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- PDB-3hjw: Structure of a functional ribonucleoprotein pseudouridine synthas... -

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Basic information

Entry
Database: PDB / ID: 3hjw
TitleStructure of a functional ribonucleoprotein pseudouridine synthase bound to a substrate RNA
Components
  • 5'-R(*GP*AP*GP*CP*GP*(FHU)P*GP*CP*GP*GP*UP*UP*U)-3'
  • 50S ribosomal protein L7AeRibosome
  • Pseudouridine synthase Cbf5
  • RNA (58-MER)
  • Ribosome biogenesis protein Nop10
KeywordsISOMERASE/RNA / protein-RNA complex / Box H/ACA / ribonucleoprotein particles / RNP / pseudouridine synthase / pseudouridylase / pseudouridylation / RNA editing / post-transcriptional modification / Isomerase / tRNA processing / Ribonucleoprotein / Ribosome biogenesis / rRNA processing / Ribosomal protein / RNA-binding / ISOMERASE-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 / rRNA binding / ribosome ...tRNA pseudouridine55 synthase / tRNA pseudouridine synthase activity / pseudouridine synthesis / tRNA pseudouridine synthesis / ribonuclease P activity / tRNA 5'-leader removal / snoRNA binding / rRNA processing / rRNA binding / ribosome / 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 / molecular replacement / Resolution: 2.35 Å
AuthorsLiang, B. / Zhou, J. / Kahen, E. / Terns, R.M. / Terns, M.P. / Li, H.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2009
Title: Structure of a functional ribonucleoprotein pseudouridine synthase bound to a substrate RNA
Authors: Liang, B. / Zhou, J. / Kahen, E. / Terns, R.M. / Terns, M.P. / Li, H.
History
DepositionMay 22, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Aug 12, 2015Group: Refinement description
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Sep 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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.db_align_beg / _struct_ref_seq.db_align_end / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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: RNA (58-MER)
E: 5'-R(*GP*AP*GP*CP*GP*(FHU)P*GP*CP*GP*GP*UP*UP*U)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,4447
Polymers79,3405
Non-polymers1052
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12860 Å2
ΔGint-86 kcal/mol
Surface area29860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)186.013, 63.026, 85.447
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 3 types, 3 molecules ABC

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


Mass: 36990.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: DSM 3638 / Gene: PF1785 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 codon plus
References: UniProt: Q7LWY0, Isomerases; Intramolecular transferases; Transferring other groups
#2: Protein Ribosome biogenesis protein Nop10 /


Mass: 6352.509 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: DSM 3638 / Gene: PF1141 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 codon plus / References: UniProt: Q8U1R4
#3: Protein 50S ribosomal protein L7Ae / Ribosome


Mass: 13083.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: DSM 3638 / Gene: PF1367, rpl7ae / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 codon plus / References: UniProt: Q8U160

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RNA chain , 2 types, 2 molecules DE

#4: RNA chain RNA (58-MER)


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


Mass: 4226.516 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 3 types, 101 molecules

#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#7: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 3.16 Å3/Da / Density % sol: 61.03 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.8 M KCl, 0.15 M Mg Acetate, 8% (w/v) PEG 6000, pH 6.5, vapor diffusion, hanging drop, temperature 303K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineID
SYNCHROTRONAPS 22-ID1
SYNCHROTRONAPS 22-BM2
Detector
TypeIDDetectorDate
MARMOSAIC 300 mm CCD1CCDDec 12, 2008
MARMOSAIC 225 mm CCD2CCDDec 12, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 51141 / % possible obs: 91.3 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.079 / Χ2: 1.613 / Net I/σ(I): 20.968
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.15-2.231.80.59228061.136151.1
2.23-2.322.30.6541681.128175.3
2.32-2.423.50.64450060.986190.3
2.42-2.555.40.54853320.937197
2.55-2.716.60.38755170.997199.3
2.71-2.9270.22455221.077199.5
2.92-3.217.40.10656051.315199.8
3.21-3.687.70.06456121.71199.9
3.68-4.637.80.05256662.509199.9
4.63-507.50.04159072.576199.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.2.0005refinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2HVY

2hvy


Resolution: 2.35→46.52 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.905 / Occupancy max: 1 / Occupancy min: 1 / SU B: 16.099 / SU ML: 0.172 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.289 / ESU R Free: 0.221 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1807 4.3 %RANDOM
Rwork0.217 ---
obs0.218 42200 98.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 96.03 Å2 / Biso mean: 37.351 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--1.18 Å20 Å20 Å2
2--0.17 Å20 Å2
3---1.01 Å2
Refinement stepCycle: LAST / Resolution: 2.35→46.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3964 1515 2 99 5580
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0225743
X-RAY DIFFRACTIONr_angle_refined_deg1.3972.3168110
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6065497
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.18423.434166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.36415758
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9431531
X-RAY DIFFRACTIONr_chiral_restr0.0770.2965
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023723
X-RAY DIFFRACTIONr_nbd_refined0.2040.22359
X-RAY DIFFRACTIONr_nbtor_refined0.2950.23725
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2268
X-RAY DIFFRACTIONr_metal_ion_refined0.3760.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.110.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0570.24
X-RAY DIFFRACTIONr_mcbond_it0.4671.52498
X-RAY DIFFRACTIONr_mcangle_it0.9424051
X-RAY DIFFRACTIONr_scbond_it1.51633355
X-RAY DIFFRACTIONr_scangle_it2.4574.54059
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 50 -
Rwork0.299 2835 -
all-2885 -
obs--92.59 %
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)
10.6756-0.3122-0.33860.51390.18920.2299-0.0062-0.06580.0397-0.05240.04790.00780.00440.0131-0.04170.01130.02410.022-0.0671-0.0023-0.064431.66514.785212.7156
21.5331-0.6249-1.27361.12121.63755.3779-0.1219-0.3876-0.0847-0.03220.1668-0.23110.01970.272-0.0449-0.05610.0682-0.01970.02560.0069-0.053453.37776.744420.0789
34.5663-0.80410.48933.14170.69122.9337-0.1211-0.273-0.13820.08910.0066-0.3726-0.0140.56120.1145-0.16460.0887-0.0160.2520.1426-0.126168.2123-1.177132.962
40.8938-0.42620.07720.8352-0.19120.04440.0028-0.2397-0.21440.07490.03540.2809-0.06480.0564-0.0382-0.03910.08870.05550.06390.0826-0.014927.40285.752129.5657
59.20470.8398-0.96422.9819-2.65782.37420.1085-0.8499-0.5137-0.1383-0.13550.0782-0.3730.03850.0271-0.0086-0.00240.0479-0.0049-0.0003-0.007119.7789-2.807124.5779
62.80941.5741-0.20332.04921.57542.4596-0.048-0.0575-0.221-0.34430.210.6495-0.92370.0686-0.1620.00020.0009-0.00030.0002-0.0003043.06834.97097.6279
71.3678-0.5513-0.12190.89840.12540.66430.0031-0.16440.0066-0.05570.05660.0467-0.09890.0203-0.05970.07290.01870.0632-0.01740.0291-0.022433.175410.507518.2371
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 337
2X-RAY DIFFRACTION2B3 - 52
3X-RAY DIFFRACTION3C4 - 123
4X-RAY DIFFRACTION4D1 - 58
5X-RAY DIFFRACTION5E5 - 17
6X-RAY DIFFRACTION6B1
7X-RAY DIFFRACTION6E2
8X-RAY DIFFRACTION7A1 - 10
9X-RAY DIFFRACTION7A338 - 390
10X-RAY DIFFRACTION7B56 - 91
11X-RAY DIFFRACTION7C124 - 125
12X-RAY DIFFRACTION7D59 - 97
13X-RAY DIFFRACTION7E19 - 80

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