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- PDB-3k16: Crystal Structure of BRCA1 BRCT D1840T in complex with a minimal ... -

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Basic information

Entry
Database: PDB / ID: 3k16
TitleCrystal Structure of BRCA1 BRCT D1840T in complex with a minimal recognition tetrapeptide with a free carboxy C-terminus
Components
  • Breast cancer type 1 susceptibility protein
  • phospho peptide
KeywordsISOMERASE / BRCA1 / BRCT domain / DNA damage response / phospho peptide interactions / Abraxas / Alternative initiation / Cell cycle / Disease mutation / DNA damage / DNA repair / DNA-binding / Fatty acid biosynthesis / Ligase / Lipid synthesis / Metal-binding / Nucleus / Phosphoprotein / Tumor suppressor / Ubl conjugation pathway / Zinc-finger
Function / homology
Function and homology information


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 / BRCA1-C complex / BRCA1-B complex / BRCA1-A complex / negative regulation of centriole replication / sex-chromosome dosage compensation / random inactivation of X chromosome / negative regulation of intracellular estrogen receptor signaling pathway ...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 / BRCA1-C complex / BRCA1-B complex / BRCA1-A complex / negative regulation of centriole replication / sex-chromosome dosage compensation / random inactivation of X chromosome / negative regulation of intracellular estrogen receptor signaling pathway / gamma-tubulin ring complex / nuclear ubiquitin ligase complex / chordate embryonic development / negative regulation of fatty acid biosynthetic process / cellular response to indole-3-methanol / DNA strand resection involved in replication fork processing / homologous recombination / lateral element / protein K6-linked ubiquitination / regulation of DNA damage checkpoint / Impaired BRCA2 binding to PALB2 / XY body / mitotic G2/M transition checkpoint / DNA repair complex / centrosome cycle / postreplication repair / RNA polymerase binding / 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 / HDR through Single Strand Annealing (SSA) / DNA-binding transcription activator activity / Impaired BRCA2 binding to RAD51 / negative regulation of gene expression via chromosomal CpG island methylation / intracellular membraneless organelle / response to ionizing radiation / mitotic G2 DNA damage checkpoint signaling / Transcriptional Regulation by E2F6 / Presynaptic phase of homologous DNA pairing and strand exchange / negative regulation of cell cycle / positive regulation of vascular endothelial growth factor production / negative regulation of reactive oxygen species metabolic process / protein autoubiquitination / regulation of DNA repair / SUMOylation of DNA damage response and repair proteins / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / ubiquitin ligase complex / Meiotic synapsis / positive regulation of DNA repair / tubulin binding / male germ cell nucleus / chromosome segregation / cellular response to ionizing radiation / TP53 Regulates Transcription of DNA Repair Genes / Nonhomologous End-Joining (NHEJ) / double-strand break repair via homologous recombination / RING-type E3 ubiquitin transferase / G2/M DNA damage checkpoint / negative regulation of cell growth / HDR through Homologous Recombination (HRR) / Meiotic recombination / Metalloprotease DUBs / fatty acid biosynthetic process / positive regulation of angiogenesis / ubiquitin-protein transferase activity / intrinsic apoptotic signaling pathway in response to DNA damage / KEAP1-NFE2L2 pathway / p53 binding / double-strand break repair / cellular response to tumor necrosis factor / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromosome / Neddylation / Processing of DNA double-strand break ends / Regulation of TP53 Activity through Phosphorylation / damaged DNA binding / transcription coactivator activity / transcription cis-regulatory region binding / regulation of cell cycle / nuclear body / protein ubiquitination / ribonucleoprotein complex / DNA repair / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / DNA damage response / positive regulation of gene expression / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / enzyme binding / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA binding / zinc ion binding / nucleoplasm / identical protein binding
Similarity search - Function
Breast cancer type 1 susceptibility protein (BRCA1) / BRCA1, serine-rich domain / BRCA1-associated / Serine-rich domain associated with BRCT / BRCT domain / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / Zinc finger, RING-type, conserved site ...Breast cancer type 1 susceptibility protein (BRCA1) / BRCA1, serine-rich domain / BRCA1-associated / Serine-rich domain associated with BRCT / BRCT domain / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / Breast cancer type 1 susceptibility protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsCampbell, S.J. / Edwards, R.A. / Glover, J.N.
CitationJournal: Structure / Year: 2010
Title: Comparison of the Structures and Peptide Binding Specificities of the BRCT Domains of MDC1 and BRCA1
Authors: Campbell, S.J. / Edwards, R.A. / Glover, J.N.
History
DepositionSep 25, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Breast cancer type 1 susceptibility protein
B: phospho peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2734
Polymers25,1792
Non-polymers942
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint-25 kcal/mol
Surface area11220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.337, 114.337, 123.867
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Breast cancer type 1 susceptibility protein / RING finger protein 53


