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- PDB-3mqk: Cbf5-Nop10-Gar1 complex binding with 17mer RNA containing ACA tri... -

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Basic information

Entry
Database: PDB / ID: 3mqk
TitleCbf5-Nop10-Gar1 complex binding with 17mer RNA containing ACA trinucleotide
Components
  • RNA (5'-R(P*CP*GP*AP*UP*CP*CP*AP*CP*A)-3')
  • RNA (5'-R(P*GP*UP*UP*CP*GP*AP*UP*CP*CP*AP*CP*AP*G)-3')
  • Ribosome biogenesis protein Nop10
  • Small nucleolar rnp gar1-like protein
  • tRNA pseudouridine synthase B
KeywordsIsomerase/RNA binding protein/rna / Protein-RNA complex / Box H/ACA / pseudouridine synthase / post-transcriptional modification / Isomerase / tRNA processing / RNA-binding / Isomerase-RNA binding protein-rna complex
Function / homology
Function and homology information


tRNA pseudouridine55 synthase / tRNA pseudouridine(55) synthase activity / rRNA pseudouridine synthesis / box H/ACA sno(s)RNA 3'-end processing / pseudouridine synthesis / tRNA pseudouridine synthesis / snRNA pseudouridine synthesis / mRNA pseudouridine synthesis / snoRNA binding / rRNA processing ...tRNA pseudouridine55 synthase / tRNA pseudouridine(55) synthase activity / rRNA pseudouridine synthesis / box H/ACA sno(s)RNA 3'-end processing / pseudouridine synthesis / tRNA pseudouridine synthesis / snRNA pseudouridine synthesis / mRNA pseudouridine synthesis / snoRNA binding / rRNA processing / ribosome biogenesis / ribonucleoprotein complex / RNA 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 / Pseudouridine synthase / tRNA pseudouridine synthase B family / Dyskerin-like ...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 / Pseudouridine synthase / 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) / PUA domain / Uncharacterised domain CHP00451 / 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 / 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: 2.8 Å
AuthorsZhou, J. / Liang, B. / Li, H.
CitationJournal: Rna / Year: 2011
Title: Structural and functional evidence of high specificity of Cbf5 for ACA trinucleotide.
Authors: Zhou, J. / Liang, B. / Li, H.
History
DepositionApr 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_seq_id
Revision 1.3Oct 30, 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: tRNA pseudouridine synthase B
B: Ribosome biogenesis protein Nop10
C: Small nucleolar rnp gar1-like protein
D: RNA (5'-R(P*GP*UP*UP*CP*GP*AP*UP*CP*CP*AP*CP*AP*G)-3')
E: RNA (5'-R(P*CP*GP*AP*UP*CP*CP*AP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)58,9295
Polymers58,9295
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7180 Å2
ΔGint-37 kcal/mol
Surface area24730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.696, 105.696, 243.925
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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


Mass: 37119.305 Da / Num. of mol.: 1 / Fragment: UNP residues 8-335
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: 6205.335 Da / Num. of mol.: 1 / Fragment: UNP residues 4-55
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 Small nucleolar rnp gar1-like protein


Mass: 8672.303 Da / Num. of mol.: 1 / Fragment: UNP residues 8-82
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
#4: RNA chain RNA (5'-R(P*GP*UP*UP*CP*GP*AP*UP*CP*CP*AP*CP*AP*G)-3')


Mass: 4117.501 Da / Num. of mol.: 1 / Source method: obtained synthetically
#5: RNA chain RNA (5'-R(P*CP*GP*AP*UP*CP*CP*AP*CP*A)-3')


Mass: 2814.759 Da / Num. of mol.: 1 / 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: 3.34 Å3/Da / Density % sol: 63.14 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 120 mM magnesium acetate tetrahydrate, 50 mM MES PH 5.6, 20% 2-Methyl-2,4-pentanediol, VAPOR DIFFUSION, HANGING DROP, temperature 303K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 19, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.8→100 Å / Num. obs: 20726 / % possible obs: 99.9 % / Redundancy: 20.6 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 48.8
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 17.4 % / Rmerge(I) obs: 0.778 / Mean I/σ(I) obs: 3.8 / Num. unique all: 2000 / % possible all: 100

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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
Starting model: PDB entry 2EY4

2ey4


Resolution: 2.8→33.378 Å / SU ML: 2.55 / σ(F): 0.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2441 1938 9.74 %RANDOM
Rwork0.1846 ---
obs0.1903 19905 96.39 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.496 Å2 / ksol: 0.307 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.5552 Å2-0 Å20 Å2
2---3.5552 Å2-0 Å2
3---7.1103 Å2
Refinement stepCycle: LAST / Resolution: 2.8→33.378 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3656 464 0 0 4120
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084264
X-RAY DIFFRACTIONf_angle_d1.2285856
X-RAY DIFFRACTIONf_dihedral_angle_d21.0661722
X-RAY DIFFRACTIONf_chiral_restr0.077667
X-RAY DIFFRACTIONf_plane_restr0.005663
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.86930.30041370.21891141X-RAY DIFFRACTION89
2.8693-2.94690.29971380.21481166X-RAY DIFFRACTION91
2.9469-3.03350.28561500.1921188X-RAY DIFFRACTION93
3.0335-3.13140.2711380.20181200X-RAY DIFFRACTION93
3.1314-3.24320.28091250.19521257X-RAY DIFFRACTION96
3.2432-3.37290.25511250.191278X-RAY DIFFRACTION96
3.3729-3.52630.27171280.18361308X-RAY DIFFRACTION98
3.5263-3.7120.23091490.17641258X-RAY DIFFRACTION98
3.712-3.94420.23241390.16531308X-RAY DIFFRACTION98
3.9442-4.24820.18971360.14371326X-RAY DIFFRACTION99
4.2482-4.67460.22761400.14071320X-RAY DIFFRACTION99
4.6746-5.34870.22271450.16571344X-RAY DIFFRACTION99
5.3487-6.72970.26741320.19581386X-RAY DIFFRACTION99
6.7297-33.38080.21141560.1891487X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -12.2349 Å / Origin y: 35.566 Å / Origin z: -8.2205 Å
111213212223313233
T0.1983 Å2-0.0928 Å2-0.0153 Å2-0.2657 Å2-0.1741 Å2--0.2436 Å2
L1.7596 °2-0.9998 °2-0.6276 °2-1.2147 °20.6707 °2--1.2551 °2
S-0.1127 Å °0.0895 Å °-0.2148 Å °-0.032 Å °0.0182 Å °0.0709 Å °0.0377 Å °-0.1137 Å °0.1127 Å °
Refinement TLS groupSelection details: all

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