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- PDB-8qqe: Crystal structure of the complex between DMC1 and the PhePP domai... -

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Basic information

Entry
Database: PDB / ID: 8qqe
TitleCrystal structure of the complex between DMC1 and the PhePP domain of BRCA2
Components
  • Breast cancer type 2 susceptibility protein
  • Meiotic recombination protein DMC1/LIM15 homolog
KeywordsRECOMBINATION / DNA BINDING PROTEIN / Meiotic recombination / RING PROTEIN / OCTAMER / AAA ATPASE
Function / homology
Function and homology information


BRCA2-MAGE-D1 complex / negative regulation of mammary gland epithelial cell proliferation / female gamete generation / mitotic recombination-dependent replication fork processing / chromosome organization involved in meiotic cell cycle / establishment of protein localization to telomere / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / double-strand break repair involved in meiotic recombination / nuclear ubiquitin ligase complex ...BRCA2-MAGE-D1 complex / negative regulation of mammary gland epithelial cell proliferation / female gamete generation / mitotic recombination-dependent replication fork processing / chromosome organization involved in meiotic cell cycle / establishment of protein localization to telomere / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / double-strand break repair involved in meiotic recombination / nuclear ubiquitin ligase complex / homologous chromosome pairing at meiosis / lateral element / telomere maintenance via recombination / DNA recombinase assembly / histone H4 acetyltransferase activity / histone H3 acetyltransferase activity / regulation of DNA damage checkpoint / mitotic recombination / Impaired BRCA2 binding to PALB2 / DNA strand invasion / HDR through MMEJ (alt-NHEJ) / gamma-tubulin binding / DNA strand exchange activity / reciprocal meiotic recombination / DNA repair complex / Defective homologous recombination repair (HRR) due to BRCA1 loss of function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function / oocyte maturation / Homologous DNA Pairing and Strand Exchange / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / response to UV-C / Resolution of D-loop Structures through Holliday Junction Intermediates / inner cell mass cell proliferation / ATP-dependent DNA damage sensor activity / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / hematopoietic stem cell proliferation / Impaired BRCA2 binding to RAD51 / female gonad development / male meiosis I / Presynaptic phase of homologous DNA pairing and strand exchange / centrosome duplication / spermatid development / response to X-ray / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / ATP-dependent activity, acting on DNA / ovarian follicle development / positive regulation of mitotic cell cycle / meiotic cell cycle / regulation of cytokinesis / condensed nuclear chromosome / secretory granule / cellular response to ionizing radiation / nucleotide-excision repair / response to gamma radiation / double-strand break repair via homologous recombination / HDR through Homologous Recombination (HRR) / brain development / Meiotic recombination / cellular senescence / double-strand break repair / chromosome / site of double-strand break / single-stranded DNA binding / spermatogenesis / double-stranded DNA binding / protease binding / chromosome, telomeric region / centrosome / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / ATP hydrolysis activity / protein-containing complex / DNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol
Similarity search - Function
Meiotic recombination protein Dmc1 / : / BRCA2, OB2 / BRCA2, OB3 / Tower domain / Breast cancer type 2 susceptibility protein, helical domain / BRCA2 helical domain superfamily / BRCA2, oligonucleotide/oligosaccharide-binding, domain 3 / Tower / BRCA2, helical ...Meiotic recombination protein Dmc1 / : / BRCA2, OB2 / BRCA2, OB3 / Tower domain / Breast cancer type 2 susceptibility protein, helical domain / BRCA2 helical domain superfamily / BRCA2, oligonucleotide/oligosaccharide-binding, domain 3 / Tower / BRCA2, helical / Tower / BRCA2 repeat / BRCA2, OB1 / Breast cancer type 2 susceptibility protein / BRCA2 repeat / BRCA2, oligonucleotide/oligosaccharide-binding, domain 1 / BRCA2 repeat profile. / 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 / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Breast cancer type 2 susceptibility protein / Meiotic recombination protein DMC1/LIM15 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.461 Å
AuthorsMiron, S. / Legrand, P. / Zinn-Justin, S.
Funding support France, European Union, 2items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-10-INSB-05-01 France
iNEXT-Discovery871037European Union
CitationJournal: Nucleic Acids Res. / Year: 2024
Title: DMC1 and RAD51 bind FxxA and FxPP motifs of BRCA2 via two separate interfaces.
Authors: Miron, S. / Legrand, P. / Dupaigne, P. / van Rossum-Fikkert, S.E. / Ristic, D. / Majeed, A. / Kanaar, R. / Zinn-Justin, S. / Zelensky, A.N.
History
DepositionOct 4, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Meiotic recombination protein DMC1/LIM15 homolog
B: Meiotic recombination protein DMC1/LIM15 homolog
C: Breast cancer type 2 susceptibility protein
D: Breast cancer type 2 susceptibility protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,0467
Polymers79,9514
Non-polymers953
Water00
1
A: Meiotic recombination protein DMC1/LIM15 homolog
B: Meiotic recombination protein DMC1/LIM15 homolog
C: Breast cancer type 2 susceptibility protein
D: Breast cancer type 2 susceptibility protein
hetero molecules

