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- PDB-2ey4: Crystal Structure of a Cbf5-Nop10-Gar1 Complex -

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Basic information

Entry
Database: PDB / ID: 2ey4
TitleCrystal Structure of a Cbf5-Nop10-Gar1 Complex
Components
  • Probable tRNA pseudouridine synthase B
  • Ribosome biogenesis protein Nop10
  • small nucleolar rnp similar to gar1
KeywordsISOMERASE/BIOSYNTHETIC PROTEIN / Trimeric complex / Structural Genomics / PSI / Protein Structure Initiative / Southeast Collaboratory for Structural Genomics / SECSG / ISOMERASE-BIOSYNTHETIC PROTEIN COMPLEX
Function / homology
Function and homology information


tRNA pseudouridine55 synthase / tRNA pseudouridine synthase activity / pseudouridine synthesis / tRNA pseudouridine synthesis / snoRNA binding / rRNA processing / ribonucleoprotein complex / RNA binding / ATP binding
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 / 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 / Rubrerythrin, domain 2 / PUA-like superfamily / Single Sheet / Thrombin, subunit H / Translation protein, beta-barrel domain superfamily / Roll / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / Probable tRNA pseudouridine synthase B / Small nucleolar rnp gar1-like protein / Ribosome biogenesis protein Nop10
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.11 Å
AuthorsRashid, R. / Liang, B. / Li, H. / Southeast Collaboratory for Structural Genomics (SECSG)
CitationJournal: Mol.Cell / Year: 2006
Title: Crystal structure of a Cbf5-Nop10-Gar1 complex and implications in RNA-guided pseudouridylation and dyskeratosis congenita.
Authors: Rashid, R. / Liang, B. / Baker, D.L. / Youssef, O.A. / He, Y. / Phipps, K. / Terns, R.M. / Terns, M.P. / Li, H.
History
DepositionNov 9, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 14, 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_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_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: Probable tRNA pseudouridine synthase B
C: small nucleolar rnp similar to gar1
D: small nucleolar rnp similar to gar1
E: Ribosome biogenesis protein Nop10
F: Ribosome biogenesis protein Nop10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,7518
Polymers107,6206
Non-polymers1312
Water3,171176
1
A: Probable tRNA pseudouridine synthase B
C: small nucleolar rnp similar to gar1
E: Ribosome biogenesis protein Nop10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8764
Polymers53,8103
Non-polymers651
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4400 Å2
ΔGint-17 kcal/mol
Surface area21570 Å2
MethodPISA
2
B: Probable tRNA pseudouridine synthase B
D: small nucleolar rnp similar to gar1
F: Ribosome biogenesis protein Nop10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8764
Polymers53,8103
Non-polymers651
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4300 Å2
ΔGint-18 kcal/mol
Surface area21480 Å2
MethodPISA
3
A: Probable tRNA pseudouridine synthase B
C: small nucleolar rnp similar to gar1
E: Ribosome biogenesis protein Nop10
hetero molecules

B: Probable tRNA pseudouridine synthase B
D: small nucleolar rnp similar to gar1
F: Ribosome biogenesis protein Nop10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,7518
Polymers107,6206
Non-polymers1312
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_454x-1,y,z-11
Buried area10600 Å2
ΔGint-46 kcal/mol
Surface area41140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.087, 75.361, 103.240
Angle α, β, γ (deg.)95.90, 96.90, 94.99
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 37663.965 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: truB / Production host: Escherichia coli (E. coli)
References: UniProt: Q7LWY0, Isomerases; Intramolecular transferases; Transferring other groups
#2: Protein small nucleolar rnp similar to gar1


Mass: 9505.268 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: DSM 3638 / Production host: Escherichia coli (E. coli) / References: GenBank: 18893970, UniProt: Q8U029*PLUS
#3: Protein Ribosome biogenesis protein Nop10 /


Mass: 6640.899 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8U1R4
#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.: 176 / 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: 2.56 Å3/Da / Density % sol: 51.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: In hanging drops, pH 6.5, VAPOR DIFFUSION, temperature 298.0K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11731
21
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 22-ID11
SYNCHROTRONAPS 8-BM20.9792, 0.9794, 0.9537
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 26, 2005
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97921
30.97941
40.95371
ReflectionResolution: 2.1→50 Å / Num. all: 93272 / Num. obs: 51837 / % possible obs: 55.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 11.8 Å2
Reflection shellHighest resolution: 2.1 Å / % possible all: 95

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Processing

Software
NameVersionClassification
CNS1.1refinement
bioteXdata reduction
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.11→39.97 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 388708.4 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.255 4967 10.1 %RANDOM
Rwork0.211 ---
obs0.211 49301 80.5 %-
all-54268 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.6809 Å2 / ksol: 0.354846 e/Å3
Displacement parametersBiso mean: 41.3 Å2
Baniso -1Baniso -2Baniso -3
1-13.29 Å2-2.68 Å2-0.09 Å2
2---4.87 Å2-4.24 Å2
3----8.42 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.11→39.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7278 0 2 176 7456
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.11→2.23 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.307 385 9.5 %
Rwork0.275 3656 -
obs--38.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3water_rep.paramwater.top

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