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- PDB-3u28: Crystal structure of a Cbf5-Nop10-Gar1 complex from Saccharomyces... -

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Basic information

Entry
Database: PDB / ID: 3u28
TitleCrystal structure of a Cbf5-Nop10-Gar1 complex from Saccharomyces cerevisiae
Components
  • H/ACA ribonucleoprotein complex subunit 1
  • H/ACA ribonucleoprotein complex subunit 3
  • H/ACA ribonucleoprotein complex subunit 4
KeywordsISOMERASE/PROTEIN BINDING / pseudouridine synthase / pseudouridylation / H/ACA RNA / Nucleolus / ISOMERASE-PROTEIN BINDING complex
Function / homology
Function and homology information


snRNA pseudouridine synthase activity / Telomere Extension By Telomerase / snoRNA guided rRNA pseudouridine synthesis / box H/ACA snoRNP complex / rRNA pseudouridine synthesis / box H/ACA sno(s)RNA 3'-end processing / snRNA pseudouridine synthesis / Isomerases; Intramolecular transferases; Transferring other groups / mRNA pseudouridine synthesis / box H/ACA snoRNA binding ...snRNA pseudouridine synthase activity / Telomere Extension By Telomerase / snoRNA guided rRNA pseudouridine synthesis / box H/ACA snoRNP complex / rRNA pseudouridine synthesis / box H/ACA sno(s)RNA 3'-end processing / snRNA pseudouridine synthesis / Isomerases; Intramolecular transferases; Transferring other groups / mRNA pseudouridine synthesis / box H/ACA snoRNA binding / pseudouridine synthase activity / rRNA modification / sno(s)RNA-containing ribonucleoprotein complex / telomerase RNA binding / snoRNA binding / chromosome, centromeric region / 90S preribosome / rRNA processing / microtubule / cell division / mRNA binding / nucleolus / DNA binding / RNA binding / cytoplasm
Similarity search - Function
Rhinovirus 14, subunit 4 - #300 / Probable tRNA pseudouridine synthase domain / 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 ...Rhinovirus 14, subunit 4 - #300 / Probable tRNA pseudouridine synthase domain / 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 / 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. / Rhinovirus 14, subunit 4 / PUA-like superfamily / Few Secondary Structures / Irregular / Thrombin, subunit H / Translation protein, beta-barrel domain superfamily / Roll / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
H/ACA ribonucleoprotein complex subunit GAR1 / H/ACA ribonucleoprotein complex subunit CBF5 / H/ACA ribonucleoprotein complex subunit NOP10
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsYe, K. / Li, S.
CitationJournal: Genes Dev. / Year: 2011
Title: Reconstitution and structural analysis of the yeast box H/ACA RNA-guided pseudouridine synthase
Authors: Li, S. / Duan, J. / Li, D. / Yang, B. / Dong, M. / Ye, K.
History
DepositionOct 2, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 1, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: H/ACA ribonucleoprotein complex subunit 4
B: H/ACA ribonucleoprotein complex subunit 3
C: H/ACA ribonucleoprotein complex subunit 1


Theoretical massNumber of molelcules
Total (without water)64,2503
Polymers64,2503
Non-polymers00
Water5,026279
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-30 kcal/mol
Surface area22730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.413, 59.386, 169.212
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein H/ACA ribonucleoprotein complex subunit 4 / Centromere-binding factor 5 / Centromere/microtubule-binding protein CBF5 / H/ACA snoRNP protein ...Centromere-binding factor 5 / Centromere/microtubule-binding protein CBF5 / H/ACA snoRNP protein CBF5 / Small nucleolar RNP protein CBF5 / p64'


Mass: 44981.797 Da / Num. of mol.: 1 / Fragment: UNP residues 3-394
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: CBF5 / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)
References: UniProt: P33322, Isomerases; Intramolecular transferases; Transferring other groups
#2: Protein H/ACA ribonucleoprotein complex subunit 3 / Nucleolar protein 10 / Nucleolar protein family A member 3 / snoRNP protein NOP10


Mass: 6649.745 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: NOP10 / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: Q6Q547
#3: Protein H/ACA ribonucleoprotein complex subunit 1 / snoRNP protein GAR1


Mass: 12618.431 Da / Num. of mol.: 1 / Fragment: UNP residues 32-124
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: GAR1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: P28007
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / 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

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.04
Details: 0.2M sodium malonate, 7%(w/v) polyethylene glycol 3350, pH 8.04, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 0.9796 Å
DetectorDetector: CCD / Date: Sep 17, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 39859 / % possible obs: 89.5 % / Redundancy: 11.2 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 26.5
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 4.2 / % possible all: 78.8

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HVY

2hvy


Resolution: 1.9→19.92 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.922 / SU B: 7.105 / SU ML: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23343 1971 5 %RANDOM
Rwork0.20355 ---
obs0.20509 37603 89.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.503 Å2
Baniso -1Baniso -2Baniso -3
1--0.7 Å20 Å20 Å2
2--0.11 Å20 Å2
3---0.6 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3749 0 0 279 4028
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223820
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3141.9795162
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0385470
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.65723.313163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.79715694
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3011531
X-RAY DIFFRACTIONr_chiral_restr0.1030.2587
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212818
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8651.52361
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.54823825
X-RAY DIFFRACTIONr_scbond_it1.97631459
X-RAY DIFFRACTIONr_scangle_it3.3524.51337
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 102 -
Rwork0.245 2467 -
obs--79.86 %
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)
10.2429-0.0546-0.46530.2320.01931.46520.0003-0.03490.01980.05210.0046-0.0323-0.04790.1006-0.00480.1362-0.0066-0.01070.0865-0.00310.08082.919-4.312-29.356
212.35010.7535-15.42470.049-0.943519.29381.5805-1.4240.45070.1101-0.48750.0756-2.45851.5842-1.0930.3494-0.1045-0.04731.78640.51821.1917-10.632-27.541-2.358
31.0359-0.70750.07781.92960.45751.27050.0456-0.0382-0.08330.09540.007-0.00080.06730.0304-0.05260.1413-0.0078-0.01710.10380.00350.04992.503-27.922-7.879
41.92170.1758-0.251.1525-0.35110.8287-0.02560.0639-0.0462-0.03340.0207-0.0883-0.01060.05130.00490.118-0.00990.00250.0864-0.00470.078625.302-9.766-54.862
52.8785-1.10961.56331.7641-0.33152.0071-0.0158-0.0938-0.07750.0544-0.04020.18220.0115-0.08930.0560.1250.00040.00710.078-0.01310.0836-12.161-0.949-37.146
67.2373-2.8219-0.78592.6213-1.46075.7279-0.4457-0.30350.56850.21860.15970.124-0.9486-0.16590.2860.39960.0311-0.15170.0274-0.0640.3196-8.39112.181-16.764
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A52 - 258
2X-RAY DIFFRACTION2A5 - 11
3X-RAY DIFFRACTION3A18 - 51
4X-RAY DIFFRACTION3A259 - 350
5X-RAY DIFFRACTION4C33 - 124
6X-RAY DIFFRACTION5B1 - 32
7X-RAY DIFFRACTION6B33 - 48

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