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- PDB-2rfk: Substrate RNA Positioning in the Archaeal H/ACA Ribonucleoprotein... -

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Basic information

Entry
Database: PDB / ID: 2rfk
TitleSubstrate RNA Positioning in the Archaeal H/ACA Ribonucleoprotein Complex
Components
  • Probable tRNA pseudouridine synthase B
  • Ribosome biogenesis protein Nop10
  • Small nucleolar rnp similar to gar1
  • guide RNA 1
  • guide RNA 2
  • target RNA
KeywordsIsomerase/RNA / PROTEIN-RNA COMPLEX / Archaeal H-ACA Ribonucleoprotein Complex / Isomerase / tRNA processing / Ribosome biogenesis / rRNA processing / Isomerase-RNA COMPLEX / Structural Genomics / Southeast Collaboratory for Structural Genomics / SECSG / PSI-2 / Protein Structure Initiative
Function / homology
Function and homology information


tRNA pseudouridine55 synthase / tRNA pseudouridine synthase activity / pseudouridine synthesis / tRNA pseudouridine synthesis / snoRNA binding / rRNA processing / ribosome biogenesis / ribonucleoprotein complex / RNA binding / ATP binding
Similarity search - Function
Probable tRNA pseudouridine synthase 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 ...Probable tRNA pseudouridine synthase 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 / Pseudouridine synthase / Pseudouridine synthase II, N-terminal / tRNA pseudouridylate synthase B, C-terminal / TruB family pseudouridylate synthase (N terminal domain) / tRNA pseudouridylate synthase B C-terminal domain / Pseudouridine synthase / Uncharacterised domain CHP00451 / PUA domain / PUA domain / Pseudouridine synthase, catalytic domain superfamily / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 / Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase / PUA domain / PUA domain profile. / PUA domain superfamily / Rubrerythrin, domain 2 / PUA-like superfamily / Single Sheet / Thrombin, subunit H / Translation protein, beta-barrel domain superfamily / Roll / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / Probable tRNA pseudouridine synthase B / Small nucleolar rnp gar1-like protein / Ribosome biogenesis protein Nop10
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.87 Å
AuthorsLiang, B. / Xue, S. / Terns, R.M. / Terns, M.P. / Li, H. / Southeast Collaboratory for Structural Genomics (SECSG)
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2007
Title: Substrate RNA positioning in the archaeal H/ACA ribonucleoprotein complex.
Authors: Liang, B. / Xue, S. / Terns, R.M. / Terns, M.P. / Li, H.
History
DepositionSep 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 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.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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 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
D: guide RNA 1
E: guide RNA 2
F: target RNA
A: Probable tRNA pseudouridine synthase B
B: Ribosome biogenesis protein Nop10
C: Small nucleolar rnp similar to gar1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,3587
Polymers72,2936
Non-polymers651
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.561, 96.561, 240.978
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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RNA chain , 3 types, 3 molecules DEF

#1: RNA chain guide RNA 1 /


Mass: 6797.132 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: RNA chain guide RNA 2 /


Mass: 8229.945 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: RNA chain target RNA


Mass: 4535.716 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Protein , 3 types, 3 molecules ABC

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


Mass: 37862.188 Da / Num. of mol.: 1 / Mutation: D85A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Plasmid: pET / Production host: Escherichia coli (E. coli)
References: UniProt: Q7LWY0, Isomerases; Intramolecular transferases; Transferring other groups
#5: Protein Ribosome biogenesis protein Nop10 /


Mass: 6352.509 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Plasmid: pET / Production host: Escherichia coli (E. coli) / References: UniProt: Q8U1R4
#6: Protein Small nucleolar rnp similar to gar1


Mass: 8515.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Plasmid: pET / Production host: Escherichia coli (E. coli) / References: UniProt: Q8U029

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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

CrystalDensity Matthews: 3.89 Å3/Da / Density % sol: 68.34 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 50 mM MES, 100 mM NH4COOCH3, 5 mM MgSO4, 1.0 M NaCl, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 303K
Components of the solutions
IDNameCrystal-IDSol-ID
1MES11
2NH4COOCH311
3MgSO411
4NaClSodium chloride11
5MES12
6NH4COOCH312
7MgSO412
8NaClSodium chloride12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 18, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.87→42.52 Å / Num. all: 29512 / Num. obs: 20534 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 5 / Redundancy: 15.1 % / Rsym value: 0.11 / Net I/σ(I): 41.9
Reflection shellResolution: 2.87→2.945 Å / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2EY4

2ey4


Resolution: 2.87→42.52 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.91 / SU B: 56.708 / SU ML: 0.46 / Cross valid method: THROUGHOUT / ESU R: 2.43 / ESU R Free: 0.466 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30042 1019 4.7 %RANDOM
Rwork0.24783 ---
obs0.25031 20534 79.97 %-
all-29512 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 48.255 Å2
Baniso -1Baniso -2Baniso -3
1-6.54 Å20 Å20 Å2
2--6.54 Å20 Å2
3----13.09 Å2
Refinement stepCycle: LAST / Resolution: 2.87→42.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3711 1293 1 0 5005
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0225247
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7252.2917389
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0925458
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.83122.733161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.58815704
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7981533
X-RAY DIFFRACTIONr_chiral_restr0.0840.2866
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023455
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2390.22525
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.23425
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.2171
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.246
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2380.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3851.52357
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.70623745
X-RAY DIFFRACTIONr_scbond_it0.87633690
X-RAY DIFFRACTIONr_scangle_it1.5474.53642
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.87→2.945 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.421 36 -
Rwork0.405 667 -
obs--35.78 %

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