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- PDB-3hay: Crystal structure of a substrate-bound full H/ACA RNP from Pyroco... -

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Basic information

Entry
Database: PDB / ID: 3hay
TitleCrystal structure of a substrate-bound full H/ACA RNP from Pyrococcus furiosus
Components
  • 5'-R(*AP*UP*AP*AP*UP*UP*(FHU)P*GP*AP*CP*UP*CP*AP*A)-3'
  • 50S ribosomal protein L7Ae
  • H/ACA RNA
  • Probable tRNA pseudouridine synthase B
  • Ribosome biogenesis protein Nop10
  • Small nucleolar rnp gar1-like protein
KeywordsISOMERASE/BIOSYNTHETIC PROTEIN/RNA / H/ACA / guide RNA / RNA-protein complex / pseudouridine synthase / Isomerase / tRNA processing / Ribonucleoprotein / Ribosome biogenesis / rRNA processing / Ribosomal protein / RNA-binding / ISOMERASE-BIOSYNTHETIC PROTEIN-RNA COMPLEX
Function / homology
Function and homology information


tRNA pseudouridine55 synthase / rRNA pseudouridine synthesis / box H/ACA sno(s)RNA 3'-end processing / pseudouridine synthesis / snRNA pseudouridine synthesis / tRNA pseudouridine synthase activity / tRNA pseudouridine synthesis / mRNA pseudouridine synthesis / positive regulation of telomerase RNA localization to Cajal body / ribonuclease P activity ...tRNA pseudouridine55 synthase / rRNA pseudouridine synthesis / box H/ACA sno(s)RNA 3'-end processing / pseudouridine synthesis / snRNA pseudouridine synthesis / tRNA pseudouridine synthase activity / tRNA pseudouridine synthesis / mRNA pseudouridine synthesis / positive regulation of telomerase RNA localization to Cajal body / ribonuclease P activity / tRNA 5'-leader removal / telomerase RNA binding / snoRNA binding / rRNA processing / ribosome biogenesis / cytosolic small ribosomal subunit / rRNA binding / structural constituent of ribosome / ribonucleoprotein complex / translation / RNA binding
Similarity search - Function
Probable tRNA pseudouridine synthase B, archaeal / H/ACA ribonucleoprotein complex subunit Nop10 , archaeal-type / H/ACA ribonucleoprotein complex, subunit Gar1/Naf1 / H/ACA RNP complex subunit Gar1/Naf1, Cbf5-binding domain / Gar1/Naf1 RNA binding region / tRNA pseudouridine synthase B family / Dyskerin-like / DKCLD (NUC011) domain / DKCLD (NUC011) domain / H/ACA ribonucleoprotein complex, subunit Nop10 ...Probable tRNA pseudouridine synthase B, archaeal / H/ACA ribonucleoprotein complex subunit Nop10 , archaeal-type / H/ACA ribonucleoprotein complex, subunit Gar1/Naf1 / H/ACA RNP complex subunit Gar1/Naf1, Cbf5-binding domain / Gar1/Naf1 RNA binding region / tRNA pseudouridine synthase B family / Dyskerin-like / DKCLD (NUC011) domain / DKCLD (NUC011) domain / H/ACA ribonucleoprotein complex, subunit Nop10 / H/ACA ribonucleoprotein complex, subunit Nop10 superfamily / Nucleolar RNA-binding protein, Nop10p family / tRNA pseudouridylate synthase B, C-terminal / tRNA pseudouridylate synthase B C-terminal domain / Pseudouridine synthase II, N-terminal / TruB family pseudouridylate synthase (N terminal domain) / Uncharacterised domain CHP00451 / PUA domain / Pseudouridine synthase, catalytic domain superfamily / Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase / PUA domain / PUA domain profile. / PUA domain superfamily / Ribosomal protein L7Ae, archaea / PUA-like superfamily / Ribosomal protein L7Ae conserved site / Ribosomal protein L7Ae signature. / Ribosomal protein L7Ae/L8/Nhp2 family / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like / Translation protein, beta-barrel domain superfamily
Similarity search - Domain/homology
RNA / RNA (> 10) / Probable tRNA pseudouridine synthase B / Small nucleolar rnp gar1-like protein / Large ribosomal subunit protein eL8 / Ribosome biogenesis protein Nop10
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.99 Å
AuthorsYe, K.
CitationJournal: Mol.Cell / Year: 2009
Title: Structural mechanism of substrate RNA recruitment in H/ACA RNA-guided pseudouridine synthase.
Authors: Duan, J. / Li, L. / Lu, J. / Wang, W. / Ye, K.
History
DepositionMay 3, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable tRNA pseudouridine synthase B
B: Small nucleolar rnp gar1-like protein
C: Ribosome biogenesis protein Nop10
D: 50S ribosomal protein L7Ae
E: H/ACA RNA
F: 5'-R(*AP*UP*AP*AP*UP*UP*(FHU)P*GP*AP*CP*UP*CP*AP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,7927
Polymers100,7266
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)189.518, 189.518, 279.045
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

