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- PDB-8r2g: Crystal structure of a BRCA2-DMC1 complex -

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Basic information

Entry
Database: PDB / ID: 8r2g
TitleCrystal structure of a BRCA2-DMC1 complex
Components
  • Breast cancer type 2 susceptibility protein
  • Meiotic recombination protein DMC1/LIM15 homologGenetic recombination
KeywordsRECOMBINATION / DNA repair / meiosis
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 / DNA recombinase assembly / establishment of protein localization to telomere / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / homologous chromosome pairing at meiosis ...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 / DNA recombinase assembly / establishment of protein localization to telomere / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / homologous chromosome pairing at meiosis / double-strand break repair involved in meiotic recombination / nuclear ubiquitin ligase complex / mitotic recombination / DNA strand invasion / histone H4 acetyltransferase activity / histone H3 acetyltransferase activity / DNA strand exchange activity / lateral element / telomere maintenance via recombination / regulation of DNA damage checkpoint / oocyte maturation / Impaired BRCA2 binding to PALB2 / HDR through MMEJ (alt-NHEJ) / gamma-tubulin binding / 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 / 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 / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / hematopoietic stem cell proliferation / ATP-dependent DNA damage sensor activity / Impaired BRCA2 binding to RAD51 / female gonad development / male meiosis I / spermatid development / Presynaptic phase of homologous DNA pairing and strand exchange / centrosome duplication / 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 / secretory granule / condensed nuclear chromosome / cellular response to ionizing radiation / nucleotide-excision repair / response to gamma radiation / double-strand break repair via homologous recombination / brain development / HDR through Homologous Recombination (HRR) / Meiotic recombination / double-strand break repair / cellular senescence / single-stranded DNA binding / site of double-strand break / chromosome / double-stranded DNA binding / spermatogenesis / 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: 3.45 Å
AuthorsDunce, J.M. / Davies, O.R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust219413/Z/19/Z United Kingdom
CitationJournal: To Be Published
Title: Crystal structure of a BRCA2-DMC1 complex
Authors: Dunce, J.M. / Davies, O.R.
History
DepositionNov 5, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release

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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
E: Meiotic recombination protein DMC1/LIM15 homolog
F: Meiotic recombination protein DMC1/LIM15 homolog
G: Meiotic recombination protein DMC1/LIM15 homolog
H: Meiotic recombination protein DMC1/LIM15 homolog
I: Breast cancer type 2 susceptibility protein
J: Breast cancer type 2 susceptibility protein
K: Breast cancer type 2 susceptibility protein
L: Breast cancer type 2 susceptibility protein
M: Breast cancer type 2 susceptibility protein
N: Breast cancer type 2 susceptibility protein
O: Breast cancer type 2 susceptibility protein


Theoretical massNumber of molelcules
Total (without water)242,19215
Polymers242,19215
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)125.400, 125.400, 364.195
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Space group name HallP4w2c
Symmetry operation#1: x,y,z
#2: -y,x,z+1/4
#3: y,-x,z+3/4
#4: x,-y,-z+1/2
#5: -x,y,-z
#6: -x,-y,z+1/2
#7: y,x,-z+3/4
#8: -y,-x,-z+1/4
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 84 through 271 or resid 291 through 335))
d_2ens_1(chain "B" and (resid 84 through 271 or resid 291 through 335))
d_3ens_1(chain "C" and resid 84 through 335)
d_4ens_1(chain "D" and (resid 84 through 271 or resid 291 through 335))
d_5ens_1(chain "E" and (resid 84 through 271 or resid 291 through 335))
d_6ens_1(chain "F" and (resid 84 through 271 or resid 291 through 335))
d_7ens_1(chain "G" and (resid 84 through 271 or resid 291 through 335))
d_8ens_1(chain "H" and (resid 84 through 271 or resid 291 through 335))
d_1ens_2(chain "I" and resid 2405 through 2412)
d_2ens_2(chain "J" and resid 2405 through 2412)
d_3ens_2chain "L"
d_1ens_3chain "K"
d_2ens_3chain "M"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1GLYGLYTHRTHRAA84 - 2715 - 192
d_12ens_1HISHISILEILEAA291 - 335212 - 256
d_21ens_1GLYGLYTHRTHRBB84 - 2715 - 192
d_22ens_1HISHISILEILEBB291 - 335212 - 256
d_31ens_1GLYGLYILEILECC84 - 3355 - 256
d_41ens_1GLYGLYTHRTHRDD84 - 2715 - 192
d_42ens_1HISHISILEILEDD291 - 335212 - 256
d_51ens_1GLYGLYTHRTHREE84 - 2715 - 192
d_52ens_1HISHISILEILEEE291 - 335212 - 256
d_61ens_1GLYGLYTHRTHRFF84 - 2715 - 192
d_62ens_1HISHISILEILEFF291 - 335212 - 256
d_71ens_1GLYGLYTHRTHRGG84 - 2715 - 192
d_72ens_1HISHISILEILEGG291 - 335212 - 256
d_81ens_1GLYGLYTHRTHRHH84 - 2715 - 192
d_82ens_1HISHISILEILEHH291 - 335212 - 256
d_11ens_2VALVALTHRTHRII2405 - 24126 - 13
d_21ens_2VALVALTHRTHRJJ2405 - 24126 - 13
d_31ens_2VALVALTHRTHRLL2405 - 24126 - 13
d_11ens_3PHEPHEPHEPHEKK2406 - 24107 - 11
d_21ens_3PHEPHEPHEPHEMM2406 - 24107 - 11

