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- PDB-6qta: Crystal structure of Rea1-MIDAS/Rsa4-UBL complex from Chaetomium ... -

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Basic information

Entry
Database: PDB / ID: 6qta
TitleCrystal structure of Rea1-MIDAS/Rsa4-UBL complex from Chaetomium thermophilum
Components
  • Midasin,Midasin
  • Ribosome assembly protein 4
KeywordsRIBOSOME / ribosome biogenesis / integrin / midas
Function / homology
Function and homology information


ribosome biogenesis / nucleolus / ATP hydrolysis activity / nucleoplasm / ATP binding
Similarity search - Function
Midasin / Midasin, AAA lid domain 7 / Midasin AAA lid domain 5 / : / Midasin AAA lid domain / Midasin AAA lid domain / Midasin AAA+ ATPase lid domain / ATPase, dynein-related, AAA domain / AAA domain (dynein-related subfamily) / von Willebrand factor (vWF) type A domain ...Midasin / Midasin, AAA lid domain 7 / Midasin AAA lid domain 5 / : / Midasin AAA lid domain / Midasin AAA lid domain / Midasin AAA+ ATPase lid domain / ATPase, dynein-related, AAA domain / AAA domain (dynein-related subfamily) / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / G-protein beta WD-40 repeat / 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 / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Ribosome assembly protein 4 / Midasin
Similarity search - Component
Biological speciesChaetomium thermophilum var. thermophilum DSM 1495 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / SAD / molecular replacement / Resolution: 1.89 Å
AuthorsAhmed, Y.L. / Thoms, M. / Hurt, E. / Sinning, I.
Funding support Germany, 1items
OrganizationGrant numberCountry
Germany
CitationJournal: Nat Commun / Year: 2019
Title: Crystal structures of Rea1-MIDAS bound to its ribosome assembly factor ligands resembling integrin-ligand-type complexes.
Authors: Ahmed, Y.L. / Thoms, M. / Mitterer, V. / Sinning, I. / Hurt, E.
History
DepositionFeb 22, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Midasin,Midasin
B: Ribosome assembly protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,74613
Polymers43,7892
Non-polymers95711
Water3,945219
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-52 kcal/mol
Surface area17250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.675, 115.675, 74.623
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-5207-

HOH

21A-5332-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Midasin,Midasin


Mass: 31464.826 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Gene: CTHT_0069750 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G0SHE6
#2: Protein Ribosome assembly protein 4 / Notchless protein homolog 1 / Ribosome biogenesis factor RSA4


Mass: 12323.778 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Gene: CTHT_0055700 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G0SC29

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Non-polymers , 4 types, 230 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 219 / 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: 2.85 Å3/Da / Density % sol: 56.85 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 2 M (NH4)2SO4, 5% PEG 400 and 0.1 M MES at pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Feb 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8729 Å / Relative weight: 1
ReflectionResolution: 1.89→36.58 Å / Num. obs: 41048 / % possible obs: 99.97 % / Redundancy: 13.2 % / Biso Wilson estimate: 29.28 Å2 / CC1/2: 0.999 / Net I/σ(I): 12.86
Reflection shellResolution: 1.89→1.95 Å / CC1/2: 0.478

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Phasing

Phasing
Method
SAD
molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
SHELXDEphasing
PHENIX1.12_2829refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6QT8 and 4WJS (UBL domain only)

6qt8

4wjs


Resolution: 1.89→36.58 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 0.25 / Phase error: 21.76
RfactorNum. reflection% reflection
Rfree0.2114 4020 5.19 %
Rwork0.1758 --
obs0.1776 77444 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 124.53 Å2 / Biso mean: 42.7495 Å2 / Biso min: 16.94 Å2
Refinement stepCycle: final / Resolution: 1.89→36.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2837 0 58 219 3114
Biso mean--68.99 50.51 -
Num. residues----359
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0182965
X-RAY DIFFRACTIONf_angle_d1.4124011
X-RAY DIFFRACTIONf_chiral_restr0.09455
X-RAY DIFFRACTIONf_plane_restr0.008517
X-RAY DIFFRACTIONf_dihedral_angle_d12.6662259
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 29 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.89-1.91230.37491080.330125762684
1.9123-1.93560.33991380.324925132651
1.9356-1.96010.34281480.307625432691
1.9601-1.98590.28081570.283724712628
1.9859-2.01310.35121300.266525762706
2.0131-2.04190.28131570.259824932650
2.0419-2.07230.30321480.240125462694
2.0723-2.10470.2391290.222925082637
2.1047-2.13920.24641300.226825532683
2.1392-2.17610.27241560.21825202676
2.1761-2.21570.2271470.197525312678
2.2157-2.25830.20891270.190225452672
2.2583-2.30440.22351150.179625662681
2.3044-2.35450.21881490.182124972646
2.3545-2.40930.23031370.172925832720
2.4093-2.46950.21151390.172424932632
2.4695-2.53630.24811040.173125462650
2.5363-2.61090.23471280.1825482676
2.6109-2.69520.21131440.16825402684
2.6952-2.79150.23651500.168725122662
2.7915-2.90320.19741470.169125292676
2.9032-3.03530.20351360.157425412677
3.0353-3.19530.15681460.158425252671
3.1953-3.39540.19871790.153124872666
3.3954-3.65750.19151420.14825232665
3.6575-4.02540.17831180.137325592677
4.0254-4.60740.14121100.13425792689
4.6074-5.8030.22821510.16225092660
5.803-45.72760.19521500.195425122662
Refinement TLS params.Method: refined / Origin x: 11.9677 Å / Origin y: 36.4946 Å / Origin z: 5.2227 Å
111213212223313233
T0.0725 Å20.0032 Å2-0.0015 Å2-0.1235 Å20.0118 Å2--0.1309 Å2
L1.3445 °2-0.5687 °2-0.2272 °2-1.2738 °2-0.0029 °2--1.6024 °2
S-0.0522 Å °-0.1587 Å °0.0428 Å °0.0072 Å °0.0681 Å °0.1091 Å °-0.057 Å °-0.0046 Å °-0.0004 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA4696 - 4997
2X-RAY DIFFRACTION1allB28 - 128
3X-RAY DIFFRACTION1allC1
4X-RAY DIFFRACTION1allD1 - 3
5X-RAY DIFFRACTION1allG5001 - 5601
6X-RAY DIFFRACTION1allS1 - 219

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