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- PDB-4u7a: The carboxy-terminal domain of Erb1 is a seven-bladed beta-propel... -

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Basic information

Entry
Database: PDB / ID: 4u7a
TitleThe carboxy-terminal domain of Erb1 is a seven-bladed beta-propeller that binds RNA.
ComponentsRibosome biogenesis protein ERB1
KeywordsPROTEIN BINDING / ribosome biogenesis / WD40 / rRNA binding / beta-propeller
Function / homology
Function and homology information


PeBoW complex / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Major pathway of rRNA processing in the nucleolus and cytosol / preribosome, large subunit precursor / ribonucleoprotein complex binding / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / rRNA processing / large ribosomal subunit rRNA binding / nucleolus ...PeBoW complex / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Major pathway of rRNA processing in the nucleolus and cytosol / preribosome, large subunit precursor / ribonucleoprotein complex binding / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / rRNA processing / large ribosomal subunit rRNA binding / nucleolus / DNA binding / nucleoplasm / nucleus
Similarity search - Function
BOP1, N-terminal domain / WD repeat BOP1/Erb1 / BOP1NT (NUC169) domain / BOP1NT (NUC169) domain / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat ...BOP1, N-terminal domain / WD repeat BOP1/Erb1 / BOP1NT (NUC169) domain / BOP1NT (NUC169) domain / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
ETHANOL / Ribosome biogenesis protein ERB1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsWegrecki, M. / Bravo, J.
CitationJournal: Plos One / Year: 2015
Title: The Carboxy-Terminal Domain of Erb1 Is a Seven-Bladed -Propeller that Binds RNA.
Authors: Wegrecki, M. / Neira, J.L. / Bravo, J.
History
DepositionJul 30, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 29, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribosome biogenesis protein ERB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,1635
Polymers93,9011
Non-polymers2624
Water6,431357
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area890 Å2
ΔGint9 kcal/mol
Surface area15320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.024, 62.431, 158.218
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ribosome biogenesis protein ERB1 / / Eukaryotic ribosome biogenesis protein 1


Mass: 93900.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: ERB1, YMR049C, YM9796.02C / Plasmid: pET28-NKI/LIC 6His/3C / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): CodonPlus / References: UniProt: Q04660
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-EOH / ETHANOL / Ethanol


Mass: 46.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 357 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10% PEG 8000, 8% ethylene glycol, 0.1M Hepes pH 7.5, 3% ethanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.6→58.07 Å / Num. obs: 67582 / % possible obs: 98.07 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.04807 / Net I/σ(I): 19.48
Reflection shellResolution: 1.6→1.657 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 2.16 / % possible all: 96.78

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2H13

2h13


Resolution: 1.6→58.073 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.174 1363 2.02 %Random selection
Rwork0.1602 ---
obs0.1605 67575 98.06 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→58.073 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2859 0 17 357 3233
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063030
X-RAY DIFFRACTIONf_angle_d1.074122
X-RAY DIFFRACTIONf_dihedral_angle_d12.0421132
X-RAY DIFFRACTIONf_chiral_restr0.047455
X-RAY DIFFRACTIONf_plane_restr0.006521
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.65720.2931280.26976417X-RAY DIFFRACTION97
1.6572-1.72350.271390.23296468X-RAY DIFFRACTION97
1.7235-1.8020.24541190.20336519X-RAY DIFFRACTION97
1.802-1.8970.20511370.18236529X-RAY DIFFRACTION98
1.897-2.01590.17121270.16036564X-RAY DIFFRACTION98
2.0159-2.17150.18811290.15496599X-RAY DIFFRACTION98
2.1715-2.39010.18561450.1616619X-RAY DIFFRACTION99
2.3901-2.73590.1681310.16796705X-RAY DIFFRACTION99
2.7359-3.44690.17791540.16116754X-RAY DIFFRACTION99
3.4469-58.11170.14551540.13847038X-RAY DIFFRACTION99
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)
11.83730.53120.04151.04430.1192.45210.0488-0.1959-0.2014-0.0644-0.09160.0320.0837-0.13760.00050.14530.01060.0040.17090.02660.193822.217616.955971.5844
22.76730.1450.76481.4655-0.97632.530.0407-0.1290.22590.0429-0.1376-0.048-0.30830.1939-0.0080.1886-0.02240.00240.19190.02080.182235.240829.780270.1147
32.53920.14320.63252.1962-1.10162.12960.0185-0.02080.3121-0.009-0.1367-0.1263-0.4720.1888-00.2456-0.01870.01290.16910.03590.233535.265135.819562.9968
40.85310.38410.34120.32430.05840.81550.03110.12590.2218-0.2779-0.1524-0.0789-0.3839-0.0221-0.00020.32360.07110.01710.20610.03960.245826.519732.793449.4816
50.79460.76170.47411.2523-0.10180.9128-0.11370.22170.339-0.3157-0.01340.0462-0.3256-0.2636-0.00030.35060.1002-0.02040.25630.03010.246820.684232.212346.7185
61.25610.51060.03671.8112-0.25381.7772-0.00040.1725-0.0243-0.1488-0.08070.2553-0.0862-0.3802-00.21220.0595-0.03250.2779-0.04430.199613.407921.140852.9407
70.99790.16750.19370.71240.02452.52270.04840.0595-0.156-0.1013-0.0550.04310.1236-0.229800.17390.00560.00010.1932-0.00770.210715.41615.120561.15
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 416 through 476 )
2X-RAY DIFFRACTION2chain 'A' and (resid 477 through 572 )
3X-RAY DIFFRACTION3chain 'A' and (resid 573 through 632 )
4X-RAY DIFFRACTION4chain 'A' and (resid 633 through 658 )
5X-RAY DIFFRACTION5chain 'A' and (resid 659 through 688 )
6X-RAY DIFFRACTION6chain 'A' and (resid 689 through 746 )
7X-RAY DIFFRACTION7chain 'A' and (resid 747 through 807 )

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