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- PDB-7mqj: Dhr1 Helicase Core -

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Basic information

Entry
Database: PDB / ID: 7mqj
TitleDhr1 Helicase Core
ComponentsProbable ATP-dependent RNA helicase DHR1
KeywordsHYDROLASE / Helicase / Ribosome Assembly
Function / homology
Function and homology information


Major pathway of rRNA processing in the nucleolus and cytosol / 90S preribosome / maturation of SSU-rRNA / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / small-subunit processome / helicase activity / ribosome biogenesis / RNA helicase activity / RNA helicase / nucleolus ...Major pathway of rRNA processing in the nucleolus and cytosol / 90S preribosome / maturation of SSU-rRNA / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / small-subunit processome / helicase activity / ribosome biogenesis / RNA helicase activity / RNA helicase / nucleolus / ATP hydrolysis activity / mitochondrion / RNA binding / nucleoplasm / ATP binding
Similarity search - Function
: / Helicase associated domain (HA2), ratchet-like / DEAD-box helicase, OB fold / Oligonucleotide/oligosaccharide-binding (OB)-fold / Helicase-associated domain / Helicase associated domain (HA2), winged-helix / Helicase associated domain (HA2) Add an annotation / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / DEAD/DEAH box helicase ...: / Helicase associated domain (HA2), ratchet-like / DEAD-box helicase, OB fold / Oligonucleotide/oligosaccharide-binding (OB)-fold / Helicase-associated domain / Helicase associated domain (HA2), winged-helix / Helicase associated domain (HA2) Add an annotation / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / 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
ADENOSINE-5'-DIPHOSPHATE / Probable ATP-dependent RNA helicase DHR1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å
AuthorsMiller, L. / Chaker-Margot, M. / Klinge, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1DP2GM123459 United States
CitationJournal: Science / Year: 2021
Title: Nucleolar maturation of the human small subunit processome.
Authors: Sameer Singh / Arnaud Vanden Broeck / Linamarie Miller / Malik Chaker-Margot / Sebastian Klinge /
Abstract: The human small subunit processome mediates early maturation of the small ribosomal subunit by coupling RNA folding to subsequent RNA cleavage and processing steps. We report the high-resolution ...The human small subunit processome mediates early maturation of the small ribosomal subunit by coupling RNA folding to subsequent RNA cleavage and processing steps. We report the high-resolution cryo–electron microscopy structures of maturing human small subunit (SSU) processomes at resolutions of 2.7 to 3.9 angstroms. These structures reveal the molecular mechanisms that enable crucial progressions during SSU processome maturation. RNA folding states within these particles are communicated to and coordinated with key enzymes that drive irreversible steps such as targeted exosome-mediated RNA degradation, protein-guided site-specific endonucleolytic RNA cleavage, and tightly controlled RNA unwinding. These conserved mechanisms highlight the SSU processome’s impressive structural plasticity, which endows this 4.5-megadalton nucleolar assembly with the distinctive ability to mature the small ribosomal subunit from within.
History
DepositionMay 5, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 29, 2021Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable ATP-dependent RNA helicase DHR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,2453
Polymers90,7931
Non-polymers4522
Water5,116284
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area940 Å2
ΔGint-20 kcal/mol
Surface area35460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.770, 130.940, 86.080
Angle α, β, γ (deg.)90.000, 106.480, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Probable ATP-dependent RNA helicase DHR1 / DEAH box RNA helicase DHR1 / Extracellular mutant protein 16


Mass: 90793.164 Da / Num. of mol.: 1 / Fragment: UNP residues 379-1174
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: ECM16, DHR1, YMR128W, YM9553.04 / Production host: Escherichia coli (E. coli) / References: UniProt: Q04217, RNA helicase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 284 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.5 Å3/Da / Density % sol: 50.84 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: PEG6000, HEPES, pH 7.0, magnesium chloride, ADP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.97919 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 2.23→39.37 Å / Num. obs: 42918 / % possible obs: 99.34 % / Redundancy: 3.4 % / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.08197 / Rpim(I) all: 0.05173 / Rrim(I) all: 0.0972 / Net I/σ(I): 11.89
Reflection shellResolution: 2.23→2.31 Å / Num. unique obs: 4275 / CC1/2: 0.784 / CC star: 0.938 / % possible all: 98.68

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Processing

Software
NameVersionClassification
PHENIX1.14_3211refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2XAU

2xau


Resolution: 2.23→39.362 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 24.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2274 2007 4.68 %
Rwork0.1794 40904 -
obs0.1817 42911 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 159.25 Å2 / Biso mean: 50.9221 Å2 / Biso min: 15.36 Å2
Refinement stepCycle: final / Resolution: 2.23→39.362 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6179 0 28 284 6491
Biso mean--50.12 43.46 -
Num. residues----773
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.23-2.28580.29431410.2559289699
2.29-2.34760.27061450.2309289699
2.3476-2.41670.27571380.2182291899
2.4167-2.49470.25841420.2085289099
2.4947-2.58380.25471430.2025291399
2.5838-2.68720.27471390.2098289499
2.6872-2.80950.26131500.2068295099
2.8095-2.95760.25451400.2004290599
2.9576-3.14280.23861380.1972910100
3.1428-3.38530.28591510.20072934100
3.3853-3.72580.20251400.17292955100
3.7258-4.26440.20231410.15072927100
4.2644-5.37050.18491460.13732949100
5.3705-39.360.19081530.1587296799
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)
12.0972-0.4335-0.43152.7309-0.17013.1704-0.0003-0.3970.26940.55980.1439-0.0974-0.2833-0.0185-0.13610.36380.0368-0.02260.2363-0.04990.254412.546444.520320.8962
21.77250.0231-0.42193.09340.59862.53040.07850.0844-0.2650.123-0.09730.1830.4521-0.2599-0.0340.2664-0.0199-0.06190.18030.00930.23575.79318.37543.6544
31.1284-0.5702-0.08882.91910.23932.08770.14240.09560.2128-0.25850.004-0.1627-0.3999-0.0963-0.13070.26230.04510.0640.18590.0280.270413.027842.621-4.2266
41.56280.08910.11331.66210.24172.85580.23840.5673-0.1142-0.6288-0.12690.0454-0.0894-0.3373-0.08150.71850.1804-0.11540.60440.03240.3144.559435.168-32.5411
51.6589-0.88290.91112.39551.39582.52360.49070.71340.3978-0.9487-0.241-0.1021-1.1966-0.3554-0.20111.04010.33450.13330.4560.23290.29467.833851.959-30.1635
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 377:587)A377 - 587
2X-RAY DIFFRACTION2(chain A and resid 588:777)A588 - 777
3X-RAY DIFFRACTION3(chain A and resid 778:920)A778 - 920
4X-RAY DIFFRACTION4(chain A and resid 921:1049)A921 - 1049
5X-RAY DIFFRACTION5(chain A and resid 1050:1174)A1050 - 1174

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