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- PDB-2kqe: Second PBZ domain of human APLF protein in complex with ribofuran... -

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Basic information

Entry
Database: PDB / ID: 2kqe
TitleSecond PBZ domain of human APLF protein in complex with ribofuranosyladenosine
ComponentsAprataxin and PNK-like factor
KeywordsLYASE / ADP-ribosylation / DNA damage / DNA repair / Metal-binding / Nucleotide-binding / Nucleus / Zinc / Zinc-finger
Function / homology
Function and homology information


ADP-D-ribose modification-dependent protein binding / regulation of isotype switching / poly-ADP-D-ribose binding / histone chaperone activity / positive regulation of DNA ligation / regulation of epithelial to mesenchymal transition / single strand break repair / DNA repair-dependent chromatin remodeling / site of DNA damage / DNA-(apurinic or apyrimidinic site) endonuclease activity ...ADP-D-ribose modification-dependent protein binding / regulation of isotype switching / poly-ADP-D-ribose binding / histone chaperone activity / positive regulation of DNA ligation / regulation of epithelial to mesenchymal transition / single strand break repair / DNA repair-dependent chromatin remodeling / site of DNA damage / DNA-(apurinic or apyrimidinic site) endonuclease activity / protein localization to chromatin / protein folding chaperone / 3'-5' exonuclease activity / embryo implantation / DNA endonuclease activity / double-strand break repair via nonhomologous end joining / double-strand break repair / site of double-strand break / histone binding / Hydrolases; Acting on ester bonds / DNA repair / nucleotide binding / DNA damage response / nucleoplasm / nucleus / metal ion binding / cytosol
Similarity search - Function
Aprataxin and PNK-like factor, PBZ domain / Aprataxin and PNK-like factor / PBZ domain / PNK, FHA domain / FHA domain / SMAD/FHA domain superfamily
Similarity search - Domain/homology
ADENOSINE / alpha-D-ribofuranose / Aprataxin and PNK-like factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsNeuhaus, D. / Eustermann, S. / Brockmann, C. / Yang, J.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Solution structures of the two PBZ domains from human APLF and their interaction with poly(ADP-ribose).
Authors: Eustermann, S. / Brockmann, C. / Mehrotra, P.V. / Yang, J.C. / Loakes, D. / West, S.C. / Ahel, I. / Neuhaus, D.
History
DepositionNov 4, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_nmr_spectrometer.model / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.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_type.id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Remark 650 HELIX DETERMINATION METHOD: AUTHOR

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aprataxin and PNK-like factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5364
Polymers10,0531
Non-polymers4833
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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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: 10053.062 Da / Num. of mol.: 1
Fragment: sequence database residues 363-451, PBZ-type 2 domain
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: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O4
#4: Sugar ChemComp-RIB / alpha-D-ribofuranose / alpha-D-ribose / D-ribose / ribose


Type: D-saccharide, alpha linking / Mass: 150.130 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
IdentifierTypeProgram
DRibfaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-ribofuranoseCOMMON NAMEGMML 1.0
a-D-RibfIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
RibSNFG CARBOHYDRATE SYMBOLGMML 1.0
Compound detailsRESIDUES 363-404 ARE NOT SHOWN IN THE COORDINATES BECAUSE STRUCTURE CALCULATIONS WERE CARRIED OUT ...RESIDUES 363-404 ARE NOT SHOWN IN THE COORDINATES BECAUSE STRUCTURE CALCULATIONS WERE CARRIED OUT ON RESIDUES 405-451 ONLY.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
3112D 1H-15N HSQC
1222D 1H-13C HSQC full-width
1322D 1H-1H NOESY
1422D 1H-1H NOESY filtered
1523D 1H-13C NOESY
1622D 1H-1H TOCSY
2722D 1H-13C HSQC full-width
2822D 1H-1H NOESY
2922D 1H-1H NOESY filtered
21023D 1H-13C NOESY
21122D 1H-1H TOCSY
NMR detailsText: The author states that NMR was carried out on a single fragment (363-451) containing both fingers F1 and F2 of APLF, but the structure calculations were carried out separately for each finger. ...Text: The author states that NMR was carried out on a single fragment (363-451) containing both fingers F1 and F2 of APLF, but the structure calculations were carried out separately for each finger. This co-ordinate file includes residues 405-451 and contains F2 as well as the unstructured regions on either side.

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Sample preparation

Details
Solution-IDContentsSolvent system
120 mM potassium pyrophosphate, 200 mM sodium chloride, 100 uM zinc sulphate, 2 mM [U-2H] DTT, 0.8 mM [U-98% 13C; U-98% 15N] APLF_363-451, 2 mM RFA, 95% H2O/5% D2O95% H2O/5% D2O
220 mM potassium pyrophosphate, 200 mM sodium chloride, 100 uM zinc sulphate, 2 mM [U-2H] DTT, 0.8 mM [U-98% 13C; U-98% 15N] APLF_363-451, 2 mM RFA, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMpotassium pyrophosphate-11
200 mMsodium chloride-21
100 uMzinc sulphate-31
2 mMDTT-4[U-2H]1
0.8 mMAPLF_363-451-5[U-98% 13C; U-98% 15N]1
2 mMRFA-61
20 mMpotassium pyrophosphate-72
200 mMsodium chloride-82
100 uMzinc sulphate-92
2 mMDTT-10[U-2H]2
0.8 mMAPLF_363-451-11[U-98% 13C; U-98% 15N]2
2 mMRFA-122
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.46ambient 278 K
20.46ambient 286 K
30.46ambient 300 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker DMXBrukerDMX6002
Bruker DRXBrukerDRX5003

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Processing

NMR software
NameDeveloperClassification
XPLOR-NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
XPLOR-NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsProtein chi angle constraints total count: 8 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 5 / Protein psi angle constraints total count: 5
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 10 / Maximum torsion angle constraint violation: 9.6 ° / Maximum upper distance constraint violation: 0.71 Å / Torsion angle constraint violation method: XPLOR-NIH

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