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- PDB-3rc3: Human Mitochondrial Helicase Suv3 -

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Basic information

Entry
Database: PDB / ID: 3rc3
TitleHuman Mitochondrial Helicase Suv3
ComponentsATP-dependent RNA helicase SUPV3L1, mitochondrial
KeywordsHYDROLASE / helicase / mitochondria / Suv3 / Nucleus
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
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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AZIDE ION / ATP-dependent RNA helicase SUPV3L1, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.08 Å
AuthorsDauter, Z. / Jedrzejczak, R. / Dauter, M. / 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 1.4Nov 8, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)77,3355
Polymers76,7281
Non-polymers6074
Water9,224512
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.390, 89.390, 88.070
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 76727.867 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

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Non-polymers , 5 types, 516 molecules

#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: N3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 512 / Source method: isolated from a natural source / Formula: H2O

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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: 53.54 %
Crystal growTemperature: 277 K / 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: 0.9754
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 14, 2006 / Details: FOCUSING MIRRORS
RadiationMonochromator: SI111 DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9754 Å / Relative weight: 1
ReflectionResolution: 2.08→50 Å / Num. obs: 47146 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 33.9 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 15
Reflection shellResolution: 2.08→2.15 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.326 / Mean I/σ(I) obs: 3.49 / % possible all: 96.5

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
SHELXDphasing
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.08→39.84 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.953 / Occupancy max: 1 / Occupancy min: 0.7 / SU B: 7.495 / SU ML: 0.105 / SU R Cruickshank DPI: 0.1571 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
RfactorNum. reflection% reflectionSelection details
Rfree0.203 965 2 %RANDOM
Rwork0.16 ---
obs0.161 47104 100 %-
all-47104 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.24 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20.26 Å20 Å2
2--0.51 Å20 Å2
3----0.77 Å2
Refinement stepCycle: LAST / Resolution: 2.08→39.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4856 0 36 512 5404
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0225004
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0211.9776785
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7545604
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.82223.867225
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.715879
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2311532
X-RAY DIFFRACTIONr_chiral_restr0.1530.2760
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213737
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1391.53040
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.95524937
X-RAY DIFFRACTIONr_scbond_it3.70631964
X-RAY DIFFRACTIONr_scangle_it5.3094.51848
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.08→2.13 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 71 -
Rwork0.198 3355 -
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)
17.0645.1450.316212.42891.60582.5846-0.04840.158-0.1297-0.22860.06530.11480.0056-0.3821-0.01690.01790.03330.00670.18930.04060.0861-16.832654.826532.1143
24.81872.5651-0.55563.0836-1.22962.2027-0.17930.261-0.1154-0.18120.2599-0.03170.0702-0.5238-0.08050.0290.02980.02990.25380.08620.0482-33.132952.451836.1766
37.60253.42780.00831.67570.13470.51980.2536-0.4334-0.00710.0828-0.0820.0045-0.1383-0.1246-0.17160.08250.04390.03660.25810.11590.1099-25.781453.390641.3964
49.07067.2523-0.05266.21350.30530.3530.1835-0.37350.22630.0683-0.08580.0916-0.12560.075-0.09780.14490.04810.07040.2625-0.00210.1515-3.677663.408645.4032
51.37810.0119-0.27781.1097-0.02340.68360.1241-0.20370.07350.07720.0026-0.0896-0.10980.1469-0.12670.0678-0.0390.01720.1201-0.07680.061825.356169.146838.2527
61.204-0.17350.26181.89180.10121.67850.08550.21710.1732-0.14920.0041-0.1175-0.28190.0319-0.08960.126-0.01450.09540.08770.01220.093628.591776.52488.9029
70.4266-0.143-0.41832.12210.46784.59150.08230.08170.24490.1045-0.0038-0.1048-0.35170.0336-0.07850.1585-0.03730.09270.03860.02690.177127.544183.089917.5927
83.9615.1635-5.6048.9169-10.978714.21860.26730.31810.52870.33220.44570.6877-0.5135-0.5584-0.71290.28960.08440.11510.0902-0.02580.247714.272987.817526.3414
92.24121.44130.03622.7310.2680.7580.0269-0.09230.07680.18220.02860.13460.0025-0.0523-0.05550.08460.01930.04660.10660.00340.0875-0.040160.853536.8625
101.12480.6779-0.65311.2322-0.80461.52680.00760.0692-0.1332-0.10570.0274-0.10990.17010.0591-0.0350.07410.01780.00290.0979-0.04340.070916.638151.61715.3147
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

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