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- PDB-2hvy: Crystal structure of an H/ACA box RNP from Pyrococcus furiosus -

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Basic information

Entry
Database: PDB / ID: 2hvy
TitleCrystal structure of an H/ACA box RNP from Pyrococcus furiosus
Components
  • 50S ribosomal protein L7Ae
  • H/ACA RNA
  • Probable tRNA pseudouridine synthase B
  • Ribosome biogenesis protein Nop10
  • Small nucleolar rnp similar to gar1
KeywordsISOMERASE/BIOSYNTHETIC PROTEIN/RNA / H/ACA RNA / RNP / PSEUDOURIDINE synthase / Guide RNA / ISOMERASE-BIOSYNTHETIC 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 / snRNA pseudouridine synthesis / tRNA pseudouridine synthesis / mRNA pseudouridine synthesis / ribonuclease P activity / tRNA 5'-leader removal ...tRNA pseudouridine55 synthase / tRNA pseudouridine(55) synthase activity / rRNA pseudouridine synthesis / box H/ACA sno(s)RNA 3'-end processing / pseudouridine synthesis / snRNA pseudouridine synthesis / tRNA pseudouridine synthesis / mRNA pseudouridine synthesis / ribonuclease P activity / tRNA 5'-leader removal / snoRNA binding / rRNA processing / ribosome biogenesis / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / RNA binding / cytoplasm
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 / tRNA pseudouridine synthase B family / Dyskerin-like / DKCLD (NUC011) domain ...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 / 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. / Ribosomal protein L7Ae, archaea / Ribosomal protein L30/S12 / Rubrerythrin, domain 2 / PUA-like superfamily / 60s Ribosomal Protein L30; Chain: A; / Single Sheet / Ribosomal protein L7Ae conserved site / Ribosomal protein L7Ae signature. / Ribosomal protein L7Ae/L8/Nhp2 family / : / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like / Thrombin, subunit H / Translation protein, beta-barrel domain superfamily / Roll / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / RNA / RNA (> 10) / Probable tRNA pseudouridine synthase B / Small nucleolar rnp gar1-like protein / Large ribosomal subunit protein eL8 / Ribosome biogenesis protein Nop10
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsYe, K.
CitationJournal: Nature / Year: 2006
Title: Crystal structure of an H/ACA box ribonucleoprotein particle
Authors: Li, L. / Ye, K.
History
DepositionJul 31, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 12, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: H/ACA RNA
A: Probable tRNA pseudouridine synthase B
B: Small nucleolar rnp similar to gar1
C: Ribosome biogenesis protein Nop10
D: 50S ribosomal protein L7Ae
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,9187
Polymers94,3455
Non-polymers5732
Water2,126118
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.031, 90.950, 114.064
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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RNA chain , 1 types, 1 molecules E

#1: RNA chain H/ACA RNA


Mass: 21021.512 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Derived from Afu-46 RNA

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Protein , 4 types, 4 molecules ABCD

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


Mass: 39453.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: truB / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Rosseta2
References: UniProt: Q7LWY0, Isomerases; Intramolecular transferases; Transferring other groups
#3: Protein Small nucleolar rnp similar to gar1 / Gar1


Mass: 12340.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: GAR1 / Plasmid: pRSFDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Rosseta2 / References: UniProt: Q8U029
#4: Protein Ribosome biogenesis protein Nop10 / Nop10


Mass: 7214.603 Da / Num. of mol.: 1 / Mutation: R2K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: NOP10 / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Rosseta2 / References: UniProt: Q8U1R4
#5: Protein 50S ribosomal protein L7Ae / L7ae


Mass: 14314.623 Da / Num. of mol.: 1 / Mutation: M2A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: rpl7ae / Plasmid: pRSFDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Rosseta2 / References: UniProt: Q8U160

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Non-polymers , 3 types, 120 molecules

#6: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#7: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.28 Å3/Da / Density % sol: 46.09 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 30% MPD, 35mM CH3COOMg, 10mM ATP, 50mM cacodylate , pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 303K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2CH3COOMg11
3ATP11
4cacodylate11
5H2O11
6MPD12
7CH3COOMg12
8ATP12
9cacodylate12
10H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 5, 2006
RadiationMonochromator: double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. all: 39340 / Num. obs: 39234 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 38
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 6.7 / Num. unique all: 1950 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2EY4

