[English] 日本語
Yorodumi
- PDB-5w7x: Crystal Structure of FHA domain of human APLF in complex with XRC... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5w7x
TitleCrystal Structure of FHA domain of human APLF in complex with XRCC1 bisphospho peptide
Components
  • Aprataxin and PNK-like factor
  • DNA repair protein XRCC1
KeywordsPROTEIN BINDING / scaffold protein / DNA repair / NHEJ
Function / homology
Function and homology information


3' overhang single-stranded DNA endodeoxyribonuclease activity / oxidized DNA binding / telomeric DNA-containing double minutes formation / ERCC4-ERCC1 complex / negative regulation of protection from non-homologous end joining at telomere / ADP-D-ribose modification-dependent protein binding / negative regulation of protein ADP-ribosylation / regulation of isotype switching / poly-ADP-D-ribose binding / histone chaperone activity ...3' overhang single-stranded DNA endodeoxyribonuclease activity / oxidized DNA binding / telomeric DNA-containing double minutes formation / ERCC4-ERCC1 complex / negative regulation of protection from non-homologous end joining at telomere / ADP-D-ribose modification-dependent protein binding / negative regulation of protein ADP-ribosylation / regulation of isotype switching / poly-ADP-D-ribose binding / histone chaperone activity / regulation of base-excision repair / regulation of epithelial to mesenchymal transition / single strand break repair / HDR through MMEJ (alt-NHEJ) / response to hydroperoxide / Resolution of AP sites via the single-nucleotide replacement pathway / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / DNA repair-dependent chromatin remodeling / site of DNA damage / protein localization to chromatin / DNA-(apurinic or apyrimidinic site) endonuclease activity / 3'-5' exonuclease activity / embryo implantation / protein folding chaperone / Gap-filling DNA repair synthesis and ligation in GG-NER / DNA endonuclease activity / hippocampus development / base-excision repair / double-strand break repair via nonhomologous end joining / Gap-filling DNA repair synthesis and ligation in TC-NER / double-strand break repair / site of double-strand break / histone binding / Hydrolases; Acting on ester bonds / chromosome, telomeric region / DNA repair / nucleotide binding / DNA damage response / chromatin / nucleolus / enzyme binding / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Aprataxin and PNK-like factor, PBZ domain / Aprataxin and PNK-like factor / DNA-repair protein Xrcc1, N-terminal / XRCC1, first (central) BRCT domain / XRCC1 N terminal domain / PBZ domain / PNK, FHA domain / FHA domain / Tumour Suppressor Smad4 - #20 / BRCT domain ...Aprataxin and PNK-like factor, PBZ domain / Aprataxin and PNK-like factor / DNA-repair protein Xrcc1, N-terminal / XRCC1, first (central) BRCT domain / XRCC1 N terminal domain / PBZ domain / PNK, FHA domain / FHA domain / Tumour Suppressor Smad4 - #20 / BRCT domain / Tumour Suppressor Smad4 / SMAD/FHA domain superfamily / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Galactose-binding-like domain superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
DNA repair protein XRCC1 / Aprataxin and PNK-like factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.005 Å
AuthorsPedersen, L.C. / Kim, K. / London, R.E.
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: Characterization of the APLF FHA-XRCC1 phosphopeptide interaction and its structural and functional implications.
Authors: Kim, K. / Pedersen, L.C. / Kirby, T.W. / DeRose, E.F. / London, R.E.
History
DepositionJun 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
D: Aprataxin and PNK-like factor
A: Aprataxin and PNK-like factor
B: Aprataxin and PNK-like factor
C: Aprataxin and PNK-like factor
H: DNA repair protein XRCC1
E: DNA repair protein XRCC1
F: DNA repair protein XRCC1
G: DNA repair protein XRCC1


Theoretical massNumber of molelcules
Total (without water)52,1398
Polymers52,1398
Non-polymers00
Water4,666259
1
D: Aprataxin and PNK-like factor
H: DNA repair protein XRCC1


