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- PDB-6hqu: Humanised RadA mutant HumRadA22 in complex with a recombined BRC ... -

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Basic information

Entry
Database: PDB / ID: 6hqu
TitleHumanised RadA mutant HumRadA22 in complex with a recombined BRC repeat 8-2
Components
  • Breast cancer type 2 susceptibility
  • DNA repair and recombination protein RadA
KeywordsONCOPROTEIN / RadA / Rad51 / BRC repeat / recombinase / ATPase / BRCA2
Function / homology
Function and homology information


BRCA2-MAGE-D1 complex / negative regulation of mammary gland epithelial cell proliferation / mitotic recombination-dependent replication fork processing / establishment of protein localization to telomere / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / nuclear ubiquitin ligase complex / lateral element / telomere maintenance via recombination / histone H4 acetyltransferase activity ...BRCA2-MAGE-D1 complex / negative regulation of mammary gland epithelial cell proliferation / mitotic recombination-dependent replication fork processing / establishment of protein localization to telomere / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / nuclear ubiquitin ligase complex / lateral element / telomere maintenance via recombination / histone H4 acetyltransferase activity / histone H3 acetyltransferase activity / regulation of DNA damage checkpoint / Impaired BRCA2 binding to PALB2 / HDR through MMEJ (alt-NHEJ) / gamma-tubulin binding / 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 / 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 / response to X-ray / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of mitotic cell cycle / regulation of cytokinesis / 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 / single-stranded DNA binding / spermatogenesis / protease binding / chromosome, telomeric region / centrosome / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / protein-containing complex / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
: / 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, 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. / P-loop containing nucleotide triphosphate hydrolases / Nucleic acid-binding, OB-fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Breast cancer type 2 susceptibility protein
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsPantelejevs, T. / Lindenburg, L. / Hyvonen, M. / Hollfelder, F.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Improved RAD51 binders through motif shuffling based on the modularity of BRC repeats.
Authors: Lindenburg, L.H. / Pantelejevs, T. / Gielen, F. / Zuazua-Villar, P. / Butz, M. / Rees, E. / Kaminski, C.F. / Downs, J.A. / Hyvonen, M. / Hollfelder, F.
History
DepositionSep 25, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 2.0Jan 11, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / database_2 ...atom_site / database_2 / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_polymer_linkage / struct_asym / struct_conn / struct_conn_type / struct_ref / struct_ref_seq / struct_sheet_range
Item: _atom_site.label_entity_id / _atom_site.label_seq_id ..._atom_site.label_entity_id / _atom_site.label_seq_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entity_nonpoly.entity_id / _pdbx_nonpoly_scheme.entity_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _struct_asym.entity_id / _struct_ref_seq.ref_id / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_label_seq_id
Revision 2.1Mar 29, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA repair and recombination protein RadA
B: DNA repair and recombination protein RadA
C: DNA repair and recombination protein RadA
D: DNA repair and recombination protein RadA
E: DNA repair and recombination protein RadA
F: DNA repair and recombination protein RadA
G: DNA repair and recombination protein RadA
H: DNA repair and recombination protein RadA
I: Breast cancer type 2 susceptibility
J: Breast cancer type 2 susceptibility
K: Breast cancer type 2 susceptibility
L: Breast cancer type 2 susceptibility
M: Breast cancer type 2 susceptibility
N: Breast cancer type 2 susceptibility
O: Breast cancer type 2 susceptibility
hetero molecules


