[English] 日本語
Yorodumi
- PDB-1t15: Crystal Structure of the Brca1 BRCT Domains in Complex with the P... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1t15
TitleCrystal Structure of the Brca1 BRCT Domains in Complex with the Phosphorylated Interacting Region from Bach1 Helicase
Components
  • BRCA1 interacting protein C-terminal helicase 1
  • Breast cancer type 1 susceptibility protein
KeywordsANTITUMOR PROTEIN / Protein-Peptide Complex
Function / homology
Function and homology information


meiotic DNA double-strand break processing involved in reciprocal meiotic recombination / cellular response to vitamin / chiasma assembly / Defective DNA double strand break response due to BRCA1 loss of function / Defective DNA double strand break response due to BARD1 loss of function / spermatogonial cell division / BRCA1-BARD1 complex / BRCA1-C complex / BRCA1-B complex / BRCA1-A complex ...meiotic DNA double-strand break processing involved in reciprocal meiotic recombination / cellular response to vitamin / chiasma assembly / Defective DNA double strand break response due to BRCA1 loss of function / Defective DNA double strand break response due to BARD1 loss of function / spermatogonial cell division / BRCA1-BARD1 complex / BRCA1-C complex / BRCA1-B complex / BRCA1-A complex / random inactivation of X chromosome / negative regulation of centriole replication / sex-chromosome dosage compensation / negative regulation of intracellular estrogen receptor signaling pathway / Cytosolic iron-sulfur cluster assembly / gamma-tubulin ring complex / double-strand break repair involved in meiotic recombination / nuclear ubiquitin ligase complex / DNA strand resection involved in replication fork processing / chordate embryonic development / cellular response to indole-3-methanol / negative regulation of fatty acid biosynthetic process / homologous recombination / lateral element / protein K6-linked ubiquitination / regulation of DNA damage checkpoint / Impaired BRCA2 binding to PALB2 / XY body / protein-DNA covalent cross-linking repair / mitotic G2/M transition checkpoint / cellular response to angiotensin / postreplication repair / DNA repair complex / RNA polymerase binding / centrosome cycle / 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) / Resolution of D-loop Structures through Holliday Junction Intermediates / negative regulation of gene expression via chromosomal CpG island methylation / intracellular non-membrane-bounded organelle / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 / DNA-binding transcription activator activity / response to ionizing radiation / seminiferous tubule development / Transcriptional Regulation by E2F6 / mitotic G2 DNA damage checkpoint signaling / Presynaptic phase of homologous DNA pairing and strand exchange / negative regulation of cell cycle / spermatid development / positive regulation of vascular endothelial growth factor production / negative regulation of reactive oxygen species metabolic process / localization / 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 / DNA helicase activity / Meiotic synapsis / positive regulation of DNA repair / tubulin binding / DNA damage checkpoint signaling / male germ cell nucleus / chromosome segregation / cellular response to ionizing radiation / nucleotide-excision repair / TP53 Regulates Transcription of DNA Repair Genes / Nonhomologous End-Joining (NHEJ) / double-strand break repair via homologous recombination / RING-type E3 ubiquitin transferase / HDR through Homologous Recombination (HRR) / G2/M DNA damage checkpoint / negative regulation of cell growth / response to toxic substance / Metalloprotease DUBs / Meiotic recombination / fatty acid biosynthetic process / ubiquitin-protein transferase activity / positive regulation of angiogenesis / intrinsic apoptotic signaling pathway in response to DNA damage / KEAP1-NFE2L2 pathway / double-strand break repair / p53 binding / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromosome / cellular response to tumor necrosis factor / Neddylation / Processing of DNA double-strand break ends / 4 iron, 4 sulfur cluster binding / 5'-3' DNA helicase activity / cellular response to hypoxia / nuclear membrane / DNA helicase / Regulation of TP53 Activity through Phosphorylation / damaged DNA binding / RNA helicase activity
Similarity search - Function
Breast cancer type 1 susceptibility protein (BRCA1) / BRCA1, serine-rich domain / BRCA1-associated / Serine-rich domain associated with BRCT / BRCT domain / ATP-dependent helicase Rad3/Chl1-like / Helicase superfamily 1/2, DinG/Rad3-like / Helicase-like, DEXD box c2 type / ATP-dependent helicase, C-terminal / DEAD2 ...Breast cancer type 1 susceptibility protein (BRCA1) / BRCA1, serine-rich domain / BRCA1-associated / Serine-rich domain associated with BRCT / BRCT domain / ATP-dependent helicase Rad3/Chl1-like / Helicase superfamily 1/2, DinG/Rad3-like / Helicase-like, DEXD box c2 type / ATP-dependent helicase, C-terminal / DEAD2 / Helicase superfamily 1/2, ATP-binding domain, DinG/Rad3-type / DEAD_2 / Helicase C-terminal domain / Superfamilies 1 and 2 helicase ATP-binding type-2 domain profile. / DEXDc2 / HELICc2 / 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 / DEAD-like helicases superfamily / Helicase superfamily 1/2, ATP-binding domain / Zinc finger, RING/FYVE/PHD-type / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Breast cancer type 1 susceptibility protein / Fanconi anemia group J protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsClapperton, J.A. / Manke, I.A. / Lowery, D.M. / Ho, T. / Haire, L.F. / Yaffe, M.B. / Smerdon, S.J.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2004
Title: Structure and mechanism of BRCA1 BRCT domain recognition of phosphorylated BACH1 with implications for cancer
Authors: Clapperton, J.A. / Manke, I.A. / Lowery, D.M. / Ho, T. / Haire, L.F. / Yaffe, M.B. / Smerdon, S.J.
History
DepositionApr 15, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Breast cancer type 1 susceptibility protein
B: BRCA1 interacting protein C-terminal helicase 1


Theoretical massNumber of molelcules
Total (without water)25,4932
Polymers25,4932
Non-polymers00
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-6 kcal/mol
Surface area11240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.837, 65.837, 93.075
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein Breast cancer type 1 susceptibility protein


Mass: 24531.234 Da / Num. of mol.: 1 / Fragment: BCRT 1, BCRT 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRCA1 / Plasmid: pGEX-4T1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P38398
#2: Protein/peptide BRCA1 interacting protein C-terminal helicase 1


Mass: 961.929 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: GenBank: 14042978, UniProt: Q9BX63*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.13 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 6.5
Details: PEG 8000, Ammonium Sulphate, MES, pH 6.5, Microbatch, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jan 17, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.85→15 Å / Num. all: 20529 / Num. obs: 19219 / % possible obs: 93.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2.5
Reflection shellResolution: 1.85→1.93 Å / % possible all: 76.8

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→15 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.222 972 5.1 %Random
Rwork0.206 ---
all-20484 --
obs-18242 --
Refinement stepCycle: LAST / Resolution: 1.85→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1750 0 0 156 1906
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.01
X-RAY DIFFRACTIONr_angle_refined_deg1.35

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more