 with zinc acetate
ComponentsEukaryotic peptide chain release factor GTP-binding subunit
KeywordsPROTEIN BINDING / Keywords 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
ACETIC ACID / Eukaryotic peptide chain release factor GTP-binding subunit
Similarity search - Component
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.3 Å
AuthorsNelson, R. / Sawaya, M.R. / Balbirnie, M. / Madsen, A.O. / Riekel, C. / Grothe, R. / Eisenberg, D.
CitationJournal: 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.
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 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_asym_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.ptnr3_symmetry / _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_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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:
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Assembly

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


Theoretical massNumber of molelcules
Total (without water)9053
Polymers7801
Non-polymers1252
Water1267
1
A: Eukaryotic peptide chain release factor GTP-binding subunit
hetero molecules

A: Eukaryotic peptide chain release factor GTP-binding subunit
hetero molecules


  • defined by author
  • 1.81 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)1,8106
Polymers1,5602
Non-polymers2514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y+1/2,-z1
Unit cell
Length a, b, c (Å)21.153, 4.870, 23.130
Angle α, β, γ (deg.)90.00, 102.93, 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: 779.755 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: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#4: 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: 1.38 Å3/Da / Density % sol: 10.32 %
Crystal growTemperature: 293 K / pH: 7
Details: ZINC SULFATE, SODIUM ACETATE, HEPES, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 7.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.975
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 22, 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: 1.3→80 Å / Num. obs: 2166 / % possible obs: 97.1 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 11.7 Å2 / Rsym value: 0.146 / Net I/σ(I): 9.8
Reflection shellResolution: 1.3→1.4 Å / Mean I/σ(I) obs: 2.6 / Rsym value: 0.426 / % possible all: 88.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: SAD / Resolution: 1.3→22.54 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.463 / SU ML: 0.025 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.043 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.152 52 4 %RANDOM
Rwork0.102 ---
obs0.103 1250 97.9 %-
all-1250 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 5.76 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å20.28 Å2
2---0.44 Å20 Å2
3---0.73 Å2
Refinement stepCycle: LAST / Resolution: 1.3→22.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms55 0 1 11 67
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02158
X-RAY DIFFRACTIONr_bond_other_d0.0010.0237
X-RAY DIFFRACTIONr_angle_refined_deg1.0771.89277
X-RAY DIFFRACTIONr_angle_other_deg0.728388
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.50455
X-RAY DIFFRACTIONr_dihedral_angle_2_deg59.93728.3336
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.092158
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0920.26
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0271
X-RAY DIFFRACTIONr_gen_planes_other00.029
X-RAY DIFFRACTIONr_nbd_refined0.2250.24
X-RAY DIFFRACTIONr_nbd_other0.1870.220
X-RAY DIFFRACTIONr_nbtor_refined0.1940.218
X-RAY DIFFRACTIONr_nbtor_other0.0830.233
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2190.24
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0390.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1710.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3390.213
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1810.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0160.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6631.543
X-RAY DIFFRACTIONr_mcbond_other0.2281.514
X-RAY DIFFRACTIONr_mcangle_it0.895249
X-RAY DIFFRACTIONr_scbond_it1.394333
X-RAY DIFFRACTIONr_scangle_it1.7154.528
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.3→1.33 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.0135 5 -
Rwork0.012 76 -
obs--87.1 %

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