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UniProt release 2.3

Published August 16, 2004

UniProtKB News

New RL line structure for electronic publications

Electronic publications have been indicated in the RL line with the '(er)' prefix that stands for electronic resource:

RL   (er) Free text.

Example:

RL   (er) Plant Gene Register PGR98-023.

Removal of the submission references to HIV data bank

We replaced all submission references to the HIV data bank by publications, thus RL lines of the type:

RL   Submitted (XXX-YYYY) to the HIV data bank.

do no longer exist in Swiss-Prot.

Change in cross-references to PDB

The structure determination method (X-ray, NMR, etc) as well as the mapping of the extent of the cross-reference on the sequence have been introduced as tertiary identifier to the PDB cross-reference line.

Former format:

DR   PDB; ENTRY_NAME; REVISION_DATE.

New format:

DR   PDB; ENTRY_NAME; Method; CHAIN[S]=RANGE.

The methods are controlled vocabulary and currently include:

  • X-ray (for X-ray crystallography)
  • NMR (for NMR spectroscopy)
  • EM (for electron microscopy and cryo-electron diffraction)
  • Fiber (for fiber diffraction)
  • IR (for infrared spectroscopy)
  • Model (for predicted models)
  • Neutron (for neutron diffraction)

Example:

DR   PDB; 1NB3; X-ray; A/B/C/D=116-335, P/R/S/T=98-105.

The tertiary identifier indicates the chain(s) and the corresponding range, of which the structure has been determined. If the range is unknown, a dash is given rather than the range positions. Example:

DR   PDB; 1IYJ; X-ray; B/D=-.

If the chains and the range is unknown, a dash is used. Example:

DR   PDB; 1N12; X-ray; -.

With the introduction of the new format, DR PDB lines can become longer than 75 characters.