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- PDB-5jh0: Crystal structure of the mitochondrial DNA packaging protein Abf2... -

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Basic information

Entry
Database: PDB / ID: 5jh0
TitleCrystal structure of the mitochondrial DNA packaging protein Abf2p in complex with DNA at 2.18 Angstrom resolution
Components
  • ARS-binding factor 2, mitochondrial
  • DNA (5'-D(*AP*AP*TP*AP*AP*TP*AP*AP*AP*TP*TP*AP*TP*AP*TP*AP*AP*TP*AP*TP*AP*A)-3')
  • DNA (5'-D(*TP*TP*AP*TP*AP*TP*TP*AP*TP*AP*TP*AP*AP*TP*TP*TP*AP*TP*TP*AP*TP*T)-3')
KeywordsDNA BINDING PROTEIN / DNA packaging
Function / homology
Function and homology information


mitochondrial chromosome packaging / Apoptosis induced DNA fragmentation / Regulation of TLR by endogenous ligand / mitochondrion inheritance / Mitochondrial transcription initiation / mitochondrial chromosome / Pyroptosis / Mitochondrial protein degradation / mitochondrial genome maintenance / DNA binding, bending ...mitochondrial chromosome packaging / Apoptosis induced DNA fragmentation / Regulation of TLR by endogenous ligand / mitochondrion inheritance / Mitochondrial transcription initiation / mitochondrial chromosome / Pyroptosis / Mitochondrial protein degradation / mitochondrial genome maintenance / DNA binding, bending / mitochondrial nucleoid / Neutrophil degranulation / mitochondrion / DNA binding / nucleus
Similarity search - Function
: / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / ARS-binding factor 2, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsChakraborty, A. / Lyonnais, S. / Sola, M.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBFU2015-70645-R Spain
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: DNA structure directs positioning of the mitochondrial genome packaging protein Abf2p.
Authors: Chakraborty, A. / Lyonnais, S. / Battistini, F. / Hospital, A. / Medici, G. / Prohens, R. / Orozco, M. / Vilardell, J. / Sola, M.
History
DepositionApr 20, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 8, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2May 1, 2024Group: 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
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: ARS-binding factor 2, mitochondrial
B: DNA (5'-D(*AP*AP*TP*AP*AP*TP*AP*AP*AP*TP*TP*AP*TP*AP*TP*AP*AP*TP*AP*TP*AP*A)-3')
C: DNA (5'-D(*TP*TP*AP*TP*AP*TP*TP*AP*TP*AP*TP*AP*AP*TP*TP*TP*AP*TP*TP*AP*TP*T)-3')
D: ARS-binding factor 2, mitochondrial
E: DNA (5'-D(*AP*AP*TP*AP*AP*TP*AP*AP*AP*TP*TP*AP*TP*AP*TP*AP*AP*TP*AP*TP*AP*A)-3')
F: DNA (5'-D(*TP*TP*AP*TP*AP*TP*TP*AP*TP*AP*TP*AP*AP*TP*TP*TP*AP*TP*TP*AP*TP*T)-3')


Theoretical massNumber of molelcules
Total (without water)65,9586
Polymers65,9586
Non-polymers00
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14830 Å2
ΔGint-41 kcal/mol
Surface area29910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.490, 113.410, 67.710
Angle α, β, γ (deg.)90.00, 103.80, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein ARS-binding factor 2, mitochondrial


Mass: 19486.270 Da / Num. of mol.: 2 / Fragment: UNP residues 27-183
Source method: isolated from a genetically manipulated source
Details: Yeast mitochondrial DNA packaging protein
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: ABF2, HIM1, YMR072W, YM9916.11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLys / References: UniProt: Q02486
#2: DNA chain DNA (5'-D(*AP*AP*TP*AP*AP*TP*AP*AP*AP*TP*TP*AP*TP*AP*TP*AP*AP*TP*AP*TP*AP*A)-3')


Mass: 6773.481 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)
#3: DNA chain DNA (5'-D(*TP*TP*AP*TP*AP*TP*TP*AP*TP*AP*TP*AP*AP*TP*TP*TP*AP*TP*TP*AP*TP*T)-3')


Mass: 6719.396 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: DNA / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.56 Å3/Da / Density % sol: 52.01 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 21% PEG 4000, 0.1 M Trisodium Citrate, 0.2 M Ammonium Acetate

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 5, 2013
RadiationMonochromator: channel cut ESRF monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.12→43.483 Å / Num. obs: 35516 / % possible obs: 96.1 % / Redundancy: 3.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.06649 / Net I/σ(I): 11.3
Reflection shellResolution: 2.12→2.18 Å / Redundancy: 1.9 % / % possible all: 68.3

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIX1.10.1_2155phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PARTIAL MODEL OBTAINED WITH SINGLE ANOMALOUS DIFFRACTION

Resolution: 2.18→43.483 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2364 1881 5.65 %
Rwork0.209 --
obs0.2106 33291 98.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.18→43.483 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2622 1792 0 75 4489
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084725
X-RAY DIFFRACTIONf_angle_d0.9486738
X-RAY DIFFRACTIONf_dihedral_angle_d25.581966
X-RAY DIFFRACTIONf_chiral_restr0.057712
X-RAY DIFFRACTIONf_plane_restr0.007561
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1801-2.23910.33011210.30762193X-RAY DIFFRACTION90
2.2391-2.3050.3241540.29112405X-RAY DIFFRACTION99
2.305-2.37940.33491400.29472398X-RAY DIFFRACTION99
2.3794-2.46440.34231420.28962436X-RAY DIFFRACTION99
2.4644-2.5630.3011480.26682418X-RAY DIFFRACTION99
2.563-2.67970.28761450.2572400X-RAY DIFFRACTION99
2.6797-2.82090.23851460.25652416X-RAY DIFFRACTION99
2.8209-2.99760.28561460.25612443X-RAY DIFFRACTION99
2.9976-3.2290.28721450.23252427X-RAY DIFFRACTION100
3.229-3.55380.25131450.20522438X-RAY DIFFRACTION100
3.5538-4.06780.21491540.19222462X-RAY DIFFRACTION100
4.0678-5.12360.20011480.17882479X-RAY DIFFRACTION100
5.1236-43.49120.18011470.16472495X-RAY DIFFRACTION100

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