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- PDB-3lwo: Structure of H/ACA RNP bound to a substrate RNA containing 5BrU -

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Basic information

Entry
Database: PDB / ID: 3lwo
TitleStructure of H/ACA RNP bound to a substrate RNA containing 5BrU
Components
  • 5'-R(*GP*AP*GP*CP*GP*(5BU)P*GP*CP*GP*GP*UP*UP*U)-3'
  • 50S ribosomal protein L7AeRibosome
  • H/ACA RNA
  • Pseudouridine synthase Cbf5
  • Ribosome biogenesis protein Nop10
KeywordsISOMERASE/RNA BINDING PROTEIN/RNA / H/ACA pseudouridine synthase / Isomerase / tRNA processing / Ribonucleoprotein / Ribosome biogenesis / rRNA processing / Ribosomal protein / RNA-binding / ISOMERASE-RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


tRNA pseudouridine55 synthase / tRNA pseudouridine synthase activity / pseudouridine synthesis / tRNA pseudouridine synthesis / ribonuclease P activity / tRNA 5'-leader removal / snoRNA binding / rRNA processing / ribosome / rRNA binding ...tRNA pseudouridine55 synthase / tRNA pseudouridine synthase activity / pseudouridine synthesis / tRNA pseudouridine synthesis / ribonuclease P activity / tRNA 5'-leader removal / snoRNA binding / rRNA processing / ribosome / rRNA binding / structural constituent of ribosome / translation / ribonucleoprotein complex / RNA binding / cytoplasm
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 / 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 / Ribosomal protein L7Ae, archaea / Ribosomal protein L30/S12 / Rubrerythrin, domain 2 / PUA-like superfamily / 60s Ribosomal Protein L30; Chain: A; / Ribosomal protein L7Ae conserved site / Ribosomal protein L7Ae signature. / Single Sheet / Ribosomal protein L7Ae/L8/Nhp2 family / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / Probable tRNA pseudouridine synthase B / Large ribosomal subunit protein eL8 / Ribosome biogenesis protein Nop10
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.855 Å
AuthorsZhou, J. / Liang, B. / Lv, C. / Yang, W. / Li, H.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Glycosidic bond conformation preference plays a pivotal role in catalysis of RNA pseudouridylation: a combined simulation and structural study.
Authors: Zhou, J. / Lv, C. / Liang, B. / Chen, M. / Yang, W. / Li, H.
History
DepositionFeb 24, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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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: 50S ribosomal protein L7Ae
D: H/ACA RNA
E: 5'-R(*GP*AP*GP*CP*GP*(5BU)P*GP*CP*GP*GP*UP*UP*U)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,3046
Polymers82,2395
Non-polymers651
Water543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11860 Å2
ΔGint-106 kcal/mol
Surface area29880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)184.523, 62.698, 85.335
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsP21212

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Components

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Protein , 3 types, 3 molecules ABC

#1: Protein Pseudouridine synthase Cbf5 / tRNA pseudouridine 55 synthase / Psi55 synthase / tRNA-uridine isomerase / tRNA pseudouridylate synthase


Mass: 38625.027 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 Ribosome biogenesis protein Nop10 /


Mass: 7242.618 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
#3: Protein 50S ribosomal protein L7Ae / Ribosome


Mass: 13414.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: PF1367, rpl7ae / Production host: Escherichia coli (E. coli) / References: UniProt: Q8U160

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RNA chain , 2 types, 2 molecules DE

#4: RNA chain H/ACA RNA


Mass: 18687.193 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: In vitro transcription
#5: RNA chain 5'-R(*GP*AP*GP*CP*GP*(5BU)P*GP*CP*GP*GP*UP*UP*U)-3'


Mass: 4269.406 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: commercial source

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Non-polymers , 2 types, 4 molecules

#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#7: Water ChemComp-HOH / water / 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
IDDensity Matthews3/Da)Density % sol (%)
1359.02
2
3
4
5
Crystal grow
Crystal-IDMethodDetails
1vapor diffusion, hanging dropVAPOR DIFFUSION, HANGING DROP
2vapor diffusion, hanging dropVAPOR DIFFUSION, HANGING DROP
3vapor diffusion, hanging dropVAPOR DIFFUSION, HANGING DROP
4vapor diffusion, hanging dropVAPOR DIFFUSION, HANGING DROP
5vapor diffusion, hanging dropVAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.5418 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Mar 21, 2009
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→100 Å / Num. obs: 23154 / % possible obs: 99.3 % / Redundancy: 13.3 % / Rsym value: 0.096
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 7.6 % / Num. unique all: 2145 / Rsym value: 0.48 / % possible all: 94.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.855→42.667 Å / SU ML: 0.88 / σ(F): 1.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2402 1184 5.12 %
Rwork0.1869 --
obs0.1897 23107 52.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.395 Å2 / ksol: 0.309 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.4337 Å20 Å2-0 Å2
2--2.1723 Å20 Å2
3----17.6456 Å2
Refinement stepCycle: LAST / Resolution: 2.855→42.667 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3881 1514 1 3 5399
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065661
X-RAY DIFFRACTIONf_angle_d1.1367991
X-RAY DIFFRACTIONf_dihedral_angle_d22.1872477
X-RAY DIFFRACTIONf_chiral_restr0.067952
X-RAY DIFFRACTIONf_plane_restr0.004753
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8552-2.98520.33331120.28532192X-RAY DIFFRACTION42
2.9852-3.14250.33631540.25682758X-RAY DIFFRACTION52
3.1425-3.33930.3191400.23232770X-RAY DIFFRACTION53
3.3393-3.5970.25521470.18852774X-RAY DIFFRACTION53
3.597-3.95880.22951520.15592801X-RAY DIFFRACTION53
3.9588-4.5310.20431440.1362824X-RAY DIFFRACTION53
4.531-5.70650.19931690.14932830X-RAY DIFFRACTION54
5.7065-42.67220.22631660.19942974X-RAY DIFFRACTION57
Refinement TLS params.Method: refined / Origin x: 37.5602 Å / Origin y: 7.6629 Å / Origin z: 21.4601 Å
111213212223313233
T0.4159 Å20.1244 Å20.0594 Å2-0.5575 Å20.0262 Å2--0.4601 Å2
L1.5932 °2-0.4483 °2-0.3974 °2-1.3041 °20.1709 °2--0.2214 °2
S-0.1565 Å °-0.5583 Å °-0.0911 Å °-0.1255 Å °0.2399 Å °0.1491 Å °-0.0535 Å °0.1727 Å °-0.0563 Å °
Refinement TLS groupSelection details: all

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