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- PDB-4hyy: Filament of octameric rings of DMC1 recombinase from Homo sapiens -

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Basic information

Entry
Database: PDB / ID: 4hyy
TitleFilament of octameric rings of DMC1 recombinase from Homo sapiens
ComponentsMeiotic recombination protein DMC1/LIM15 homolog
KeywordsRECOMBINATION / RecA homolog / DNA strand exchange / DNA / nucleus
Function / homology
Function and homology information


female gamete generation / chromosome organization involved in meiotic cell cycle / DNA recombinase assembly / homologous chromosome pairing at meiosis / double-strand break repair involved in meiotic recombination / DNA strand invasion / mitotic recombination / DNA strand exchange activity / lateral element / reciprocal meiotic recombination ...female gamete generation / chromosome organization involved in meiotic cell cycle / DNA recombinase assembly / homologous chromosome pairing at meiosis / double-strand break repair involved in meiotic recombination / DNA strand invasion / mitotic recombination / DNA strand exchange activity / lateral element / reciprocal meiotic recombination / oocyte maturation / ATP-dependent DNA damage sensor activity / male meiosis I / spermatid development / ATP-dependent activity, acting on DNA / ovarian follicle development / condensed nuclear chromosome / meiotic cell cycle / Meiotic recombination / single-stranded DNA binding / chromosome / site of double-strand break / double-stranded DNA binding / spermatogenesis / chromosome, telomeric region / ATP hydrolysis activity / DNA binding / ATP binding / identical protein binding / nucleus
Similarity search - Function
Meiotic recombination protein Dmc1 / DNA recombination and repair protein, RecA-like / DNA recombination and repair protein Rad51-like, C-terminal / Rad51 / DNA recombination and repair protein RecA, monomer-monomer interface / RecA family profile 2. / DNA recombination and repair protein RecA-like, ATP-binding domain / RecA family profile 1. / DNA repair Rad51/transcription factor NusA, alpha-helical / Helix-hairpin-helix domain ...Meiotic recombination protein Dmc1 / DNA recombination and repair protein, RecA-like / DNA recombination and repair protein Rad51-like, C-terminal / Rad51 / DNA recombination and repair protein RecA, monomer-monomer interface / RecA family profile 2. / DNA recombination and repair protein RecA-like, ATP-binding domain / RecA family profile 1. / DNA repair Rad51/transcription factor NusA, alpha-helical / Helix-hairpin-helix domain / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Meiotic recombination protein DMC1/LIM15 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.603 Å
AuthorsDu, L. / Luo, Y.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2013
Title: Structure of a filament of stacked octamers of human DMC1 recombinase.
Authors: Du, L. / Luo, Y.
History
DepositionNov 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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: Meiotic recombination protein DMC1/LIM15 homolog
B: Meiotic recombination protein DMC1/LIM15 homolog
C: Meiotic recombination protein DMC1/LIM15 homolog
D: Meiotic recombination protein DMC1/LIM15 homolog


Theoretical massNumber of molelcules
Total (without water)118,2704
Polymers118,2704
Non-polymers00
Water1,72996
1
A: Meiotic recombination protein DMC1/LIM15 homolog
B: Meiotic recombination protein DMC1/LIM15 homolog

A: Meiotic recombination protein DMC1/LIM15 homolog
B: Meiotic recombination protein DMC1/LIM15 homolog

A: Meiotic recombination protein DMC1/LIM15 homolog
B: Meiotic recombination protein DMC1/LIM15 homolog

A: Meiotic recombination protein DMC1/LIM15 homolog
B: Meiotic recombination protein DMC1/LIM15 homolog


Theoretical massNumber of molelcules
Total (without water)236,5408
Polymers236,5408
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area19440 Å2
ΔGint-92 kcal/mol
Surface area77560 Å2
MethodPISA
2
C: Meiotic recombination protein DMC1/LIM15 homolog
D: Meiotic recombination protein DMC1/LIM15 homolog

C: Meiotic recombination protein DMC1/LIM15 homolog
D: Meiotic recombination protein DMC1/LIM15 homolog

C: Meiotic recombination protein DMC1/LIM15 homolog
D: Meiotic recombination protein DMC1/LIM15 homolog

C: Meiotic recombination protein DMC1/LIM15 homolog
D: Meiotic recombination protein DMC1/LIM15 homolog


