1MRF

PREPARATION, CHARACTERIZATION AND CRYSTALLIZATION OF AN ANTIBODY FAB FRAGMENT THAT RECOGNIZES RNA. CRYSTAL STRUCTURES OF NATIVE FAB AND THREE FAB-MONONUCLEOTIDE COMPLEXES


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Preparation, characterization and crystallization of an antibody Fab fragment that recognizes RNA. Crystal structures of native Fab and three Fab-mononucleotide complexes.

Pokkuluri, P.R.Bouthillier, F.Li, Y.Kuderova, A.Lee, J.Cygler, M.

(1994) J.Mol.Biol. 243: 283-297

  • DOI: 10.1006/jmbi.1994.1654
  • Primary Citation of Related Structures:  1MRC, 1MRD, 1MRE

  • PubMed Abstract: 
  • Fab fragments from Jel 103, an antibody which specifically binds to single-stranded poly(rl), were prepared by papain digestion, separated into eight isoforms and characterized by mass spectrometry. One of the purified isoforms yielded crystals suita ...

    Fab fragments from Jel 103, an antibody which specifically binds to single-stranded poly(rl), were prepared by papain digestion, separated into eight isoforms and characterized by mass spectrometry. One of the purified isoforms yielded crystals suitable for structural studies by X-ray diffraction and its crystal structure was determined to 2.4 A resolution. Soaking the crystals in solutions containing either of the mononucleotides inosine-5'-diphosphate, guanosine-5'-diphosphate or deoxyinosine-5'-monophosphate resulted in binding of the nucleotide in a single binding site. However, adenosine-5'-diphosphate does not bind to this antibody. The recognition of the base is achieved through hydrogen bonds to the C6 carbonyl oxygen and the imino NH group of the purine in a pattern similar to that of the base-base interactions in a double-stranded nucleic acid. Additional binding energy is provided by stacking of the base and the Tyr32L side-chain and by interaction of the alpha-phosphate with the antibody in an anionic binding site. Most of the side-chains interacting with the nucleotide come from the light chain. Surprisingly, this antibody shares the VL sequence with another nucleic acid-binding antibody, BV04-1. The latter binds to a single stranded DNA with a high preference for thymine bases. The structures of the unliganded and complexed Jel 103 Fab are compared to those of BV-04-1 Fab and while they show similarity in recognition of the base of the immunodominant nucleotide, their 5' phosphates occupy different positions, suggesting different orientation of the nucleic acid bound to these two antibodies. Differences in the conformations of the L1 loops between the two Fabs have been noted.


    Organizational Affiliation

    Biotechnology Research Institute, National Research Council of Canada, Montreal, Quebec.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
IGG2B-KAPPA JEL103 FAB (LIGHT CHAIN)
L
219N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
IGG2B-KAPPA JEL103 FAB (HEAVY CHAIN)
H
215N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
L
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
DI
Query on DI

Download SDF File 
Download CCD File 
L
2'-DEOXYINOSINE-5'-MONOPHOSPHATE
C10 H13 N4 O7 P
PHNGFPPXDJJADG-RRKCRQDMSA-N
 Ligand Interaction
IMD
Query on IMD

Download SDF File 
Download CCD File 
L
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Work: 0.184 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 66.200α = 90.00
b = 75.500β = 90.00
c = 104.600γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORrefinement
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-02-14
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance