3ROG

Crystal Structure of Mouse Apolipoprotein A-I Binding Protein in Complex with Thymidine 3'-monophosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Identification of unknown protein function using metabolite cocktail screening.

Shumilin, I.A.Cymborowski, M.Chertihin, O.Jha, K.N.Herr, J.C.Lesley, S.A.Joachimiak, A.Minor, W.

(2012) Structure 20: 1715-1725

  • DOI: https://doi.org/10.1016/j.str.2012.07.016
  • Primary Citation of Related Structures:  
    3RNO, 3RO7, 3ROE, 3ROG, 3ROX, 3ROZ, 3RPH, 3RPZ, 3RQ2, 3RQ5, 3RQ6, 3RQ8, 3RQH, 3RQQ, 3RQX, 3RRB, 3RRE, 3RRF, 3RRJ, 3RS8, 3RS9, 3RSF, 3RSG, 3RSQ, 3RSS, 3RT7, 3RT9, 3RTA, 3RTB, 3RTC, 3RTD, 3RTE, 3RTG, 3RU2, 3RU3

  • PubMed Abstract: 

    Proteins of unknown function comprise a significant fraction of sequenced genomes. Defining the roles of these proteins is vital to understanding cellular processes. Here, we describe a method to determine a protein function based on the identification of its natural ligand(s) by the crystallographic screening of the binding of a metabolite library, followed by a focused search in the metabolic space. The method was applied to two protein families with unknown function, PF01256 and YjeF_N. The PF01256 proteins, represented by YxkO from Bacillus subtilis and the C-terminal domain of Tm0922 from Thermotoga maritima, were shown to catalyze ADP/ATP-dependent NAD(P)H-hydrate dehydratation, a previously described orphan activity. The YjeF_N proteins, represented by mouse apolipoprotein A-I binding protein and the N-terminal domain of Tm0922, were found to interact with an adenosine diphosphoribose-related substrate and likely serve as ADP-ribosyltransferases. Crystallographic screening of metabolites serves as an efficient tool in functional analyses of uncharacterized proteins.


  • Organizational Affiliation

    Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA. ias2n@virginia.edu


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Apolipoprotein A-I-binding protein265Mus musculusMutation(s): 0 
Gene Names: AibpApoa1bp
UniProt & NIH Common Fund Data Resources
Find proteins for Q8K4Z3 (Mus musculus)
Explore Q8K4Z3 
Go to UniProtKB:  Q8K4Z3
IMPC:  MGI:2180167
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8K4Z3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
T3P
Query on T3P

Download Ideal Coordinates CCD File 
B [auth A]THYMIDINE-3'-PHOSPHATE
C10 H15 N2 O8 P
XXYIANZGUOSQHY-XLPZGREQSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.094α = 90
b = 126.094β = 90
c = 110.962γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-07-18
    Type: Initial release
  • Version 1.1: 2012-10-31
    Changes: Database references
  • Version 1.2: 2022-04-13
    Changes: Database references, Derived calculations, Structure summary
  • Version 1.3: 2023-09-13
    Changes: Data collection, Refinement description
  • Version 1.4: 2023-12-06
    Changes: Data collection