Theoretical massNumber of molelcules
Total (without water)235,81231
Polymers232,20015
Non-polymers3,61216
Water3,855214
1
A: DNA repair and recombination protein RadA
I: Breast cancer type 2 susceptibility
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9744
Polymers29,5222
Non-polymers4522
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-30 kcal/mol
Surface area11420 Å2
MethodPISA
2
B: DNA repair and recombination protein RadA
J: Breast cancer type 2 susceptibility
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9744
Polymers29,5222
Non-polymers4522
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-31 kcal/mol
Surface area11620 Å2
MethodPISA
3
C: DNA repair and recombination protein RadA
K: Breast cancer type 2 susceptibility
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9744
Polymers29,5222
Non-polymers4522
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-24 kcal/mol
Surface area10640 Å2
MethodPISA
4
D: DNA repair and recombination protein RadA
L: Breast cancer type 2 susceptibility
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9744
Polymers29,5222
Non-polymers4522
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-31 kcal/mol
Surface area11170 Å2
MethodPISA
5
E: DNA repair and recombination protein RadA
M: Breast cancer type 2 susceptibility
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9744
Polymers29,5222
Non-polymers4522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-33 kcal/mol
Surface area11570 Å2
MethodPISA
6
F: DNA repair and recombination protein RadA
N: Breast cancer type 2 susceptibility
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9744
Polymers29,5222
Non-polymers4522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-27 kcal/mol
Surface area10670 Å2
MethodPISA
7
G: DNA repair and recombination protein RadA
O: Breast cancer type 2 susceptibility
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9744
Polymers29,5222
Non-polymers4522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-28 kcal/mol
Surface area9920 Å2
MethodPISA
8
H: DNA repair and recombination protein RadA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9943
Polymers25,5421
Non-polymers4522
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area730 Å2
ΔGint-19 kcal/mol
Surface area10100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.403, 75.473, 114.792
Angle α, β, γ (deg.)90.000, 97.060, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
DNA repair and recombination protein RadA


Mass: 25542.064 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) (archaea)
Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: radA, PF1926 / Plasmid: pBAT4 / Production host: Escherichia coli (E. coli)
#2: Protein/peptide
Breast cancer type 2 susceptibility


Mass: 3980.434 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P51587*PLUS
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / References: UniProt: P51587*PLUS / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 2.12 Å3/Da / Density % sol: 41.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.5 / Details: 0.2 M NH4Cl, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.966→85.87 Å / Num. obs: 137994 / % possible obs: 99.8 % / Redundancy: 3.8 % / Biso Wilson estimate: 45.47 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.046 / Rrim(I) all: 0.091 / Net I/σ(I): 7.4 / Num. measured all: 522829
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.966-1.9723.92.388554814410.2721.4042.7780.5100
9.121-85.873.50.039502214540.9970.0240.04626.398.3

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Processing

Software
NameVersionClassification
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KDD

5kdd


Resolution: 1.97→85.87 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.894 / SU R Cruickshank DPI: 0.219 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.211 / SU Rfree Blow DPI: 0.167 / SU Rfree Cruickshank DPI: 0.172
RfactorNum. reflection% reflectionSelection details
Rfree0.271 6853 4.97 %RANDOM
Rwork0.263 ---
obs0.263 137876 99.7 %-
Displacement parametersBiso max: 150.89 Å2 / Biso mean: 68.12 Å2 / Biso min: 29.86 Å2
Baniso -1Baniso -2Baniso -3
1--4.2997 Å20 Å217.1159 Å2
2--9.2558 Å20 Å2
3----4.956 Å2
Refine analyzeLuzzati coordinate error obs: 0.5 Å
Refinement stepCycle: final / Resolution: 1.97→85.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13981 0 224 215 14420
Biso mean--59.91 56.49 -
Num. residues----1815
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d5176SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes2543HARMONIC5
X-RAY DIFFRACTIONt_it14373HARMONIC20
X-RAY DIFFRACTIONt_nbd4SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1906SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact16558SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d14373HARMONIC20.011
X-RAY DIFFRACTIONt_angle_deg19352HARMONIC21.28
X-RAY DIFFRACTIONt_omega_torsion2.2
X-RAY DIFFRACTIONt_other_torsion17.24
LS refinement shellResolution: 1.97→1.98 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2812 135 4.89 %
Rwork0.2792 2623 -
all0.2793 2758 -
obs--99.05 %

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