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- PDB-7w1r: Crystal structure of human Suv3 monomer -

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Basic information

Entry
Database: PDB / ID: 7w1r
TitleCrystal structure of human Suv3 monomer
ComponentsATP-dependent RNA helicase SUPV3L1, mitochondrial
KeywordsHYDROLASE / Mitochondrial Helicase
Function / homology
Function and homology information


mitochondrial ncRNA surveillance / mitochondrial mRNA surveillance / mitochondrial RNA surveillance / mitochondrial degradosome / mitochondrial mRNA catabolic process / positive regulation of mitochondrial RNA catabolic process / mitochondrial RNA 3'-end processing / mitochondrial RNA catabolic process / Mitochondrial RNA degradation / 3'-5' RNA helicase activity ...mitochondrial ncRNA surveillance / mitochondrial mRNA surveillance / mitochondrial RNA surveillance / mitochondrial degradosome / mitochondrial mRNA catabolic process / positive regulation of mitochondrial RNA catabolic process / mitochondrial RNA 3'-end processing / mitochondrial RNA catabolic process / Mitochondrial RNA degradation / 3'-5' RNA helicase activity / RNA catabolic process / DNA duplex unwinding / mitochondrial nucleoid / DNA helicase activity / mitochondrion organization / helicase activity / double-stranded RNA binding / positive regulation of cell growth / DNA recombination / RNA helicase activity / RNA helicase / mitochondrial matrix / negative regulation of apoptotic process / protein homodimerization activity / ATP hydrolysis activity / mitochondrion / DNA binding / RNA binding / ATP binding / identical protein binding / nucleus
Similarity search - Function
Suv3, C-terminal domain 1 / Suv3, N-terminal / Suv3, DEXQ-box helicase domain / Suv3 helical N-terminal domain / Suv3 C-terminal domain 1 / Mitochondrial degradasome RNA helicase subunit, C-terminal domain / Mitochondrial degradasome RNA helicase subunit C terminal / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. ...Suv3, C-terminal domain 1 / Suv3, N-terminal / Suv3, DEXQ-box helicase domain / Suv3 helical N-terminal domain / Suv3 C-terminal domain 1 / Mitochondrial degradasome RNA helicase subunit, C-terminal domain / Mitochondrial degradasome RNA helicase subunit C terminal / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Helicase, C-terminal / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ATP-dependent RNA helicase SUPV3L1, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsJain, M. / Yuan, H.S.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Academia Sinica (Taiwan)AS-IA-110-L02 Taiwan
CitationJournal: Protein Sci. / Year: 2022
Title: Dimeric assembly of human Suv3 helicase promotes its RNA unwinding function in mitochondrial RNA degradosome for RNA decay.
Authors: Jain, M. / Golzarroshan, B. / Lin, C.L. / Agrawal, S. / Tang, W.H. / Wu, C.J. / Yuan, H.S.
History
DepositionNov 20, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 11, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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

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Assembly

Deposited unit
A: ATP-dependent RNA helicase SUPV3L1, mitochondrial


Theoretical massNumber of molelcules
Total (without water)75,8421
Polymers75,8421
Non-polymers00
Water00
1
A: ATP-dependent RNA helicase SUPV3L1, mitochondrial

A: ATP-dependent RNA helicase SUPV3L1, mitochondrial


Theoretical massNumber of molelcules
Total (without water)151,6842
Polymers151,6842
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_565-x+y,-x+1,z+1/31
Unit cell
Length a, b, c (Å)92.409, 92.409, 88.057
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Space group name HallP32
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3

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Components

#1: Protein ATP-dependent RNA helicase SUPV3L1, mitochondrial / Suppressor of var1 3-like protein 1 / SUV3-like protein 1


Mass: 75842.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SUPV3L1, SUV3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8IYB8, RNA helicase

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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: 2.86 Å3/Da / Density % sol: 57.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.005 M Magnesium sulfate heptahydrate, 0.05 M MES monohydrate pH 6.0, 5% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: May 16, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.2→40 Å / Num. obs: 13937 / % possible obs: 95.76 % / Redundancy: 3.7 % / Biso Wilson estimate: 113.08 Å2 / Rsym value: 0.052 / Net I/σ(I): 33.1
Reflection shellResolution: 3.2→3.31 Å / Num. unique obs: 1079 / Rsym value: 0.488

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RC3

3rc3


Resolution: 3.2→36.43 Å / SU ML: 0.4701 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 40.4933
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2864 1345 10.1 %
Rwork0.2396 11973 -
obs0.2445 13318 95.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 124.1 Å2
Refinement stepCycle: LAST / Resolution: 3.2→36.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4168 0 0 0 4168
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00894251
X-RAY DIFFRACTIONf_angle_d1.76455738
X-RAY DIFFRACTIONf_chiral_restr0.1104654
X-RAY DIFFRACTIONf_plane_restr0.0051720
X-RAY DIFFRACTIONf_dihedral_angle_d5.9264543
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.310.38311100.3216972X-RAY DIFFRACTION78.35
3.31-3.440.34671350.27151111X-RAY DIFFRACTION89.45
3.44-3.60.31221320.24181218X-RAY DIFFRACTION97.83
3.6-3.790.30871360.27471265X-RAY DIFFRACTION99.86
3.79-4.030.32261360.26871259X-RAY DIFFRACTION100
4.03-4.340.2961380.26961253X-RAY DIFFRACTION100
4.34-4.770.29271420.22371241X-RAY DIFFRACTION100
4.77-5.460.28291380.24711259X-RAY DIFFRACTION99.93
5.46-6.860.32271450.26561244X-RAY DIFFRACTION99.93
6.89-36.430.23481330.19771151X-RAY DIFFRACTION92.11
Refinement TLS params.Method: refined / Origin x: -2.58084573106 Å / Origin y: 38.2445226981 Å / Origin z: -0.0434505076228 Å
111213212223313233
T0.237062815223 Å2-0.168051001975 Å2-0.115733361658 Å2-0.0675119493824 Å20.0057349411565 Å2--0.630158244015 Å2
L1.15859141644 °2-0.464327095322 °2-0.249355463537 °2-2.01227854619 °20.294828795078 °2--4.94247118303 °2
S0.113012971656 Å °-0.0334547969885 Å °-0.258236578636 Å °0.199957126319 Å °0.372301047882 Å °0.273868860529 Å °0.46409449249 Å °-0.188215926389 Å °1.07657547733 Å °
Refinement TLS groupSelection details: all

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