Theoretical massNumber of molelcules
Total (without water)236,5408
Polymers236,5408
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area19330 Å2
ΔGint-96 kcal/mol
Surface area75270 Å2
MethodPISA
3
A: Meiotic recombination protein DMC1/LIM15 homolog
B: Meiotic recombination protein DMC1/LIM15 homolog

A: Meiotic recombination protein DMC1/LIM15 homolog
B: Meiotic recombination protein DMC1/LIM15 homolog

A: Meiotic recombination protein DMC1/LIM15 homolog
B: Meiotic recombination protein DMC1/LIM15 homolog

A: Meiotic recombination protein DMC1/LIM15 homolog
B: Meiotic recombination protein DMC1/LIM15 homolog

C: Meiotic recombination protein DMC1/LIM15 homolog
D: Meiotic recombination protein DMC1/LIM15 homolog

C: Meiotic recombination protein DMC1/LIM15 homolog
D: Meiotic recombination protein DMC1/LIM15 homolog

C: Meiotic recombination protein DMC1/LIM15 homolog
D: Meiotic recombination protein DMC1/LIM15 homolog

C: Meiotic recombination protein DMC1/LIM15 homolog
D: Meiotic recombination protein DMC1/LIM15 homolog


Theoretical massNumber of molelcules
Total (without water)473,08016
Polymers473,08016
Non-polymers00
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation1_556x,y,z+11
crystal symmetry operation2_556-x,-y,z+11
crystal symmetry operation3_556-y,x,z+11
crystal symmetry operation4_556y,-x,z+11
Buried area42900 Å2
ΔGint-208 kcal/mol
Surface area148700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.997, 123.997, 91.713
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4

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Components

#1: Protein
Meiotic recombination protein DMC1/LIM15 homolog


Mass: 29567.510 Da / Num. of mol.: 4 / Fragment: ATPase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DMC1, DMC1H, LIM15 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Rosetta2 (DE3) / References: UniProt: Q14565
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.98 Å3/Da / Density % sol: 58.73 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 6% PEG 3350, 0.5 M NaCl, 0.05 M MgCl2, 0.05 M HEPES-NACl, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 294.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Sep 24, 2010 / Details: Mirror
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.6→47.5 Å / Num. all: 43421 / Num. obs: 42118 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 25.7
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 6 % / Rmerge(I) obs: 0.419 / Mean I/σ(I) obs: 2.7 / Num. unique all: 6906 / Rsym value: 0.419 / % possible all: 82.1

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Processing

Software
NameVersionClassification
MxDCdata collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1V5W

1v5w


Resolution: 2.603→47.45 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.929 / SU B: 22.484 / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.452 / ESU R Free: 0.292 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24615 2085 5.1 %RANDOM
Rwork0.17851 ---
all0.18187 40632 --
obs0.18187 39104 96.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 67.35 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.603→47.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7536 0 0 96 7632
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0197668
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9061.95710316
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5265956
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.86823.516364
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.601151352
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2951560
X-RAY DIFFRACTIONr_chiral_restr0.1310.21144
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025784
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.603→2.67 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 140 -
Rwork0.296 2298 -
obs--79.49 %
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)
15.06810.6289-0.02582.22210.11990.09350.0868-0.45560.16910.2524-0.06830.0501-0.06470.0602-0.01850.1378-0.02870.01430.11-0.03680.01276.0627-42.0866-22.5246
24.5993-3.0102-0.15363.79640.180.0308-0.3127-0.56920.0220.56240.31040.16220.04150.01810.00230.13090.05210.02770.1222-0.01910.0205-25.4648-34.0794-22.5163
35.13151.4301-0.01572.3014-0.26660.4994-0.18270.56520.0591-0.2410.195-0.0390.05270.0503-0.01230.169-0.03030.02680.13860.0020.007313.3094-40.0301-63.5794
46.324-2.54120.14663.05340.0320.25610.28440.8835-0.1689-0.4176-0.28530.017-0.0288-0.02780.00090.20610.03070.02130.2417-0.0410.0111-18.9915-37.9174-63.4442
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A84 - 338
2X-RAY DIFFRACTION2B84 - 338
3X-RAY DIFFRACTION3C84 - 338
4X-RAY DIFFRACTION4D84 - 338

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