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- PDB-6o16: Crystal structure of murine DHX37 in complex with RNA -

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Basic information

Entry
Database: PDB / ID: 6o16
TitleCrystal structure of murine DHX37 in complex with RNA
Components
  • DEAH (Asp-Glu-Ala-His) box polypeptide 37
  • RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
KeywordsHYDROLASE/RNA / RNA helicase / ribosome biogenesis / RNA-dependent ATPase / HYDROLASE-RNA complex
Function / homology
Function and homology information


Major pathway of rRNA processing in the nucleolus and cytosol / positive regulation of male gonad development / U3 snoRNA binding / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosome assembly / helicase activity / brain development / ribosome biogenesis / nuclear membrane / nucleolus ...Major pathway of rRNA processing in the nucleolus and cytosol / positive regulation of male gonad development / U3 snoRNA binding / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosome assembly / helicase activity / brain development / ribosome biogenesis / nuclear membrane / nucleolus / RNA binding / ATP binding / cytoplasm
Similarity search - Function
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 / 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. ...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 / 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
RNA / DEAH (Asp-Glu-Ala-His) box polypeptide 37
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.875 Å
AuthorsBoneberg, F. / Brandmann, T. / Kobel, L. / van den Heuvel, J. / Bargsten, K. / Bammert, L. / Kutay, U. / Jinek, M.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science FoundationNCCR RNA & Disease Switzerland
CitationJournal: Rna / Year: 2019
Title: Molecular mechanism of the RNA helicase DHX37 and its activation by UTP14A in ribosome biogenesis.
Authors: Boneberg, F.M. / Brandmann, T. / Kobel, L. / van den Heuvel, J. / Bargsten, K. / Bammert, L. / Kutay, U. / Jinek, M.
History
DepositionFeb 18, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1May 29, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DEAH (Asp-Glu-Ala-His) box polypeptide 37
B: DEAH (Asp-Glu-Ala-His) box polypeptide 37
C: RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
D: RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')


Theoretical massNumber of molelcules
Total (without water)223,4644
Polymers223,4644
Non-polymers00
Water0
1
A: DEAH (Asp-Glu-Ala-His) box polypeptide 37
C: RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')


Theoretical massNumber of molelcules
Total (without water)111,7322
Polymers111,7322
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-34 kcal/mol
Surface area38440 Å2
MethodPISA
2
B: DEAH (Asp-Glu-Ala-His) box polypeptide 37
D: RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')


Theoretical massNumber of molelcules
Total (without water)111,7322
Polymers111,7322
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-31 kcal/mol
Surface area38470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.829, 137.593, 94.225
Angle α, β, γ (deg.)90.00, 93.34, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DEAH (Asp-Glu-Ala-His) box polypeptide 37


Mass: 108715.477 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Dhx37
Production host: Spodoptera aff. frugiperda 2 RZ-2014 (butterflies/moths)
References: UniProt: Q6NZL1
#2: RNA chain RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')


Mass: 3016.700 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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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: 2.65 Å3/Da / Density % sol: 53.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M Bis-Tris propane pH 7.0, 0.2 M NaNO3, 15% (w/v) polyethylene glycol (PEG)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.0077 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Aug 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0077 Å / Relative weight: 1
ReflectionResolution: 2.875→47.032 Å / Num. obs: 93431 / % possible obs: 97.88 % / Redundancy: 3.4 % / Biso Wilson estimate: 64.06 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.1026 / Rpim(I) all: 0.06542 / Rrim(I) all: 0.122 / Net I/σ(I): 9.76
Reflection shellResolution: 2.8875→2.98 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.625 / Mean I/σ(I) obs: 1.57 / Num. unique obs: 4209 / CC1/2: 0.872 / Rpim(I) all: 0.4113 / Rrim(I) all: 0.7505 / % possible all: 86.19

