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- PDB-6yfv: Crystal structure of Mtr4-Red1 minimal complex from Chaetomium th... -

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Basic information

Entry
Database: PDB / ID: 6yfv
TitleCrystal structure of Mtr4-Red1 minimal complex from Chaetomium thermophilum
Components
  • ATP dependent RNA helicase (Dob1)-like protein
  • Red1
KeywordsRNA BINDING PROTEIN / ncRNA degradation / MTREC / nuclear exosome
Function / homology
Function and homology information


exosome (RNase complex) / RNA catabolic process / maturation of 5.8S rRNA / hydrolase activity / RNA helicase activity / RNA binding / ATP binding / metal ion binding / nucleus
Similarity search - Function
NURS complex subunit red1 / rRNA-processing arch domain / Mtr4-like, beta-barrel domain / ATP-dependent RNA helicase Ski2, C-terminal / ATP-dependent RNA helicase Ski2-like / : / DSHCT (NUC185) domain / Exosome RNA helicase MTR4-like, stalk / DSHCT / : ...NURS complex subunit red1 / rRNA-processing arch domain / Mtr4-like, beta-barrel domain / ATP-dependent RNA helicase Ski2, C-terminal / ATP-dependent RNA helicase Ski2-like / : / DSHCT (NUC185) domain / Exosome RNA helicase MTR4-like, stalk / DSHCT / : / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ATP dependent RNA helicase (Dob1)-like protein / Zinc-finger domain-containing protein
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.75 Å
AuthorsDobrev, N. / Ahmed, Y.L. / Sinning, I.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation Germany
CitationJournal: Nat Commun / Year: 2021
Title: The zinc-finger protein Red1 orchestrates MTREC submodules and binds the Mtl1 helicase arch domain.
Authors: Dobrev, N. / Ahmed, Y.L. / Sivadas, A. / Soni, K. / Fischer, T. / Sinning, I.
History
DepositionMar 26, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 23, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: ATP dependent RNA helicase (Dob1)-like protein
B: Red1
C: ATP dependent RNA helicase (Dob1)-like protein
D: Red1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,6167
Polymers69,2474
Non-polymers3693
Water00
1
A: ATP dependent RNA helicase (Dob1)-like protein
B: Red1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6893
Polymers34,6232
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: ATP dependent RNA helicase (Dob1)-like protein
D: Red1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9274
Polymers34,6232
Non-polymers3042
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)172.186, 172.186, 145.078
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 654 through 664 or resid 666...
21(chain C and (resid 654 through 664 or resid 666 through 865))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPILEILE(chain A and (resid 654 through 664 or resid 666...AA654 - 6642 - 12
12GLUGLUASPASP(chain A and (resid 654 through 664 or resid 666...AA666 - 79614 - 144
13GLYGLYASNASN(chain A and (resid 654 through 664 or resid 666...AA800 - 864148 - 212
14SERSERSERSER(chain A and (resid 654 through 664 or resid 666...AA865213
15ASPASPSERSER(chain A and (resid 654 through 664 or resid 666...AA654 - 8652 - 213
16ASPASPSERSER(chain A and (resid 654 through 664 or resid 666...AA654 - 8652 - 213
17ASPASPSERSER(chain A and (resid 654 through 664 or resid 666...AA654 - 8652 - 213
18ASPASPSERSER(chain A and (resid 654 through 664 or resid 666...AA654 - 8652 - 213
19ASPASPSERSER(chain A and (resid 654 through 664 or resid 666...AA654 - 8652 - 213
21ASPASPILEILE(chain C and (resid 654 through 664 or resid 666 through 865))CC654 - 6642 - 12
22GLUGLUSERSER(chain C and (resid 654 through 664 or resid 666 through 865))CC666 - 86514 - 213

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Components

#1: Protein ATP dependent RNA helicase (Dob1)-like protein


Mass: 24388.902 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Gene: CTHT_0001850 / Plasmid: pET24d / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: G0RZ64
#2: Protein Red1


Mass: 10234.464 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Gene: CTHT_0014920 / Details (production host): pET21d / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: G0S1V1
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
Has protein modificationY

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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: 4.49 Å3/Da / Density % sol: 72.6 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M MES pH 6.5 30% PEG 300

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.2741 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2741 Å / Relative weight: 1
ReflectionResolution: 2.75→49.71 Å / Num. obs: 33467 / % possible obs: 99.95 % / Redundancy: 39.1 % / Biso Wilson estimate: 86.84 Å2 / Rmerge(I) obs: 0.129 / Net I/σ(I): 25.61
Reflection shellResolution: 2.75→2.848 Å / Rmerge(I) obs: 3.048

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
SHELXDEphasing
PHENIX1.12_2829refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.75→49.706 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.31 / Phase error: 28.58
RfactorNum. reflection% reflection
Rfree0.2573 1705 5.1 %
Rwork0.2152 --
obs0.2174 33460 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 338.21 Å2 / Biso mean: 105.8642 Å2 / Biso min: 43.66 Å2
Refinement stepCycle: final / Resolution: 2.75→49.706 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4571 0 17 0 4588
Biso mean--137.33 --
Num. residues----569
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014710
X-RAY DIFFRACTIONf_angle_d1.3416377
X-RAY DIFFRACTIONf_chiral_restr0.073677
X-RAY DIFFRACTIONf_plane_restr0.009840
X-RAY DIFFRACTIONf_dihedral_angle_d9.4593313
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1940X-RAY DIFFRACTION16.19TORSIONAL
12C1940X-RAY DIFFRACTION16.19TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.7502-2.83110.3721390.343226052744
2.8311-2.92250.34511410.291225922733
2.9225-3.02690.33161390.268425882727
3.0269-3.14810.31991280.276726072735
3.1481-3.29130.31041260.278626212747
3.2913-3.46480.28971370.240526432780
3.4648-3.68180.25471430.22426042747
3.6818-3.9660.27321570.209326162773
3.966-4.36490.23091540.184726382792
4.3649-4.9960.19971390.171826752814
4.996-6.29240.2281440.218127052849
6.2924-49.71390.27421580.210628613019

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