A: Meiotic recombination protein DMC1/LIM15 homolog
B: Meiotic recombination protein DMC1/LIM15 homolog
C: Breast cancer type 2 susceptibility protein
D: Breast cancer type 2 susceptibility protein
hetero molecules

A: Meiotic recombination protein DMC1/LIM15 homolog
B: Meiotic recombination protein DMC1/LIM15 homolog
C: Breast cancer type 2 susceptibility protein
D: Breast cancer type 2 susceptibility protein
hetero molecules

A: Meiotic recombination protein DMC1/LIM15 homolog
B: Meiotic recombination protein DMC1/LIM15 homolog
C: Breast cancer type 2 susceptibility protein
D: Breast cancer type 2 susceptibility protein
hetero molecules


  • defined by author
  • Evidence: gel filtration, A dimer is observed in the asymmetric unit, which is assembled into a ring-shaped octamer using the crystallographic symmetries. Size Exclusion Chromatography coupled to ...Evidence: gel filtration, A dimer is observed in the asymmetric unit, which is assembled into a ring-shaped octamer using the crystallographic symmetries. Size Exclusion Chromatography coupled to Multi-Angle Light Scattering also shows that DMC1 bound to PhePP assembles into an octamer in solution.
  • 320 kDa, 16 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)320,18628
Polymers319,80516
Non-polymers38112
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation15_555y,-x,z1
crystal symmetry operation16_555-y,x,z1
Buried area31000 Å2
ΔGint-290 kcal/mol
Surface area96080 Å2
Unit cell
Length a, b, c (Å)234.383, 234.383, 234.383
Angle α, β, γ (deg.)90, 90, 90
Int Tables number211
Space group name H-MI432

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Components

#1: Protein Meiotic recombination protein DMC1/LIM15 homolog


Mass: 37656.887 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DMC1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14565
#2: Protein/peptide Breast cancer type 2 susceptibility protein


Mass: 2318.714 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRCA2 / Production host: Escherichia coli #1/H766 (bacteria) / References: UniProt: P51587
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
Has ligand of interestN

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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: 4.05 Å3/Da / Density % sol: 69.5 % / Description: 0
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6 / Details: 0.1M MES at pH 6, 2.4 M sodium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.965459 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 2, 2022 / Details: CRL
RadiationMonochromator: Diamond [110] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965459 Å / Relative weight: 1
ReflectionResolution: 3.46→47.84 Å / Num. obs: 14667 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 76.3 % / Biso Wilson estimate: 155 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.228 / Rpim(I) all: 0.026 / Rrim(I) all: 0.229 / Net I/σ(I): 22.9
Reflection shellResolution: 3.46→3.55 Å / Redundancy: 76.3 % / Rmerge(I) obs: 6.345 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1058 / CC1/2: 0.541 / Rpim(I) all: 0.728 / Rrim(I) all: 6.387 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
MxCuBE3data collection
XDS20220820data reduction
MOLREP11.9.02phasing
STARANISOdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.461→47.84 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.923 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.505
Details: 3 TLS groups automatic LSSR NCS restraints target LSSR refinement using PDB 6R3P B chain
RfactorNum. reflection% reflectionSelection details
Rfree0.2609 708 5 %RANDOM
Rwork0.2484 ---
obs0.2491 13996 95.4 %-
Displacement parametersBiso mean: 169.03 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.53 Å
Refinement stepCycle: LAST / Resolution: 3.461→47.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4374 0 3 0 4377
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0064448HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.85980HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1589SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes753HARMONIC5
X-RAY DIFFRACTIONt_it4448HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion599SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact3294SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.42
X-RAY DIFFRACTIONt_other_torsion18.43
LS refinement shellResolution: 3.461→3.54 Å
RfactorNum. reflection% reflection
Rfree0.4321 27 -
Rwork0.3149 --
obs--41.02 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
17.2442-0.8831-0.04346.33881.09752.2960.20210.54420.11190.54420.140.41760.11190.4176-0.3421-0.304-0.1155-0.086-0.1259-0.1520.263639.321516.898190.5148
28.3154-1.43412.43518.31540.79968.31550.02360.1236-0.00390.12360.19120.2304-0.00390.2304-0.21480.304-0.0347-0.01980.304-0.01380.30443.8017-12.354558.7342
38.3154-0.36442.50384.0475-1.45611.68760.1279-0.1570.0591-0.157-0.0485-0.11170.0591-0.1117-0.0794-0.3040.1305-0.152-0.2405-0.09740.128840.126-16.274490.2787
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|83 - A|339 A|501 - A|502 }A83 - 339
2X-RAY DIFFRACTION1{ A|83 - A|339 A|501 - A|502 }A501 - 502
3X-RAY DIFFRACTION2{ A|28 - A|82 }A28 - 82
4X-RAY DIFFRACTION3{ B|81 - B|339 B|401 - B|401 C|2402 - C|2414 }B81 - 339
5X-RAY DIFFRACTION3{ B|81 - B|339 B|401 - B|401 C|2402 - C|2414 }B401
6X-RAY DIFFRACTION3{ B|81 - B|339 B|401 - B|401 C|2402 - C|2414 }C2402 - 2414

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