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- PDB-8rs8: Crystal structure of BRCA1 BRCTs in complex with a RIF1 phosphopeptide -

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Basic information

Entry
Database: PDB / ID: 8rs8
TitleCrystal structure of BRCA1 BRCTs in complex with a RIF1 phosphopeptide
Components
  • Breast cancer type 1 susceptibility protein
  • Telomere-associated protein RIF1
KeywordsPEPTIDE BINDING PROTEIN / DNA damage repair
Function / homology
Function and homology information


histone H2AK127 ubiquitin ligase activity / histone H2AK129 ubiquitin ligase activity / Defective DNA double strand break response due to BRCA1 loss of function / Defective DNA double strand break response due to BARD1 loss of function / BRCA1-BARD1 complex / chromosome, telomeric repeat region / BRCA1-C complex / BRCA1-B complex / BRCA1-A complex / negative regulation of centriole replication ...histone H2AK127 ubiquitin ligase activity / histone H2AK129 ubiquitin ligase activity / Defective DNA double strand break response due to BRCA1 loss of function / Defective DNA double strand break response due to BARD1 loss of function / BRCA1-BARD1 complex / chromosome, telomeric repeat region / BRCA1-C complex / BRCA1-B complex / BRCA1-A complex / negative regulation of centriole replication / sex-chromosome dosage compensation / negative regulation of intracellular estrogen receptor signaling pathway / random inactivation of X chromosome / nuclear ubiquitin ligase complex / ubiquitin-modified histone reader activity / chordate embryonic development / positive regulation of isotype switching / cellular response to indole-3-methanol / gamma-tubulin ring complex / negative regulation of fatty acid biosynthetic process / DNA strand resection involved in replication fork processing / homologous recombination / lateral element / Regulation of MITF-M-dependent genes involved in DNA replication, damage repair and senescence / protein K6-linked ubiquitination / regulation of DNA damage checkpoint / Impaired BRCA2 binding to PALB2 / XY body / mitotic G2/M transition checkpoint / male pronucleus / female pronucleus / centrosome cycle / RNA polymerase binding / postreplication repair / DNA repair complex / Homologous DNA Pairing and Strand Exchange / 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 / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / Resolution of D-loop Structures through Holliday Junction Intermediates / intracellular membraneless organelle / HDR through Single Strand Annealing (SSA) / response to ionizing radiation / negative regulation of gene expression via chromosomal CpG island methylation / positive regulation of double-strand break repair via nonhomologous end joining / Impaired BRCA2 binding to RAD51 / negative regulation of gene expression, epigenetic / mitotic G2 DNA damage checkpoint signaling / Transcriptional Regulation by E2F6 / telomere maintenance in response to DNA damage / negative regulation of cell cycle / negative regulation of reactive oxygen species metabolic process / Presynaptic phase of homologous DNA pairing and strand exchange / positive regulation of vascular endothelial growth factor production / somatic stem cell population maintenance / ubiquitin ligase complex / spindle midzone / negative regulation of double-strand break repair via homologous recombination / subtelomeric heterochromatin formation / SUMOylation of DNA damage response and repair proteins / regulation of DNA repair / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / protein autoubiquitination / condensed chromosome / Meiotic synapsis / telomere maintenance / tubulin binding / positive regulation of DNA repair / male germ cell nucleus / cellular response to leukemia inhibitory factor / cellular response to ionizing radiation / chromosome segregation / Nonhomologous End-Joining (NHEJ) / TP53 Regulates Transcription of DNA Repair Genes / double-strand break repair via homologous recombination / G2/M DNA damage checkpoint / negative regulation of cell growth / RING-type E3 ubiquitin transferase / Meiotic recombination / HDR through Homologous Recombination (HRR) / Metalloprotease DUBs / positive regulation of angiogenesis / intrinsic apoptotic signaling pathway in response to DNA damage / fatty acid biosynthetic process / ubiquitin-protein transferase activity / KEAP1-NFE2L2 pathway / p53 binding / cellular response to tumor necrosis factor / double-strand break repair / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / site of double-strand break / chromosome / Neddylation / Processing of DNA double-strand break ends / nuclear membrane / Regulation of TP53 Activity through Phosphorylation / damaged DNA binding / transcription coactivator activity / transcription cis-regulatory region binding
Similarity search - Function
Telomere-associated protein Rif1, N-terminal / Rap1-interacting factor 1 N terminal / Breast cancer type 1 susceptibility protein (BRCA1) / BRCA1, serine-rich domain / BRCA1-associated / Serine-rich domain associated with BRCT / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain ...Telomere-associated protein Rif1, N-terminal / Rap1-interacting factor 1 N terminal / Breast cancer type 1 susceptibility protein (BRCA1) / BRCA1, serine-rich domain / BRCA1-associated / Serine-rich domain associated with BRCT / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Armadillo-like helical / Armadillo-type fold / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
IMIDAZOLE / DI(HYDROXYETHYL)ETHER / Breast cancer type 1 susceptibility protein / Telomere-associated protein RIF1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.31 Å
AuthorsDay, M. / Pearl, L.H. / Oliver, A.W.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cancer Research UKC302/A24386 United Kingdom
CitationJournal: Nat Commun / Year: 2025
Title: The human RIF1-Long isoform interacts with BRCA1 to promote recombinational fork repair under DNA replication stress.
Authors: Dong, Q. / Day, M. / Saito, Y. / Parker, E. / Watts, L.P. / Kanemaki, M.T. / Oliver, A.W. / Pearl, L.H. / Hiraga, S.I. / Donaldson, A.D.
History
DepositionJan 24, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Breast cancer type 1 susceptibility protein
B: Breast cancer type 1 susceptibility protein
C: Breast cancer type 1 susceptibility protein
D: Breast cancer type 1 susceptibility protein
E: Telomere-associated protein RIF1
F: Telomere-associated protein RIF1
G: Telomere-associated protein RIF1
H: Telomere-associated protein RIF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,67248
Polymers104,1318
Non-polymers2,54140
Water18,0331001
1
A: Breast cancer type 1 susceptibility protein
E: Telomere-associated protein RIF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,59111
Polymers26,0332
Non-polymers5599
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Breast cancer type 1 susceptibility protein
F: Telomere-associated protein RIF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,53610
Polymers26,0332
Non-polymers5048
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Breast cancer type 1 susceptibility protein
G: Telomere-associated protein RIF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,01517
Polymers26,0332
Non-polymers98215
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Breast cancer type 1 susceptibility protein
H: Telomere-associated protein RIF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,52910
Polymers26,0332
Non-polymers4978
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.840, 173.716, 74.522
Angle α, β, γ (deg.)90.000, 89.050, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein / Protein/peptide , 2 types, 8 molecules ABCDEFGH