Theoretical massNumber of molelcules
Total (without water)13,0352
Polymers13,0352
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area840 Å2
ΔGint-4 kcal/mol
Surface area6100 Å2
MethodPISA
2
A: Aprataxin and PNK-like factor
E: DNA repair protein XRCC1


Theoretical massNumber of molelcules
Total (without water)13,0352
Polymers13,0352
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area890 Å2
ΔGint-5 kcal/mol
Surface area6130 Å2
MethodPISA
3
B: Aprataxin and PNK-like factor
F: DNA repair protein XRCC1


Theoretical massNumber of molelcules
Total (without water)13,0352
Polymers13,0352
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area770 Å2
ΔGint-5 kcal/mol
Surface area5940 Å2
MethodPISA
4
C: Aprataxin and PNK-like factor
G: DNA repair protein XRCC1


Theoretical massNumber of molelcules
Total (without water)13,0352
Polymers13,0352
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area760 Å2
ΔGint-5 kcal/mol
Surface area6110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.119, 36.799, 98.284
Angle α, β, γ (deg.)90.00, 90.86, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Aprataxin and PNK-like factor / Apurinic-apyrimidinic endonuclease APLF / PNK and APTX-like FHA domain-containing protein / XRCC1- ...Apurinic-apyrimidinic endonuclease APLF / PNK and APTX-like FHA domain-containing protein / XRCC1-interacting protein 1


Mass: 11921.815 Da / Num. of mol.: 4 / Fragment: UNP residues 1-105
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APLF, C2orf13, PALF, XIP1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8IW19, DNA-(apurinic or apyrimidinic site) lyase
#2: Protein/peptide
DNA repair protein XRCC1 / X-ray repair cross-complementing protein 1


Mass: 1112.878 Da / Num. of mol.: 4 / Fragment: UNP residues 514-522 / Source method: obtained synthetically / Details: bisphosphopeptide of XRCC1 / Source: (synth.) Homo sapiens (human) / References: UniProt: P18887
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 40.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.6mM XRCC1 bisphosphopeptide 0.6mM APLF 0.5M lithium chloride 0.1M Tris 28% PEG 6000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.514 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Nov 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.514 Å / Relative weight: 1
ReflectionResolution: 2.005→25.497 Å / Num. obs: 28032 / % possible obs: 97.9 % / Redundancy: 4.8 % / Rpim(I) all: 0.031 / Rsym value: 0.065 / Net I/σ(I): 13.4
Reflection shellResolution: 2.005→2.05 Å / Redundancy: 2.4 % / Num. unique obs: 1098 / Rpim(I) all: 0.214 / Rsym value: 0.295 / % possible all: 75.3

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5W7W

5w7w


Resolution: 2.005→25.497 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.24
RfactorNum. reflection% reflectionSelection details
Rfree0.2291 1390 4.97 %random
Rwork0.1922 ---
obs0.194 27941 96.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.005→25.497 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3347 0 0 259 3606
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033462
X-RAY DIFFRACTIONf_angle_d0.5814722
X-RAY DIFFRACTIONf_dihedral_angle_d18.6011296
X-RAY DIFFRACTIONf_chiral_restr0.045514
X-RAY DIFFRACTIONf_plane_restr0.004610
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0054-2.0770.28881000.2431926X-RAY DIFFRACTION71
2.077-2.16020.26951430.22012702X-RAY DIFFRACTION99
2.1602-2.25840.2391480.20242696X-RAY DIFFRACTION100
2.2584-2.37740.28971360.21612739X-RAY DIFFRACTION100
2.3774-2.52620.30331460.23312704X-RAY DIFFRACTION100
2.5262-2.72110.35231400.24542713X-RAY DIFFRACTION99
2.7211-2.99450.28051450.23932704X-RAY DIFFRACTION99
2.9945-3.42690.23231480.19662729X-RAY DIFFRACTION100
3.4269-4.31420.17611370.1572781X-RAY DIFFRACTION100
4.3142-25.49890.19111470.16862857X-RAY DIFFRACTION99

+
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://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