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Protein , 4 types, 4 molecules ABCD

#1: Protein Probable tRNA pseudouridine synthase B / tRNA pseudouridine 55 synthase / Psi55 synthase / tRNA-uridine isomerase / tRNA pseudouridylate synthase


Mass: 39453.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: truB, PF1785 / Production host: Escherichia coli (E. coli)
References: UniProt: Q7LWY0, Isomerases; Intramolecular transferases; Transferring other groups
#2: Protein Small nucleolar rnp gar1-like protein / Gar1


Mass: 12340.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: PF1791 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8U029
#3: Protein Ribosome biogenesis protein Nop10


Mass: 7214.603 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: PF1141 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8U1R4
#4: Protein 50S ribosomal protein L7Ae


Mass: 14314.623 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: rpl7ae, PF1367 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8U160

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RNA chain , 2 types, 2 molecules EF

#5: RNA chain H/ACA RNA


Mass: 22949.637 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: RNA WAS PREPARED BY IN VITRO TRANSCRIPTION
#6: RNA chain 5'-R(*AP*UP*AP*AP*UP*UP*(FHU)P*GP*AP*CP*UP*CP*AP*A)-3'


Mass: 4452.682 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 1 types, 1 molecules

#7: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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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: 293 K / Method: vapor diffusion, hanging drop / pH: 4.9
Details: 1.5M lithium sulfate, 50mM sodium acetate (pH 4.9), VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorDate: Nov 15, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4.99→50 Å / Num. obs: 13408 / % possible obs: 99.5 % / Redundancy: 10.2 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 34.4
Reflection shellResolution: 5→5.18 Å / Rmerge(I) obs: 0.481 / Mean I/σ(I) obs: 4.7 / % possible all: 99.8

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HAX

3hax


Resolution: 4.99→20 Å / Cor.coef. Fo:Fc: 0.891 / Cor.coef. Fo:Fc free: 0.873 / SU B: 127.599 / SU ML: 1.398 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 1.323 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.36657 654 5 %RANDOM
Rwork0.32281 ---
obs0.32494 12531 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 263.788 Å2
Baniso -1Baniso -2Baniso -3
1-10.06 Å25.03 Å20 Å2
2--10.06 Å20 Å2
3----15.09 Å2
Refinement stepCycle: LAST / Resolution: 4.99→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4572 1754 1 0 6327
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0226634
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9712.3179361
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5615571
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.8923.403191
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.7315875
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4741535
X-RAY DIFFRACTIONr_chiral_restr0.0550.21118
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.024283
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.160.22456
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2860.24271
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1070.2133
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1730.249
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0950.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.1851.52972
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.33524664
X-RAY DIFFRACTIONr_scbond_it0.45734714
X-RAY DIFFRACTIONr_scangle_it0.9994.54697
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 4.992→5.113 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.509 42 -
Rwork0.379 850 -
obs--98.67 %

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