#1: Protein
Breast cancer type 1 susceptibility protein / RING finger protein 53 / RING-type E3 ubiquitin transferase BRCA1


Mass: 24772.480 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRCA1, RNF53 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P38398, RING-type E3 ubiquitin transferase
#2: Protein/peptide
Telomere-associated protein RIF1 / Rap1-interacting factor 1 homolog


Mass: 1260.314 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q5UIP0

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Non-polymers , 4 types, 1041 molecules

#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 37 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1001 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.29 Å3/Da / Density % sol: 46.28 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop
Details: 55.5 mM MES, 44.5 mM Imidazole, 120 mM Diethylene glycol, 120 mM Triethylene-glycol, 120 mM Tetraethylene glycol, 120 mM Pentaethylene glycol, 20% (v/v) Ethylene glycol, 10% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.918 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.31→56.55 Å / Num. obs: 219241 / % possible obs: 98.06 % / Redundancy: 2.6 % / Biso Wilson estimate: 18.63 Å2 / CC1/2: 0.995 / Net I/σ(I): 9.12
Reflection shellResolution: 1.31→1.357 Å / Num. unique obs: 20958 / CC1/2: 0.326

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.31→56.55 Å / SU ML: 0.1824 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.5828
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1787 10833 4.95 %
Rwork0.141 208162 -
obs0.1428 218995 98.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.03 Å2
Refinement stepCycle: LAST / Resolution: 1.31→56.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7034 0 165 1001 8200
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00867640
X-RAY DIFFRACTIONf_angle_d1.008510302
X-RAY DIFFRACTIONf_chiral_restr0.0821105
X-RAY DIFFRACTIONf_plane_restr0.00751322
X-RAY DIFFRACTIONf_dihedral_angle_d14.26642847
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.31-1.320.3773280.34926402X-RAY DIFFRACTION91.37
1.32-1.340.36333130.33476559X-RAY DIFFRACTION93.22
1.34-1.360.34723500.316790X-RAY DIFFRACTION94.39
1.36-1.370.31583290.29676687X-RAY DIFFRACTION94.48
1.37-1.390.30593390.26876631X-RAY DIFFRACTION94.97
1.39-1.410.29423310.25866743X-RAY DIFFRACTION94.23
1.41-1.430.30133520.24436442X-RAY DIFFRACTION91.67
1.43-1.450.28513920.23016947X-RAY DIFFRACTION99.22
1.45-1.480.26643600.227091X-RAY DIFFRACTION99.14
1.48-1.50.25393820.22166902X-RAY DIFFRACTION98.97
1.5-1.530.27643510.21837070X-RAY DIFFRACTION98.81
1.53-1.550.25993520.1916992X-RAY DIFFRACTION99.06
1.55-1.580.24213760.16256980X-RAY DIFFRACTION99.18
1.58-1.620.1933250.14147079X-RAY DIFFRACTION99.24
1.62-1.650.19533750.12837012X-RAY DIFFRACTION99.65
1.65-1.690.16743400.11917101X-RAY DIFFRACTION99.79
1.69-1.730.17343790.11747028X-RAY DIFFRACTION99.76
1.73-1.780.1833690.12017041X-RAY DIFFRACTION99.7
1.78-1.830.18783750.12597051X-RAY DIFFRACTION99.49
1.83-1.890.17413840.12346998X-RAY DIFFRACTION99.43
1.89-1.960.15973540.11177087X-RAY DIFFRACTION99.4
1.96-2.040.1563830.10487036X-RAY DIFFRACTION99.81
2.04-2.130.16353700.10697060X-RAY DIFFRACTION99.91
2.13-2.240.15554000.10727023X-RAY DIFFRACTION99.84
2.24-2.380.14033840.10687009X-RAY DIFFRACTION99.56
2.38-2.560.15773800.11417066X-RAY DIFFRACTION99.6
2.56-2.820.16463700.12077122X-RAY DIFFRACTION99.79
2.82-3.230.16373590.13497013X-RAY DIFFRACTION99.26
3.23-4.070.15653760.13377099X-RAY DIFFRACTION99.61
4.07-56.550.17683550.16177101X-RAY DIFFRACTION99.08

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