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.875→47.032 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 33.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2948 4684 5.02 %
Rwork0.2703 --
obs0.2715 93377 97.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.875→47.032 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12605 394 0 0 12999
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00513321
X-RAY DIFFRACTIONf_angle_d0.79218142
X-RAY DIFFRACTIONf_dihedral_angle_d16.7378147
X-RAY DIFFRACTIONf_chiral_restr0.1222089
X-RAY DIFFRACTIONf_plane_restr0.0062242
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.875-2.90760.5226840.4611545X-RAY DIFFRACTION52
2.9076-2.94180.38221570.36573074X-RAY DIFFRACTION100
2.9418-2.97770.37351650.36053000X-RAY DIFFRACTION100
2.9777-3.01540.36961600.34933004X-RAY DIFFRACTION100
3.0154-3.05510.36421560.34643071X-RAY DIFFRACTION100
3.0551-3.09690.35331590.35063021X-RAY DIFFRACTION100
3.0969-3.14120.36631540.32213018X-RAY DIFFRACTION100
3.1412-3.1880.38761730.33012994X-RAY DIFFRACTION100
3.188-3.23780.38651450.33453076X-RAY DIFFRACTION100
3.2378-3.29090.37041700.31143014X-RAY DIFFRACTION100
3.2909-3.34760.35471650.3083031X-RAY DIFFRACTION100
3.3476-3.40850.36221430.30422967X-RAY DIFFRACTION99
3.4085-3.4740.39361670.30733001X-RAY DIFFRACTION99
3.474-3.54490.37031490.30273028X-RAY DIFFRACTION100
3.5449-3.6220.31751710.29633034X-RAY DIFFRACTION99
3.622-3.70620.31731470.28493006X-RAY DIFFRACTION99
3.7062-3.79880.31951590.27553007X-RAY DIFFRACTION99
3.7988-3.90150.30171590.26472945X-RAY DIFFRACTION99
3.9015-4.01620.3011590.27063035X-RAY DIFFRACTION98
4.0162-4.14580.26141540.25892953X-RAY DIFFRACTION98
4.1458-4.29390.2931650.25152969X-RAY DIFFRACTION98
4.2939-4.46570.23141530.25152963X-RAY DIFFRACTION98
4.4657-4.66870.31371600.24142957X-RAY DIFFRACTION98
4.6687-4.91460.23581590.23943020X-RAY DIFFRACTION99
4.9146-5.22220.27171580.24233002X-RAY DIFFRACTION99
5.2222-5.62480.26041570.26372981X-RAY DIFFRACTION99
5.6248-6.18970.25451580.24893013X-RAY DIFFRACTION99
6.1897-7.08280.28441630.26052974X-RAY DIFFRACTION99
7.0828-8.91360.20731590.21682971X-RAY DIFFRACTION98
8.9136-47.03870.21431560.21823019X-RAY DIFFRACTION99
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)
10.727-0.10220.16491.8159-0.34370.85510.0084-0.1285-0.0680.2960.03760.4740.317-0.0764-0.00340.5616-0.03210.10140.3985-0.0040.4037-29.142911.905-48.1323
20.44170.6680.42171.55040.09180.8712-0.0983-0.19040.08980.47530.0351-0.0101-0.07850.0163-00.47830.0822-0.0310.4480.0220.3969-18.890336.8493-47.6694
30.7070.6283-1.5510.1024-0.4827-0.04110.40.22840.02850.4391-0.1363-0.06681.34350.70690-3.2743-1.4481-0.1452-0.4745-0.07710.30482.307647.7904-62.3466
40.6736-0.10920.00210.7384-0.32470.38860.02090.17190.1203-0.3464-0.04310.16960.1406-0.079600.9858-0.0536-0.00560.5520.03140.4891-21.180236.9506-4.423
50.6594-0.1097-0.55941.273-0.02470.45260.09320.18560.0345-0.2714-0.12280.5441-0.1698-0.303200.53240.0969-0.0850.6364-0.00460.6262-41.760120.15522.04
61.29040.3088-0.04661.69130.02120.86930.10040.1038-0.1227-0.1014-0.0509-0.0087-0.0277-0.01610.01460.2801-0.01910.05290.2499-0.02940.1951-18.92371.3484-4.7257
70.1941-0.50260.74460.3397-0.59461.08940.0792-0.1013-0.03240.0336-0.1145-0.17120.0320.103900.4948-0.01480.01990.49940.0360.58982.0333-6.121217.7228
80.02450.10920.01710.05050.04930.0314-0.09-0.16790.12770.05990.0872-0.11710.3843-0.10300.64910.0886-0.02290.626-0.00930.6197-31.409834.3702-52.4956
90.0394-0.1266-0.03720.06270.064-0.0607-0.1793-0.4815-0.1706-0.28330.2371-0.0358-0.9147-0.325700.5122-0.0433-0.05340.7670.1010.7186-33.65986.26491.6582
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 231 through 707 )
2X-RAY DIFFRACTION2chain 'A' and (resid 708 through 895 )
3X-RAY DIFFRACTION3chain 'A' and (resid 896 through 1149 )
4X-RAY DIFFRACTION4chain 'B' and (resid 231 through 423 )
5X-RAY DIFFRACTION5chain 'B' and (resid 424 through 736 )
6X-RAY DIFFRACTION6chain 'B' and (resid 737 through 925 )
7X-RAY DIFFRACTION7chain 'B' and (resid 926 through 1148 )
8X-RAY DIFFRACTION8chain 'C' and (resid 1 through 10 )
9X-RAY DIFFRACTION9chain 'D' and (resid 1 through 10 )

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