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- PDB-5em2: Crystal structure of the Erb1-Ytm1 complex -

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Basic information

Entry
Database: PDB / ID: 5em2
TitleCrystal structure of the Erb1-Ytm1 complex
Components
  • Ribosome biogenesis protein ERB1
  • Ribosome biogenesis protein YTM1
KeywordsRIBOSOME / ribosome biogenesis / complex / WD40 / transcription
Function / homology
Function and homology information


maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / preribosome, large subunit precursor / ribonucleoprotein complex binding / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nucleolus / nucleoplasm
Similarity search - Function
WD repeat WDR12/Ytm1 / BOP1, N-terminal domain / WD repeat BOP1/Erb1 / BOP1NT (NUC169) domain / BOP1NT (NUC169) domain / NLE / NLE (NUC135) domain / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H ...WD repeat WDR12/Ytm1 / BOP1, N-terminal domain / WD repeat BOP1/Erb1 / BOP1NT (NUC169) domain / BOP1NT (NUC169) domain / NLE / NLE (NUC135) domain / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Ribosome biogenesis protein ERB1 / Ribosome biogenesis protein YTM1
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.67 Å
AuthorsAhmed, Y.L. / Sinning, I.
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: Concerted removal of the Erb1-Ytm1 complex in ribosome biogenesis relies on an elaborate interface.
Authors: Thoms, M. / Ahmed, Y.L. / Maddi, K. / Hurt, E. / Sinning, I.
History
DepositionNov 5, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2016Group: Database references
Revision 1.2May 8, 2024Group: 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 / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribosome biogenesis protein ERB1
B: Ribosome biogenesis protein YTM1
C: Ribosome biogenesis protein ERB1
D: Ribosome biogenesis protein YTM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,70916
Polymers193,0024
Non-polymers70712
Water3,297183
1
A: Ribosome biogenesis protein ERB1
B: Ribosome biogenesis protein YTM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,8989
Polymers96,5012
Non-polymers3977
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3440 Å2
ΔGint6 kcal/mol
Surface area32930 Å2
MethodPISA
2
C: Ribosome biogenesis protein ERB1
D: Ribosome biogenesis protein YTM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,8117
Polymers96,5012
Non-polymers3105
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint2 kcal/mol
Surface area33440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.662, 81.353, 141.695
Angle α, β, γ (deg.)90.000, 100.230, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain C
12chain B
22chain D

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUMETMETchain AAA432 - 80119 - 388
21LEULEUMETMETchain CCC432 - 80119 - 388
12ALAALAGLYGLYchain BBB10 - 48714 - 491
22ALAALAGLYGLYchain DDD10 - 48714 - 491

NCS ensembles :
ID
1
2

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Components

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


Mass: 43174.348 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Gene: ERB1, CTHT_0057570 / Plasmid: pET24d / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2 / References: UniProt: G0SCK6
#2: Protein Ribosome biogenesis protein YTM1


Mass: 53326.594 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Gene: YTM1, CTHT_0061460 / Plasmid: YEplac112 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): W303 / References: UniProt: G0SFB5
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.69 Å3/Da / Density % sol: 54.34 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 20-28% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionRedundancy: 5.2 % / Number: 306061 / Rmerge(I) obs: 0.163 / D res high: 2.67 Å / D res low: 48.61 Å / Num. obs: 58449 / % possible obs: 99.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsRedundancy
2.672.7411.1765.2
11.6448.6110.0375.1
ReflectionResolution: 2.67→48.61 Å / Num. obs: 58449 / % possible obs: 99.8 % / Redundancy: 5.2 % / Biso Wilson estimate: 44.75 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.163 / Rpim(I) all: 0.077 / Net I/σ(I): 10.6 / Num. measured all: 306061
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.67-2.745.21.1761.52326645040.5290.567100
11.64-48.615.10.03736.537887450.9990.01898.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.605
Highest resolutionLowest resolution
Rotation48.61 Å2.95 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.3.11data scaling
MOLREPphasing
REFMACrefinement
PHENIXrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.67→48.609 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 27.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2509 5574 4.92 %
Rwork0.221 107833 -
obs0.2225 58449 99.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 126.91 Å2 / Biso mean: 50.8885 Å2 / Biso min: 23.9 Å2
Refinement stepCycle: final / Resolution: 2.67→48.609 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12526 0 45 183 12754
Biso mean--47.83 39.92 -
Num. residues----1631
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00312861
X-RAY DIFFRACTIONf_angle_d0.91717481
X-RAY DIFFRACTIONf_chiral_restr0.0351985
X-RAY DIFFRACTIONf_plane_restr0.0052238
X-RAY DIFFRACTIONf_dihedral_angle_d13.9274635
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3382X-RAY DIFFRACTION6.925TORSIONAL
12C3382X-RAY DIFFRACTION6.925TORSIONAL
21B3982X-RAY DIFFRACTION6.925TORSIONAL
22D3982X-RAY DIFFRACTION6.925TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.67-2.70040.37272080.33083544375299
2.7004-2.73210.36931700.3353627379799
2.7321-2.76540.36092030.331435763779100
2.7654-2.80040.3661490.33013667381699
2.8004-2.83730.35072010.32493568376999
2.8373-2.87620.3412130.32063585379899
2.8762-2.91720.33061770.32153608378599
2.9172-2.96080.3281880.29913564375299
2.9608-3.0070.31731630.2943578374199
3.007-3.05630.30072100.29063550376099
3.0563-3.1090.30732090.28623481369098
3.109-3.16550.31541880.27663640382899
3.1655-3.22640.35411640.27713621378599
3.2264-3.29230.24922130.25223531374499
3.2923-3.36380.25291750.25053573374899
3.3638-3.44210.21741690.2373561373099
3.4421-3.52810.2961590.22993675383499
3.5281-3.62350.29452010.21393501370298
3.6235-3.73010.20772120.21733577378999
3.7301-3.85040.24031940.206736103804100
3.8504-3.9880.24161800.194936413821100
3.988-4.14760.21861810.187936153796100
4.1476-4.33620.23051550.170736553810100
4.3362-4.56470.18042000.15936043804100
4.5647-4.85040.1541700.151536143784100
4.8504-5.22450.21921850.159836033788100
5.2245-5.74950.21281710.189236373808100
5.7495-6.57980.19231780.19936123790100
6.5798-8.28310.24692060.201136173823100
8.2831-48.61680.22911820.19053598378099
Refinement TLS params.Method: refined / Origin x: 9.4289 Å / Origin y: 15.6363 Å / Origin z: 38.4202 Å
111213212223313233
T0.3383 Å2-0.0325 Å20.0134 Å2-0.2579 Å2-0.0655 Å2--0.304 Å2
L0.2602 °2-0.0975 °20.0233 °2-0.2496 °2-0.1845 °2--0.2896 °2
S0.0173 Å °-0.0593 Å °0.0392 Å °0.0163 Å °-0.0512 Å °0.0502 Å °0.0598 Å °-0.0817 Å °0.0312 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA432 - 801
2X-RAY DIFFRACTION1allB10 - 487
3X-RAY DIFFRACTION1allC432 - 801
4X-RAY DIFFRACTION1allD10 - 487
5X-RAY DIFFRACTION1allE1 - 11
6X-RAY DIFFRACTION1allF1
7X-RAY DIFFRACTION1allG1 - 183

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