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- PDB-6qtb: Crystal structure of Rea1-MIDAS/Ytm1-UBL complex from Chaetomium ... -

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Basic information

Entry
Database: PDB / ID: 6qtb
TitleCrystal structure of Rea1-MIDAS/Ytm1-UBL complex from Chaetomium thermophilum
Components
  • Midasin,Midasin
  • Ribosome biogenesis protein YTM1
KeywordsRIBOSOME / ribosome biogenesis / integrin / midas
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 / 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 / WD repeat WDR12/Ytm1 / ATPase, dynein-related, AAA domain / AAA domain (dynein-related subfamily) ...Midasin / Midasin, AAA lid domain 7 / Midasin AAA lid domain 5 / : / Midasin AAA lid domain / Midasin AAA lid domain / Midasin AAA+ ATPase lid domain / WD repeat WDR12/Ytm1 / ATPase, dynein-related, AAA domain / AAA domain (dynein-related subfamily) / NLE / NLE (NUC135) domain / 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 biogenesis protein YTM1 / Midasin
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 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 / struct_ncs_dom_lim
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 / _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: Midasin,Midasin
B: Ribosome biogenesis protein YTM1
D: Midasin,Midasin
E: Ribosome biogenesis protein YTM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,1439
Polymers85,8184
Non-polymers3255
Water7,314406
1
A: Midasin,Midasin
B: Ribosome biogenesis protein YTM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0254
Polymers42,9092
Non-polymers1162
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-19 kcal/mol
Surface area15770 Å2
MethodPISA
2
D: Midasin,Midasin
E: Ribosome biogenesis protein YTM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1175
Polymers42,9092
Non-polymers2083
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint-17 kcal/mol
Surface area15300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.553, 83.176, 77.686
Angle α, β, γ (deg.)90.000, 117.720, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain B
21chain E
12(chain A and (resid 4699 through 4734 or resid 4777 through 4886 or resid 4891 through 4994))
22(chain D and resid 4699 through 4994)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111VALVALSERSERchain BBB12 - 9815 - 101
211VALVALSERSERchain EED12 - 9815 - 101
112PROPROGLYGLY(chain A and (resid 4699 through 4734 or resid 4777 through 4886 or resid 4891 through 4994))AA4699 - 473411 - 46
122LYSLYSSERSER(chain A and (resid 4699 through 4734 or resid 4777 through 4886 or resid 4891 through 4994))AA4777 - 488652 - 161
132GLUGLUGLUGLU(chain A and (resid 4699 through 4734 or resid 4777 through 4886 or resid 4891 through 4994))AA4891 - 4994166 - 269
212PROPROGLUGLU(chain D and resid 4699 through 4994)DC4699 - 499411 - 269

NCS ensembles :
ID
1
2

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Components

#1: Protein Midasin,Midasin


Mass: 31464.826 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)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0069750 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: G0SHE6
#2: Protein Ribosome biogenesis protein YTM1 /


Mass: 11444.034 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 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G0SFB5
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 406 / 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: 2.52 Å3/Da / Density % sol: 51.15 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 3 M NaCl and 0.1 M Tris (pH 8.5)

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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: Mar 31, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8729 Å / Relative weight: 1
ReflectionResolution: 1.84→39.62 Å / Num. obs: 73123 / % possible obs: 99.97 % / Redundancy: 13.3 % / CC1/2: 0.999 / Net I/σ(I): 13.33
Reflection shellResolution: 1.84→1.9 Å / CC1/2: 0.664

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
PHENIX1.12_2829refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6QT8 and 5EM2

6qt8

5em2


Resolution: 1.89→36.58 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 0.02 / Phase error: 23.43
RfactorNum. reflection% reflection
Rfree0.2127 7365 5.17 %
Rwork0.19 --
obs0.1912 73123 98.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 100.68 Å2 / Biso mean: 39.6132 Å2 / Biso min: 12.97 Å2
Refinement stepCycle: final / Resolution: 1.89→36.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5368 0 20 406 5794
Biso mean--61.33 45.1 -
Num. residues----679
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0185475
X-RAY DIFFRACTIONf_angle_d1.4947409
X-RAY DIFFRACTIONf_chiral_restr0.092865
X-RAY DIFFRACTIONf_plane_restr0.01949
X-RAY DIFFRACTIONf_dihedral_angle_d10.4473319
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11B846X-RAY DIFFRACTION11.156TORSIONAL
12E846X-RAY DIFFRACTION11.156TORSIONAL
21A2348X-RAY DIFFRACTION11.156TORSIONAL
22D2348X-RAY DIFFRACTION11.156TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.84-1.86090.36922330.33884472470599
1.8609-1.88280.35352690.31784566483599
1.8828-1.90580.34042650.29574448471398
1.9058-1.92990.2812360.28714546478298
1.9299-1.95530.31862790.26324444472399
1.9553-1.98210.292470.25064651489899
1.9821-2.01040.2522280.23514481470999
2.0104-2.04040.24652560.22134600485699
2.0404-2.07230.24152190.21354489470898
2.0723-2.10620.24262210.20714582480399
2.1062-2.14260.23962440.20944587483199
2.1426-2.18150.22862310.20934574480599
2.1815-2.22350.23312260.21484584481099
2.2235-2.26890.22942080.19914562477099
2.2689-2.31820.22842400.19594613485399
2.3182-2.37210.21982560.19564505476199
2.3721-2.43140.24122440.1964586483099
2.4314-2.49710.24352910.19264476476799
2.4971-2.57060.2422580.19634489474798
2.5706-2.65360.20892340.19664463469797
2.6536-2.74840.23712120.19624445465796
2.7484-2.85840.2172580.20314438469697
2.8584-2.98840.21362390.19754525476497
2.9884-3.14590.21692410.18774443468497
3.1459-3.3430.20192750.17974450472598
3.343-3.60090.19842850.17084496478198
3.6009-3.9630.17062620.15564434469697
3.963-4.53570.17062330.14324419465297
4.5357-5.71180.18632240.16954417464195
5.7118-39.62470.18662510.18914374462595
Refinement TLS params.Method: refined / Origin x: 10.7712 Å / Origin y: 8.8868 Å / Origin z: 18.7265 Å
111213212223313233
T0.2051 Å20.0189 Å2-0.0336 Å2-0.1906 Å20.0043 Å2--0.1662 Å2
L1.2917 °20.3783 °2-0.6042 °2-0.213 °2-0.1107 °2--0.3836 °2
S0.022 Å °-0.0367 Å °0.0364 Å °-0.006 Å °-0.0346 Å °0.0269 Å °-0.0265 Å °0.0161 Å °-0.0004 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA4698 - 4994
2X-RAY DIFFRACTION1allB12 - 98
3X-RAY DIFFRACTION1allC1
4X-RAY DIFFRACTION1allD4699 - 4995
5X-RAY DIFFRACTION1allE12 - 98
6X-RAY DIFFRACTION1allF1
7X-RAY DIFFRACTION1allG1 - 3
8X-RAY DIFFRACTION1allS1 - 406

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