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- PDB-3uai: Structure of the Shq1-Cbf5-Nop10-Gar1 complex from Saccharomyces ... -

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Basic information

Entry
Database: PDB / ID: 3uai
TitleStructure of the Shq1-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
  • Protein SHQ1
KeywordsISOMERASE/CHAPERONE / H/ACA RNP assembly intermediate / H/ACA RNA / Nuclear / ISOMERASE-CHAPERONE complex
Function / homology
Function and homology information


snRNA pseudouridine synthase activity / Telomere Extension By Telomerase / box H/ACA snoRNP assembly / snoRNA guided rRNA pseudouridine synthesis / rRNA pseudouridine synthesis / box H/ACA snoRNP complex / box H/ACA sno(s)RNA 3'-end processing / Isomerases; Intramolecular transferases; Transferring other groups / snRNA pseudouridine synthesis / mRNA pseudouridine synthesis ...snRNA pseudouridine synthase activity / Telomere Extension By Telomerase / box H/ACA snoRNP assembly / snoRNA guided rRNA pseudouridine synthesis / rRNA pseudouridine synthesis / box H/ACA snoRNP complex / box H/ACA sno(s)RNA 3'-end processing / Isomerases; Intramolecular transferases; Transferring other groups / snRNA pseudouridine synthesis / 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 / unfolded protein binding / microtubule / cell division / mRNA binding / nucleolus / DNA binding / RNA binding / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Rhinovirus 14, subunit 4 - #300 / Probable tRNA pseudouridine synthase domain / Shq1 protein domain / Protein Shq1 / : / SHQ1 protein, Shq1 domain / SHQ1-like, CS domain / H/ACA ribonucleoprotein complex, subunit Gar1/Naf1 / H/ACA RNP complex subunit Gar1/Naf1, Cbf5-binding domain / Gar1/Naf1 RNA binding region ...Rhinovirus 14, subunit 4 - #300 / Probable tRNA pseudouridine synthase domain / Shq1 protein domain / Protein Shq1 / : / SHQ1 protein, Shq1 domain / SHQ1-like, CS domain / 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) / Uncharacterised domain CHP00451 / CS domain / CS domain profile. / PUA domain / 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 / HSP20-like chaperone / PUA-like superfamily / Few Secondary Structures / Irregular / Thrombin, subunit H / Translation protein, beta-barrel domain superfamily / 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 / Protein SHQ1 / H/ACA ribonucleoprotein complex subunit NOP10
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.06 Å
AuthorsYe, K.
CitationJournal: Embo J. / Year: 2011
Title: Structure of the Shq1-Cbf5-Nop10-Gar1 complex and implications for H/ACA RNP biogenesis and dyskeratosis congenita
Authors: Li, S. / Duan, J. / Li, D. / Ma, S. / Ye, K.
History
DepositionOct 21, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Nov 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
D: Protein SHQ1


Theoretical massNumber of molelcules
Total (without water)107,1784
Polymers107,1784
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7620 Å2
ΔGint-42 kcal/mol
Surface area38780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.995, 100.995, 272.329
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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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: Core domain, UNP residues 3-394
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: 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: 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: Core domain, UNP residues 32-124
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288c / Gene: GAR1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: P28007
#4: Protein Protein SHQ1 / Small nucleolar RNAs of the box H/ACA family quantitative accumulation protein 1


Mass: 42928.047 Da / Num. of mol.: 1 / Fragment: Shq1 specific domain, UNP residues 147-504
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288c / Gene: SHQ1 / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: P40486

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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: 3.24 Å3/Da / Density % sol: 62.03 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Bis-Tris, 20%(w/v) polyethylene glycol monomethyl ether 5000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9789 Å
DetectorDetector: CCD / Date: Jun 6, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 3.06→50 Å / Num. obs: 27487 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.1 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 58.4
Reflection shellResolution: 3.06→3.11 Å / Redundancy: 14.7 % / Rmerge(I) obs: 0.684 / Mean I/σ(I) obs: 5.6 / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UAH, 3U28

3uah

3u28


Resolution: 3.06→20 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.907 / SU B: 37.907 / SU ML: 0.311 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.434 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27526 1370 5 %RANDOM
Rwork0.21886 ---
obs0.22162 25934 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 100.637 Å2
Baniso -1Baniso -2Baniso -3
1-1.62 Å20 Å20 Å2
2--1.62 Å20 Å2
3----3.24 Å2
Refinement stepCycle: LAST / Resolution: 3.06→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6627 0 0 0 6627
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0226755
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.211.9739128
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9335817
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.11524.241316
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.102151242
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6061546
X-RAY DIFFRACTIONr_chiral_restr0.0860.21020
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215035
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_it0.3791.54100
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.72826647
X-RAY DIFFRACTIONr_scbond_it0.90332655
X-RAY DIFFRACTIONr_scangle_it1.6034.52481
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.062→3.14 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 96 -
Rwork0.279 1821 -
obs--99.33 %
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)
13.5128-0.9419-1.88263.39491.16484.02890.0527-0.18390.13690.12490.0677-0.1647-0.22780.1545-0.12040.22290.0232-0.04930.03610.03610.1474-15.49870.38745.8027
24.13341.4266-1.04873.54570.15530.38110.33180.40210.45140.0815-0.23590.8194-0.0665-0.3014-0.0960.73680.0932-0.03950.93810.18110.685-45.73260.083260.0043
35.01481.2563-0.91893.433-1.31163.94590.00590.2830.0636-0.54410.14110.65470.286-0.8377-0.14710.2332-0.0024-0.05270.42330.00770.1575-38.7158-10.662563.1534
44.87752.13982.86426.56122.15519.81360.0411-0.54760.36370.2349-0.19460.1096-0.4370.06970.15350.38970.16750.2040.653-0.19940.5473-41.13252.101699.793
54.5933-1.5545-1.77425.1693-1.255612.6511-0.13340.60640.1727-0.24240.3243-0.09340.00020.012-0.19090.27640.05320.02830.27470.12040.1443-18.41289.49130.4386
65.1344-1.9805-5.99165.1941-2.151211.50820.2129-0.5420.83890.55240.5442-0.4138-0.92780.2948-0.75711.0299-0.07760.00060.23-0.27330.9241-14.747124.131951.0848
72.9328-1.69790.75043.1887-0.78492.71590.09320.055-0.5999-0.0924-0.1365-0.30030.24760.4940.04330.57550.17960.05510.2476-0.02220.55471.9993-27.087436.1539
83.06480.1342-0.43623.2877-0.192.37110.0393-0.2897-0.02940.1543-0.1835-0.32150.08730.02220.14410.0516-0.00090.02350.23860.03170.0664-22.9622-15.892886.3749
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A52 - 258
2X-RAY DIFFRACTION2A18 - 51
3X-RAY DIFFRACTION3A259 - 347
4X-RAY DIFFRACTION4A348 - 378
5X-RAY DIFFRACTION5B1 - 32
6X-RAY DIFFRACTION6B33 - 48
7X-RAY DIFFRACTION7C33 - 124
8X-RAY DIFFRACTION8D164 - 506

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