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- PDB-2aus: Crystal structure of the archaeal box H/ACA sRNP Nop10-Cbf5 complex -

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Basic information

Entry
Database: PDB / ID: 2aus
TitleCrystal structure of the archaeal box H/ACA sRNP Nop10-Cbf5 complex
Components
  • Ribosome biogenesis protein Nop10
  • pseudouridine synthase
KeywordsISOMERASE/STRUCTURAL PROTEIN / ISOMERASE / STRUCTURAL PROTEIN / ISOMERASE-STRUCTURAL PROTEIN COMPLEX
Function / homology
Function and homology information


tRNA pseudouridine55 synthase / tRNA pseudouridine synthase activity / pseudouridine synthesis / tRNA pseudouridine synthesis / snoRNA binding / rRNA processing / RNA binding
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. / Rubrerythrin, domain 2 / PUA-like superfamily / Single Sheet / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Ribosome biogenesis protein Nop10 / Probable tRNA pseudouridine synthase B
Similarity search - Component
Biological speciesPyrococcus abyssi (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsCharron, C. / Manival, X. / Charpentier, B. / Fourmann, J.-B. / Godard, F. / Branlant, C.
CitationJournal: Nucleic Acids Res. / Year: 2006
Title: Crystal structure determination and site-directed mutagenesis of the Pyrococcus abyssi aCBF5-aNOP10 complex reveal crucial roles of the C-terminal domains of both proteins in H/ACA sRNP activity
Authors: Manival, X. / Charron, C. / Fourmann, J.B. / Godard, F. / Charpentier, B. / Branlant, C.
History
DepositionAug 29, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 11, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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
C: pseudouridine synthase
D: Ribosome biogenesis protein Nop10
A: pseudouridine synthase
B: Ribosome biogenesis protein Nop10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,56111
Polymers89,9564
Non-polymers6067
Water4,504250
1
C: pseudouridine synthase
D: Ribosome biogenesis protein Nop10
hetero molecules

C: pseudouridine synthase
D: Ribosome biogenesis protein Nop10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,46610
Polymers89,9564
Non-polymers5116
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
MethodPQS
2
A: pseudouridine synthase
B: Ribosome biogenesis protein Nop10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3286
Polymers44,9782
Non-polymers3504
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8340 Å2
ΔGint-78 kcal/mol
Surface area32860 Å2
MethodPISA
3
C: pseudouridine synthase
D: Ribosome biogenesis protein Nop10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2335
Polymers44,9782
Non-polymers2553
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-25 kcal/mol
Surface area17430 Å2
MethodPISA
4
A: pseudouridine synthase
B: Ribosome biogenesis protein Nop10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3286
Polymers44,9782
Non-polymers3504
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-29 kcal/mol
Surface area17330 Å2
MethodPISA
5
A: pseudouridine synthase
B: Ribosome biogenesis protein Nop10
hetero molecules

A: pseudouridine synthase
B: Ribosome biogenesis protein Nop10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,65612
Polymers89,9564
Non-polymers7018
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
MethodPQS
Unit cell
Length a, b, c (Å)136.430, 136.820, 59.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological assembly is a tetramer generated from the heterodimer in the asymmetric unit by the operation: -x, -y, z.

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Components

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


Mass: 37792.199 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus abyssi (archaea) / Plasmid: pGex-6p1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9V1A5, Isomerases; Intramolecular transferases; Transferring other groups
#2: Protein Ribosome biogenesis protein Nop10 / / Nop10


Mass: 7185.565 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus abyssi (archaea) / Plasmid: pGex-6p1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9V0E3
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 3.27 Å3/Da / Density % sol: 62.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: potassium phosphate, sodium acetate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID14-410.9686
SYNCHROTRONESRF BM1420.9777
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDSep 25, 2004
MARRESEARCH2CCDFeb 14, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.96861
20.97771
ReflectionResolution: 2.1→30 Å / Num. all: 65534 / Num. obs: 65534 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rsym value: 0.068
Reflection shellResolution: 2.1→2.2 Å / % possible all: 100

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Processing

Software
NameClassification
XDSdata scaling
XDSdata reduction
SOLVEphasing
CNSrefinement
RefinementMethod to determine structure: SAD / Resolution: 2.1→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.252 3334 random
Rwork0.224 --
all0.225 65534 -
obs0.225 65534 -
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5776 0 27 250 6053
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.49148

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