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- PDB-3hjy: Structure of a functional ribonucleoprotein pseudouridine synthas... -

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Basic information

Entry
Database: PDB / ID: 3hjy
TitleStructure of a functional ribonucleoprotein pseudouridine synthase bound to a substrate RNA
Components
  • 5'-R(*GP*GP*AP*GP*CP*GP*UP*GP*CP*GP*GP*UP*UP*U)-3'
  • 5'-R(*GP*GP*GP*CP*UP*CP*CP*GP*GP*AP*AP*AP*CP*CP*GP*CP*GP*GP*CP*GP*C)-3'
  • RNA (25-MER)
  • Ribosome biogenesis protein Nop10
  • pseudouridine synthase CBf5
KeywordsISOMERASE/RNA / protein-RNA complex / Box H/ACA / ribonucleoprotein particles / RNP / pseudouridine synthase / pseudouridylase / pseudouridylation / RNA editing / post-transcriptional modification / Isomerase / tRNA processing / Ribonucleoprotein / Ribosome biogenesis / rRNA processing / ISOMERASE-RNA COMPLEX
Function / homology
Function and homology information


tRNA pseudouridine55 synthase / tRNA pseudouridine(55) synthase activity / pseudouridine synthesis / tRNA pseudouridine synthesis / snoRNA binding / rRNA processing / ribonucleoprotein complex / RNA binding
Similarity search - Function
H/ACA ribonucleoprotein complex, subunit Nop10 / Probable tRNA pseudouridine synthase B, archaeal / H/ACA ribonucleoprotein complex subunit Nop10 , archaeal-type / 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 ...H/ACA ribonucleoprotein complex, subunit Nop10 / Probable tRNA pseudouridine synthase B, archaeal / H/ACA ribonucleoprotein complex subunit Nop10 , archaeal-type / 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 / 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) / Pseudouridine synthase / Uncharacterised domain CHP00451 / PUA domain / PUA domain / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 / Pseudouridine synthase, catalytic domain superfamily / Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase / PUA domain / PUA domain superfamily / PUA domain profile. / Rubrerythrin, domain 2 / PUA-like superfamily / Single Sheet / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / Probable tRNA pseudouridine synthase B / Ribosome biogenesis protein Nop10
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.65 Å
AuthorsLiang, B. / Zhou, J. / Kahen, E. / Terns, R.M. / Terns, M.P. / Li, H.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2009
Title: Structure of a functional ribonucleoprotein pseudouridine synthase bound to a substrate RNA
Authors: Liang, B. / Zhou, J. / Kahen, E. / Terns, R.M. / Terns, M.P. / Li, H.
History
DepositionMay 22, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Sep 6, 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
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: pseudouridine synthase CBf5
B: Ribosome biogenesis protein Nop10
C: 5'-R(*GP*GP*GP*CP*UP*CP*CP*GP*GP*AP*AP*AP*CP*CP*GP*CP*GP*GP*CP*GP*C)-3'
D: RNA (25-MER)
E: 5'-R(*GP*GP*AP*GP*CP*GP*UP*GP*CP*GP*GP*UP*UP*U)-3'


Theoretical massNumber of molelcules
Total (without water)62,5765
Polymers62,5765
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9100 Å2
ΔGint-58 kcal/mol
Surface area27460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)238.341, 238.341, 127.369
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein pseudouridine synthase CBf5 / tRNA pseudouridine 55 synthase / Psi55 synthase / tRNA-uridine isomerase / tRNA pseudouridylate synthase


Mass: 36990.188 Da / Num. of mol.: 1 / Fragment: Cbf5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: DSM 3638 / Gene: PF1785 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 codon plus
References: UniProt: Q7LWY0, Isomerases; Intramolecular transferases; Transferring other groups
#2: Protein Ribosome biogenesis protein Nop10


Mass: 6352.509 Da / Num. of mol.: 1 / Fragment: Nop10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: DSM 3638 / Gene: PF1141 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 codon plus / References: UniProt: Q8U1R4
#3: RNA chain 5'-R(*GP*GP*GP*CP*UP*CP*CP*GP*GP*AP*AP*AP*CP*CP*GP*CP*GP*GP*CP*GP*C)-3'


