1UBQ

STRUCTURE OF UBIQUITIN REFINED AT 1.8 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Observed: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of ubiquitin refined at 1.8 A resolution.

Vijay-Kumar, S.Bugg, C.E.Cook, W.J.

(1987) J Mol Biol 194: 531-544

  • DOI: 10.1016/0022-2836(87)90679-6
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The crystal structure of human erythrocytic ubiquitin has been refined at 1.8 A resolution using a restrained least-squares procedure. The crystallographic R-factor for the final model is 0.176. Bond lengths and bond angles in the molecule have root- ...

    The crystal structure of human erythrocytic ubiquitin has been refined at 1.8 A resolution using a restrained least-squares procedure. The crystallographic R-factor for the final model is 0.176. Bond lengths and bond angles in the molecule have root-mean-square deviations from ideal values of 0.016 A and 1.5 degrees, respectively. A total of 58 water molecules per molecule of ubiquitin are included in the final model. The last four residues in the molecule appear to have partial occupancy or large thermal motion. The overall structure of ubiquitin is extremely compact and tightly hydrogen-bonded; approximately 87% of the polypeptide chain is involved in hydrogen-bonded secondary structure. Prominent secondary structural features include three and one-half turns of alpha-helix, a short piece of 3(10)-helix, a mixed beta-sheet that contains five strands, and seven reverse turns. There is a marked hydrophobic core formed between the beta-sheet and alpha-helix. The molecule features a number of unusual secondary structural features, including a parallel G1 beta-bulge, two reverse Asx turns, and a symmetrical hydrogen-bonding region that involves the two helices and two of the reverse turns.


    Related Citations: 
    • Comparison of the Three-Dimensional Structures of Human, Yeast, and Oat Ubiquitin
      Vijay-Kumar, S., Bugg, C.E., Wilkinson, K.D., Vierstra, R.D., Hatfield, P.M., Cook, W.J.
      (1987) J Biol Chem 262: 6396
    • Three-Dimensional Structure of Ubiquitin at 2.8 Angstroms Resolution
      Vijay-Kumar, S., Bugg, C.E., Wilkinson, K.D., Cook, W.J.
      (1985) Proc Natl Acad Sci U S A 82: 3582
    • Crystallization and Preliminary X-Ray Investigation of Ubiquitin, a Non-Histone Chromosomal Protein
      Cook, W.J., Suddath, F.L., Bugg, C.E., Goldstein, G.
      (1979) J Mol Biol 130: 353
    • Molecular Conservation of 74 Amino Acid Sequence of Ubiquitin between Cattle and Man
      Schlesinger, D.H., Goldstein, G.
      (1975) Nature 255: 423

    Organizational Affiliation

    Howard Hughes Medical Institute, Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas 75235-9050, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
UBIQUITINA76Homo sapiensMutation(s): 0 
Gene Names: UBC
Find proteins for P0CG48 (Homo sapiens)
Explore P0CG48 
Go to UniProtKB:  P0CG48
NIH Common Fund Data Resources
PHAROS  P0CG48
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Observed: 0.176 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.84α = 90
b = 42.77β = 90
c = 28.95γ = 90
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1987-04-16
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance