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- PDB-3lwq: Structure of H/ACA RNP bound to a substrate RNA containing 3MU -

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Basic information

Entry
Database: PDB / ID: 3lwq
TitleStructure of H/ACA RNP bound to a substrate RNA containing 3MU
Components
  • 5'-R(*GP*AP*GP*CP*GP*(UR3)P*GP*CP*GP*GP*UP*UP*U)-3
  • H/ACA RNA
  • Large ribosomal subunit protein eL8
  • Probable tRNA pseudouridine synthase B
  • Ribosome biogenesis protein Nop10
KeywordsISOMERASE/RNA BINDING PROTEIN/RNA / H/ACA pseudouridine synthase / Isomerase / tRNA processing / Ribonucleoprotein / Ribosome biogenesis / rRNA processing / Ribosomal protein / RNA-binding / ISOMERASE-RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


tRNA pseudouridine55 synthase / tRNA pseudouridine(55) 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(55) 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 / 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 / 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 / Resolution: 2.678 Å
AuthorsZhou, J. / Liang, B. / Lv, C. / Yang, W. / Li, H.
CitationJournal: Biochemistry / Year: 2010
Title: Functional and Structural Impact of Target Uridine Substitutions on the H/ACA Ribonucleoprotein Particle Pseudouridine Synthase .
Authors: Zhou, J. / Liang, B. / Li, H.
History
DepositionFeb 24, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / entity_name_com / entity_src_gen / pdbx_entity_src_syn / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref / struct_ref_seq / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _entity.pdbx_ec / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_seq_type / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_seq_id / _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: Probable tRNA pseudouridine synthase B
B: Ribosome biogenesis protein Nop10
C: Large ribosomal subunit protein eL8
D: H/ACA RNA
E: 5'-R(*GP*AP*GP*CP*GP*(UR3)P*GP*CP*GP*GP*UP*UP*U)-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,2396
Polymers82,1745
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11430 Å2
ΔGint-62 kcal/mol
Surface area29950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)189.152, 64.333, 84.045
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 Probable tRNA pseudouridine synthase B / tRNA pseudouridine(55) synthase / Psi55 synthase / tRNA pseudouridylate synthase / tRNA-uridine isomerase


Mass: 38625.027 Da / Num. of mol.: 1
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, tRNA pseudouridine55 synthase
#2: Protein Ribosome biogenesis protein Nop10


Mass: 7242.618 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: nop10, PF1141 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8U1R4
#3: Protein Large ribosomal subunit protein eL8 / 50S ribosomal protein L7Ae / Ribosomal protein L8e


Mass: 13414.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: rpl7ae, PF1367 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8U160

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RNA chain , 2 types, 2 molecules DE

#4: RNA chain H/ACA RNA


Mass: 18687.193 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: In vitro transcription
#5: RNA chain 5'-R(*GP*AP*GP*CP*GP*(UR3)P*GP*CP*GP*GP*UP*UP*U)-3


Mass: 4204.537 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: commercial source

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Non-polymers , 1 types, 1 molecules

#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Details

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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
13.1160.47
2
3
4
5
Crystal grow
Crystal-IDMethodDetails
1vapor diffusion, hanging dropVAPOR DIFFUSION, HANGING DROP
2vapor diffusion, hanging dropVAPOR DIFFUSION, HANGING DROP
3vapor diffusion, hanging dropVAPOR DIFFUSION, HANGING DROP
4vapor diffusion, hanging dropVAPOR DIFFUSION, HANGING DROP
5vapor diffusion, hanging dropVAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.5418 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: May 25, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 25347 / % possible obs: 86.6 % / Redundancy: 6.3 % / Rsym value: 0.093
Reflection shellResolution: 2.65→2.7 Å / Redundancy: 4.8 % / Num. unique all: 1405 / Rsym value: 0.634 / % possible all: 99.4

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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 / Resolution: 2.678→32.974 Å / SU ML: 0.97 / σ(F): 1.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2714 1284 5.09 %
Rwork0.2108 --
obs0.2139 25208 45.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.247 Å2 / ksol: 0.338 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.4594 Å2-0 Å20 Å2
2---17.9229 Å2-0 Å2
3---13.4635 Å2
Refinement stepCycle: LAST / Resolution: 2.678→32.974 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3842 1514 1 0 5357
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085622
X-RAY DIFFRACTIONf_angle_d1.227940
X-RAY DIFFRACTIONf_dihedral_angle_d22.0422441
X-RAY DIFFRACTIONf_chiral_restr0.071947
X-RAY DIFFRACTIONf_plane_restr0.004747
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6781-2.78530.32671380.25862625X-RAY DIFFRACTION45
2.7853-2.9120.35661640.26023064X-RAY DIFFRACTION52
2.912-3.06540.34511390.26712797X-RAY DIFFRACTION51
3.0654-3.25730.4057610.30941135X-RAY DIFFRACTION26
3.2573-3.50850.30161560.23073122X-RAY DIFFRACTION53
3.5085-3.86110.2721310.21392164X-RAY DIFFRACTION37
3.8611-4.41870.21571550.16712598X-RAY DIFFRACTION44
4.4187-5.56270.21141780.16033126X-RAY DIFFRACTION53
5.5627-32.97680.28781620.21623293X-RAY DIFFRACTION56
Refinement TLS params.Method: refined / Origin x: 38.3395 Å / Origin y: 9.6463 Å / Origin z: 20.9564 Å
111213212223313233
T0.306 Å20.0391 Å20.0213 Å2-0.3549 Å2-0.0068 Å2--0.3072 Å2
L1.0398 °2-0.184 °20.18 °2-1.5058 °2-0.2466 °2--0.6372 °2
S-0.0991 Å °-0.1542 Å °-0.0536 Å °-0.0433 Å °0.1671 Å °0.1924 Å °0.0719 Å °0.0022 Å °-0.0554 Å °
Refinement TLS groupSelection details: all

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