2KQE

Second PBZ domain of human APLF protein in complex with ribofuranosyladenosine

• PDB DOI: https://doi.org/10.2210/pdb2KQE/pdb
• BMRB: 16596

• Classification: LYASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-11-04 Released: 2010-01-19 
• Deposition Author(s): Neuhaus, D., Eustermann, S., Brockmann, C., Yang, J.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Literature

Solution structures of the two PBZ domains from human APLF and their interaction with poly(ADP-ribose).

Eustermann, S., Brockmann, C., Mehrotra, P.V., Yang, J.C., Loakes, D., West, S.C., Ahel, I., Neuhaus, D.

(2010) Nat Struct Mol Biol 17: 241-243

• PubMed: 20098424 
• DOI: https://doi.org/10.1038/nsmb.1747
• Primary Citation of Related Structures:  
  2KQB, 2KQC, 2KQE


• PubMed Abstract: 
  

  Addition of poly(ADP-ribose) (PAR) is an important post-translational modification in higher eukaryotes. Several DNA repair and checkpoint proteins possess specific PAR-binding zinc-finger (PBZ) modules critical for function. Here, we present solution structures of the two PBZ modules of aprataxin and PNK-like factor (APLF), revealing a novel type of zinc finger. By combining in vivo PAR-binding data with NMR interaction data using PAR fragments, we propose a structural basis for PBZ-PAR recognition.

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Organizational Affiliation: 

MRC Laboratory of Molecular Biology, Cambridge, UK.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 10.54 kDa 
• Atom Count: 410 
• Modelled Residue Count: 47 
• Deposited Residue Count: 89 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aprataxin and PNK-like factor	A	89	Homo sapiens	Mutation(s): 0  Gene Names: APLF, C2orf13, PALF, XIP1 EC: 4.2.99.18
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IW19 (Homo sapiens) Explore Q8IW19  Go to UniProtKB:  Q8IW19
PHAROS:  Q8IW19 GTEx:  ENSG00000169621

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADN	C [auth A]	ADENOSINE C10 H13 N5 O4 OIRDTQYFTABQOQ-KQYNXXCUSA-N
RIB	D [auth A]	alpha-D-ribofuranose C5 H10 O5 HMFHBZSHGGEWLO-AIHAYLRMSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-01-19 
Deposition Author(s): Neuhaus, D., Eustermann, S., Brockmann, C., Yang, J.

Revision History  

• Version 1.0: 2010-01-19
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary