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- PDB-3rc8: Human Mitochondrial Helicase Suv3 in Complex with Short RNA Fragment -

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Basic information

Entry
Database: PDB / ID: 3rc8
TitleHuman Mitochondrial Helicase Suv3 in Complex with Short RNA Fragment
Components
  • ATP-dependent RNA helicase SUPV3L1, mitochondrial
  • RNA fragment
KeywordsHYDROLASE/RNA / Helicaase / Suv3 / Mitochondria / RNA / Helicase / HYDROLASE-RNA complex
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 / ATP hydrolysis activity / protein homodimerization activity / mitochondrion / DNA binding / RNA binding / ATP binding / identical protein binding / nucleus
Similarity search - Function
Rna Polymerase Sigma Factor; Chain: A - #140 / Zinc Finger, Delta Prime; domain 3 - #40 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1080 / 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 ...Rna Polymerase Sigma Factor; Chain: A - #140 / Zinc Finger, Delta Prime; domain 3 - #40 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1080 / 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 / Zinc Finger, Delta Prime; domain 3 / Rna Polymerase Sigma Factor; Chain: A / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / 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 nucleotide triphosphate hydrolases / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
RNA / ATP-dependent RNA helicase SUPV3L1, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsDauter, Z. / Jedrzejczak, R. / Dauter, M. / Wang, J. / Szczesny, R. / Stepien, P.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2011
Title: Human Suv3 protein reveals unique features among SF2 helicases.
Authors: Jedrzejczak, R. / Wang, J. / Dauter, M. / Szczesny, R.J. / Stepien, P.P. / Dauter, Z.
History
DepositionMar 30, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 2, 2011Group: Database references
Revision 1.3Mar 28, 2012Group: Database references
Revision 1.4Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)77,8972
Polymers77,8972
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-14 kcal/mol
Surface area29140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.430, 94.430, 88.030
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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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: 76071.328 Da / Num. of mol.: 1 / Fragment: Residues 47-722
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SUPV3L1, SUV3 / Plasmid: pDEST-HISMBP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: Q8IYB8, RNA helicase
#2: RNA chain RNA fragment


Mass: 1826.157 Da / Num. of mol.: 1 / Source method: obtained synthetically

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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: 2.92 Å3/Da / Density % sol: 57.84 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 6% PEG 3350, 0.1 M Na citrate, 10 % glycerol, pH 6.5, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR300 / Detector: CCD / Date: Sep 18, 2006 / Details: Focusing mirrors
RadiationMonochromator: SI111 DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. all: 19411 / Num. obs: 19411 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 75.2 Å2 / Rmerge(I) obs: 0.075 / Χ2: 1.065 / Net I/σ(I): 11.6
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2
2.9-35.50.4074.4619570.925
3-3.125.50.276.9319160.998
3.12-3.275.60.1989.7619721.051
3.27-3.445.50.14713.6519101.197
3.44-3.655.60.10717.5319551.133
3.65-3.935.60.08420.6719231.091
3.93-4.335.60.06724.4619651.011
4.33-4.955.60.06525.8919421.124
4.95-6.235.60.06127.119301.113
6.23-305.50.03935.1519411.004

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
SERGUIdata collection
HKL-2000data reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3RC3

3rc3


Resolution: 2.9→30 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.898 / WRfactor Rfree: 0.2345 / WRfactor Rwork: 0.1801 / Occupancy max: 1 / Occupancy min: 0.7 / FOM work R set: 0.8314 / SU B: 32.062 / SU ML: 0.28 / SU R Cruickshank DPI: 0.2763 / SU Rfree: 0.3654 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.365 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2378 991 5.1 %RANDOM
Rwork0.1772 ---
all0.1803 19389 --
obs0.1803 19389 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 117.91 Å2 / Biso mean: 63.801 Å2 / Biso min: 17.13 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å2-0.21 Å20 Å2
2---0.43 Å20 Å2
3---0.64 Å2
Refinement stepCycle: LAST / Resolution: 2.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4868 107 0 0 4975
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0225098
X-RAY DIFFRACTIONr_angle_refined_deg1.661.9966929
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.385607
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3723.839224
X-RAY DIFFRACTIONr_dihedral_angle_3_deg2015876
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.91532
X-RAY DIFFRACTIONr_chiral_restr0.110.2784
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213786
X-RAY DIFFRACTIONr_mcbond_it0.731.53053
X-RAY DIFFRACTIONr_mcangle_it1.4324955
X-RAY DIFFRACTIONr_scbond_it2.0732045
X-RAY DIFFRACTIONr_scangle_it3.574.51974
LS refinement shellResolution: 2.903→2.978 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 72 -
Rwork0.251 1361 -
all-1433 -
obs--100 %
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)
14.8821-1.08241.60750.4330.26662.5443-0.0618-0.104-0.0265-0.0665-0.02460.0471-0.2661-0.1440.08630.04360.05510.01390.14570.07030.223-15.485662.725230.7623
24.16511.89020.47582.5223-0.34191.60250.079-0.12790.068-0.03650.07150.0106-0.2141-0.6039-0.15050.05260.09940.02880.28140.07320.0395-31.697965.835534.9194
312.5552.33151.79451.466-0.51250.97190.1559-0.80470.1160.25620.06450.21-0.138-0.3112-0.22040.07290.08310.00830.31340.07850.1796-24.407164.302340.0085
44.68961.71192.43540.67760.85314.85060.3369-0.20410.43860.2276-0.13840.0938-0.039-0.186-0.19850.2504-0.0179-0.04420.13820.01850.2269-0.144266.920144.2283
51.4818-0.08720.00981.76750.32791.56970.06550.0013-0.0411-0.0371-0.0638-0.124-0.01560.218-0.00170.0168-0.02630.02090.1032-0.00750.085329.315764.60136.5208
62.10050.9080.30662.1544-0.42982.3424-0.07750.3403-0.0807-0.3227-0.0726-0.2097-0.10150.31690.15010.1482-0.01240.08430.17370.02480.07833.088770.79746.6661
73.5284-3.8233-2.34444.95831.26173.6288-0.1449-0.20390.17320.26680.1873-0.2215-0.14450.2833-0.04250.142-0.09950.03080.15660.01350.086834.429179.051813.835
89.79437.4068-15.45125.6087-11.570426.30550.76770.01840.510.5522-0.01720.4016-1.7995-0.5044-0.75050.29210.1210.04160.14680.05310.313222.353885.531123.949
91.31910.93070.23291.49770.22290.67810.08060.01480.08060.1378-0.00060.0248-0.0593-0.0675-0.07990.04350.03820.02450.05550.00760.09692.469663.386735.5273
102.01590.3015-0.82441.04820.00791.40790.01890.1583-0.1258-0.10.0415-0.09790.12330.0127-0.06030.04570.0248-0.00960.0577-0.03760.035315.68249.504513.9751
113.1616-2.45896.031913.1041-16.660526.56720.138-0.4298-0.07280.4871-0.00340.2394-0.9492-0.7091-0.13460.19360.0334-0.00020.1241-0.02880.147318.21565.286116.5381
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A58 - 72
2X-RAY DIFFRACTION2A87 - 151
3X-RAY DIFFRACTION3A152 - 175
4X-RAY DIFFRACTION4A176 - 187
5X-RAY DIFFRACTION5A188 - 347
6X-RAY DIFFRACTION6A348 - 445
7X-RAY DIFFRACTION7A457 - 487
8X-RAY DIFFRACTION8A495 - 508
9X-RAY DIFFRACTION9A509 - 551
10X-RAY DIFFRACTION10A552 - 689
11X-RAY DIFFRACTION11E4 - 9

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