2ey4


Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.906 / SU B: 16.054 / SU ML: 0.196 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: TLS isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.369 / ESU R Free: 0.26 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27807 1914 4.9 %RANDOM
Rwork0.23786 ---
all0.23984 37072 --
obs0.23984 36983 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.191 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å20 Å20 Å2
2--2.4 Å20 Å2
3----2.14 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4512 1235 32 118 5897
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0226019
X-RAY DIFFRACTIONr_angle_refined_deg1.0452.258420
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8155563
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.48223.617188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.90215860
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3151532
X-RAY DIFFRACTIONr_chiral_restr0.0810.2989
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.023993
X-RAY DIFFRACTIONr_nbd_refined0.1550.22440
X-RAY DIFFRACTIONr_nbtor_refined0.2880.23940
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1110.2236
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1340.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1340.25
X-RAY DIFFRACTIONr_mcbond_it0.1931.52950
X-RAY DIFFRACTIONr_mcangle_it0.34124605
X-RAY DIFFRACTIONr_scbond_it0.37933913
X-RAY DIFFRACTIONr_scangle_it0.6414.53815
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 120 -
Rwork0.298 2680 -
obs--100 %
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)
13.7651.31580.33634.25490.49725.9757-0.0430.35110.1627-0.72080.02740.0321-0.61120.07440.01560.0174-0.00250.0083-0.23950.0453-0.1293-16.5316.90624.554
21.10171.07940.88583.11522.64733.94990.0450.0341-0.0111-0.0448-0.0025-0.0317-0.04680.0772-0.0425-0.1520.00120.0237-0.22580.059-0.1433-22.284-10.80826.801
35.32011.5123.47136.63850.24558.3969-0.05410.3976-0.3463-0.01750.43590.45560.1475-0.5827-0.3818-0.1394-0.06020.00110.02680.1048-0.0894-39.097-21.753-3.893
411.9114-4.7286-3.14212.40261.964514.66030.0945-0.51660.0350.4836-0.1282-0.82760.38131.33880.03370.00720.08930.0128-0.06180.0709-0.0055-11.316-25.89826.756
53.8311-1.41771.6387.83071.37456.737-0.1637-0.31160.07341.01030.0134-0.62880.37290.22980.15030.1445-0.0672-0.0608-0.24960.119-0.0398-17.69-18.86948.647
66.0688-0.48981.0857.2712-1.38355.71590.3528-0.4769-1.0090.3542-0.0706-0.36471.08250.3774-0.28220.41930.0479-0.1987-0.14530.12880.0946-16.001-38.56850.694
710.61912.2352-5.1450.5049-0.91733.2912-0.07540.13510.4611-0.23810.01540.44210.094-0.2650.060.18470.127-0.0765-0.0736-0.07250.0928-37.14317.16335.056
8000000-0.9841-1.1426-0.3215-0.28441.53792.2616-0.48580.3318-0.55380.8903-0.2004-0.18870.75780.47061.0112-43.698-5.60333.845
94.5124-1.05980.45884.8918-2.76433.39410.14630.4216-0.3137-0.30660.41411.06790.719-0.8938-0.56040.105-0.1905-0.06520.05690.12030.1369-36.735-24.63839.843
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AB11 - 388 - 35
2X-RAY DIFFRACTION1AB253 - 337250 - 334
3X-RAY DIFFRACTION2AB39 - 25236 - 249
4X-RAY DIFFRACTION3BC1 - 748 - 81
5X-RAY DIFFRACTION4CD3 - 303 - 30
6X-RAY DIFFRACTION4CF2011
7X-RAY DIFFRACTION5CD31 - 5531 - 55
8X-RAY DIFFRACTION6DE4 - 1244 - 124
9X-RAY DIFFRACTION7EA1 - 91 - 9
10X-RAY DIFFRACTION7EA49 - 6149 - 61
11X-RAY DIFFRACTION8EA10 - 1610 - 16
12X-RAY DIFFRACTION8EA42 - 4842 - 48
13X-RAY DIFFRACTION9EA17 - 4117 - 41

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