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(0.712196352296, 0.70096969991, 0.0376541575962), (-0.69918271103, 0.713120906548, -0.0510108737545), (-0.0626090438682, 0.0100026222257, 0.997988003522)58.4408410966, 28.0878455775, 2.96307551114
2given(0.0175111096248, 0.999743169637, 0.0143859585521), (-0.994492811904, 0.0189025196004, -0.103086089381), (-0.103331544607, -0.0125015805604, 0.994568400047)120.290991827, 7.0241369424, 2.91689856742
3given(-0.688107588791, 0.722933332226, 0.0622522562205), (-0.725490781897, -0.68391266803, -0.0769843353615), (-0.0130794354495, -0.0981369434205, 0.995086965398)146.563824688, -52.8075486975, -3.66087352237
4given(-0.997165590741, -0.0033744954867, 0.0751624734937), (0.000469581615194, -0.999253370284, -0.0386326477085), (0.0752367206528, -0.0384878520585, 0.996422661881)122.982571552, -116.439083399, -4.8599942582
5given(-0.713537414862, -0.700454152028, 0.0151108735371), (0.700610917453, -0.7132743133, 0.0195983757522), (-0.00294956572309, 0.024571017342, 0.999693735685)65.4676245806, -144.697690505, 1.65203828099
6given(-0.0196496580846, -0.996129509582, -0.0856731642787), (0.998586590056, -0.023785948699, 0.0475294730192), (-0.0493833281397, -0.0846181350826, 0.995188955986)7.01260375331, -123.045180093, 0.0981275620757
7given(0.697877122231, -0.712564069743, -0.0722493513988), (0.715578055388, 0.697959100262, 0.0283044344317), (0.0302583693064, -0.0714530676246, 0.996984899692)-20.9347882983, -62.5629777895, -3.54328054121
8given(-0.98693472252, 0.144871062148, -0.0705140328996), (-0.139074999443, -0.986950757734, -0.0811563080566), (-0.0813510787493, -0.0702892392864, 0.994203915113)129.081618027, -98.9881406742, 7.10042882081
9given(-0.0795655849272, -0.994171804895, -0.0727443471861), (0.995896480829, -0.0824360319127, 0.0373430062401), (-0.04312211924, -0.0694746212284, 0.996651272932)15.0123502095, -124.315667437, 3.59258507262
10given(-0.921883842701, -0.224187820497, -0.316022153825), (0.259564207937, -0.962877499693, -0.0741170867156), (-0.28767447319, -0.150355384759, 0.945852343523)124.636492929, -114.28896617, -6.26977105738

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Components

#1: Protein
Meiotic recombination protein DMC1/LIM15 homolog / Genetic recombination


Mass: 28868.811 Da / Num. of mol.: 8
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 / Fanconi anemia group D1 protein


Mass: 1605.961 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRCA2, FACD, FANCD1 / Production host: Escherichia coli (E. coli) / References: UniProt: P51587

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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: 2.96 Å3/Da / Density % sol: 58.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 50 mM HEPES-NaOH pH 7.4, 50 mM MgCl2, 500 mM NaCl, 8 % PEG 3350, 20 % glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.45→182.098 Å / Num. obs: 22688 / % possible obs: 57.7 % / Redundancy: 12.2 % / Biso Wilson estimate: 84.4 Å2 / Rpim(I) all: 0.072 / Rrim(I) all: 0.247 / Net I/σ(I): 8
Reflection shellResolution: 3.452→3.692 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1134 / Rpim(I) all: 0.561 / Rrim(I) all: 1.5 / % possible all: 16.1

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487model building
XDSdata reduction
Aimlessdata scaling
autoPROCdata processing
PHASERphasing
STARANISOdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.45→118.57 Å / SU ML: 0.5719 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.451
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3057 1072 4.74 %
Rwork0.2635 21553 -
obs0.2655 22625 57.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 94.23 Å2
Refinement stepCycle: LAST / Resolution: 3.45→118.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15352 0 0 0 15352
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001915639
X-RAY DIFFRACTIONf_angle_d0.479721045
X-RAY DIFFRACTIONf_chiral_restr0.04152334
X-RAY DIFFRACTIONf_plane_restr0.00362729
X-RAY DIFFRACTIONf_dihedral_angle_d10.73635768
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.314439052202
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.386871911502
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS0.442228239472
ens_1d_5AAX-RAY DIFFRACTIONTorsion NCS0.296122528959
ens_1d_6AAX-RAY DIFFRACTIONTorsion NCS0.326396501961
ens_1d_7AAX-RAY DIFFRACTIONTorsion NCS0.296342765419
ens_1d_8AAX-RAY DIFFRACTIONTorsion NCS0.286185725469
ens_2d_2IIX-RAY DIFFRACTIONTorsion NCS1.03821756482
ens_2d_3IIX-RAY DIFFRACTIONTorsion NCS1.4592611217
ens_3d_2KKX-RAY DIFFRACTIONTorsion NCS1.52161072832
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.45-3.610.3514240.384538X-RAY DIFFRACTION11.7
3.61-3.80.4241730.36761297X-RAY DIFFRACTION28.39
3.8-4.040.3769790.30441766X-RAY DIFFRACTION38.36
4.04-4.350.31471170.26922296X-RAY DIFFRACTION50.06
4.35-4.790.33111640.25993083X-RAY DIFFRACTION66.73
4.79-5.480.29811770.24643502X-RAY DIFFRACTION74.93
5.48-6.90.30461990.28554096X-RAY DIFFRACTION86.44
6.9-118.570.27272390.24054975X-RAY DIFFRACTION99.3

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