Mass: 6797.132 Da / Num. of mol.: 1 / Fragment: guide RNA_A / Source method: obtained synthetically
#4: RNA chain RNA (25-MER)


Mass: 7900.740 Da / Num. of mol.: 1 / Fragment: guide RNA_B / Source method: obtained synthetically
#5: RNA chain 5'-R(*GP*GP*AP*GP*CP*GP*UP*GP*CP*GP*GP*UP*UP*U)-3'


Mass: 4535.716 Da / Num. of mol.: 1 / Fragment: substrate RNA / Source method: obtained synthetically
Has protein modificationY

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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: 2.72 Å3/Da / Density % sol: 59.62 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2.0mM CoCl2, 30mM CaCl2, 2.0mM Spermine, 2.0M LiCl, pH 6.5, vapor diffusion, hanging drop, temperature 303K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineID
SYNCHROTRONAPS 22-ID1
SYNCHROTRONAPS 22-BM2
Detector
TypeIDDetectorDate
MARMOSAIC 300 mm CCD1CCDMar 16, 2008
MARMOSAIC 225 mm CCD2CCDMar 16, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.65→49.33 Å / Num. obs: 22492

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
DENZOdata reduction
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2EY4

2ey4


Resolution: 3.65→49.33 Å / Cor.coef. Fo:Fc: 0.887 / Cor.coef. Fo:Fc free: 0.865 / Occupancy max: 1 / Occupancy min: 1 / SU B: 58.757 / SU ML: 0.401 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.939 / ESU R Free: 0.502 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.306 1208 5.1 %RANDOM
Rwork0.276 ---
obs0.277 22492 97.8 %-
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 max: 289.55 Å2 / Biso mean: 132.735 Å2 / Biso min: 58.38 Å2
Baniso -1Baniso -2Baniso -3
1--6.76 Å2-3.38 Å20 Å2
2---6.76 Å20 Å2
3---10.14 Å2
Refinement stepCycle: LAST / Resolution: 3.65→49.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2989 1271 0 0 4260
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0224540
X-RAY DIFFRACTIONr_angle_refined_deg1.5052.336428
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9225378
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.60322.727132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.59815576
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3141527
X-RAY DIFFRACTIONr_chiral_restr0.0860.2759
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022945
X-RAY DIFFRACTIONr_nbd_refined0.2390.22013
X-RAY DIFFRACTIONr_nbtor_refined0.3120.22935
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2138
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2270.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1590.21
X-RAY DIFFRACTIONr_mcbond_it0.9111.51961
X-RAY DIFFRACTIONr_mcangle_it1.65623081
X-RAY DIFFRACTIONr_scbond_it1.23733352
X-RAY DIFFRACTIONr_scangle_it2.274.53347
LS refinement shellResolution: 3.648→3.743 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 80 -
Rwork0.329 1378 -
all-1458 -
obs--83.51 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.0264-1.25370.01143.83651.7431.53930.1338-0.3403-0.40380.3159-0.26810.28130.4491-0.31790.13440.1911-0.07020.0264-0.11060.1036-0.0155-112.952233.271239.7419
21.40620.3171-3.752.79920.013210.2713-0.2371-0.2598-0.0856-0.2306-0.1607-0.0745-0.12850.13540.3978-0.05030.03610.0452-0.034-0.056-0.2284-104.691556.100737.0987
34.7505-1.60391.061412.7254-2.03462.97720.52591.22910.1199-1.7875-0.5120.11090.5789-0.5724-0.01390.25180.2554-0.1199-0.41970.1627-0.0177-126.045532.95218.4115
41.05031.5111-0.56245.28391.23681.64710.49690.5706-0.5601-1.1096-0.88471.30330.4562-0.48720.38780.34910.1187-0.1369-0.5084-0.09510.2996-118.550822.023724.4636
55.0715-2.94364.012623.933-9.96055.79530.90911.1251-0.72-2.25670.13322.66410.44880.4963-1.04230.01840.1582-0.43290.0449-0.2790.5705-132.463333.800718.0899
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 337
2X-RAY DIFFRACTION2B3 - 55
3X-RAY DIFFRACTION3C1 - 21
4X-RAY DIFFRACTION4D1 - 25
5X-RAY DIFFRACTION5E4 - 16

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