Mass: 24648.449 Da / Num. of mol.: 1 / Fragment: BRCT Domain / Mutation: D1840T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRCA1, RNF53 / Plasmid: pLM1-CD6 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold
References: UniProt: P38398, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein/peptide phospho peptide


Mass: 530.464 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Sequence occurs naturally in humans in the Abraxas/CCDC98 protein. Synthesized by the Alberta Peptide Institute.
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
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: 4.67 Å3/Da / Density % sol: 73.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8.5
Details: Li2SO4, Tris-HCl, NiCl2, pH 8.5, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97934 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jul 15, 2008
RadiationMonochromator: DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.95→38.66 Å / Num. obs: 10632 / % possible obs: 99.6 % / Redundancy: 19.7 % / Rmerge(I) obs: 0.084 / Χ2: 0.989 / Net I/σ(I): 10.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.95-3.0610.70.6759840.642196.1
3.06-3.1817.80.46610480.6621100
3.18-3.3221.10.33910320.7031100
3.32-3.521.70.22710430.7791100
3.5-3.7221.60.15410460.9131100
3.72-421.50.10610581.0511100
4-4.4121.40.08810661.2741100
4.41-5.0420.90.08110661.3161100
5.04-6.3520.70.06911011.1991100
6.35-5018.90.04311881.091199.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 47.24 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.94 Å38.67 Å
Translation2.94 Å38.67 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→38.66 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.91 / WRfactor Rfree: 0.287 / WRfactor Rwork: 0.215 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.771 / SU B: 38.12 / SU ML: 0.327 / SU R Cruickshank DPI: 0.557 / SU Rfree: 0.375 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.557 / ESU R Free: 0.375 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.288 480 4.8 %RANDOM
Rwork0.224 ---
obs0.227 10051 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 114.09 Å2 / Biso mean: 57.243 Å2 / Biso min: 22.43 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å2-0.21 Å20 Å2
2---0.42 Å20 Å2
3---0.63 Å2
Refinement stepCycle: LAST / Resolution: 3→38.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1730 0 2 6 1738
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0221774
X-RAY DIFFRACTIONr_angle_refined_deg1.0641.9442406
X-RAY DIFFRACTIONr_dihedral_angle_1_deg12.1695213
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.79223.7882
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.77415.049304
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.3741511
X-RAY DIFFRACTIONr_chiral_restr0.0720.2268
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0211332
X-RAY DIFFRACTIONr_mcbond_it1.2291.51072
X-RAY DIFFRACTIONr_mcangle_it2.33221746
X-RAY DIFFRACTIONr_scbond_it3.2993702
X-RAY DIFFRACTIONr_scangle_it5.5334.5660
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.446 34 -
Rwork0.322 680 -
all-714 -
obs--99.44 %
Refinement TLS params.Method: refined / Origin x: -18.919 Å / Origin y: 48.8269 Å / Origin z: -4.003 Å
111213212223313233
T0.0549 Å20.0147 Å20.0267 Å2-0.4555 Å20.0939 Å2--0.0341 Å2
L14.6258 °22.8701 °2-1.3389 °2-2.9684 °2-0.9515 °2--1.4052 °2
S-0.116 Å °1.4749 Å °0.1349 Å °-0.2535 Å °0.066 Å °-0.1855 Å °0.2517 Å °-0.2305 Å °0.05 Å °

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