3E47

Crystal Structure of the Yeast 20S Proteasome in Complex with Homobelactosin C


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Inhibitor-binding mode of homobelactosin C to proteasomes: new insights into class I MHC ligand generation

Groll, M.Larionov, O.V.Huber, R.de Meijere, A.

(2006) Proc.Natl.Acad.Sci.Usa 103: 4576-4579

  • DOI: 10.1073/pnas.0600647103
  • Primary Citation of Related Structures:  2FNY

  • PubMed Abstract: 
  • Most class I MHC ligands are generated from the vast majority of cellular proteins by proteolysis within the ubiquitin-proteasome pathway and are presented on the cell surface by MHC class I molecules. Here, we present the crystallographic analysis o ...

    Most class I MHC ligands are generated from the vast majority of cellular proteins by proteolysis within the ubiquitin-proteasome pathway and are presented on the cell surface by MHC class I molecules. Here, we present the crystallographic analysis of yeast 20S proteasome in complex with the inhibitor homobelactosin C. The structure reveals a unique inhibitor-binding mode and provides information about the composition of proteasomal primed substrate-binding sites. IFN-gamma inducible substitution of proteasomal constitutive subunits by immunosubunits modulates characteristics of generated peptides, thus producing fragments with higher preference for binding to MHC class I molecules. The structural data for the proteasome:homobelactosin C complex provide an explanation for involvement of immunosubunits in antigen generation and open perspectives for rational design of ligands, inhibiting exclusively constitutive proteasomes or immunoproteasomes.


    Organizational Affiliation

    Ludwig Maximilians Universität, Adolf Butenandt Institut, Butenandtstrasse 5, Gebäude B, D-81377 Munich, Germany. mgroll@med.uni-muenchen.de




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proteasome component Y7
A, O
250Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: PRE8 (PRS4)
EC: 3.4.25.1
Find proteins for P23639 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P23639
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Proteasome component Y13
B, P
244Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: PRE9 (PRS5)
EC: 3.4.25.1
Find proteins for P23638 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P23638
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Proteasome component PRE6
C, Q
241Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: PRE6
EC: 3.4.25.1
Find proteins for P40303 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P40303
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Proteasome component PUP2
D, R
242Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: PUP2 (DOA5)
EC: 3.4.25.1
Find proteins for P32379 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32379
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Proteasome component PRE5
E, S
233Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: PRE5
EC: 3.4.25.1
Find proteins for P40302 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P40302
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Proteasome component C1
F, T
244Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: PRE10 (PRC1, PRS1)
EC: 3.4.25.1
Find proteins for P21242 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P21242
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Proteasome component C7-alpha
G, U
243Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: SCL1 (PRC2, PRS2)
EC: 3.4.25.1
Find proteins for P21243 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P21243
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Proteasome component PUP1
H, V
222Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: PUP1
EC: 3.4.25.1
Find proteins for P25043 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P25043
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Proteasome component PUP3
I, W
204Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: PUP3
EC: 3.4.25.1
Find proteins for P25451 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P25451
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Proteasome component C11
J, X
198Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: PRE1
EC: 3.4.25.1
Find proteins for P22141 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P22141
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Proteasome component PRE2
K, Y
212Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: PRE2 (DOA3, PRG1)
EC: 3.4.25.1
Find proteins for P30656 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P30656
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Proteasome component C5
L, Z
222Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: PRE7 (PRS3, PTS1)
EC: 3.4.25.1
Find proteins for P23724 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P23724
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Proteasome component PRE4
M, 1
233Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: PRE4
EC: 3.4.25.1
Find proteins for P30657 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P30657
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Proteasome component PRE3
N, 2
196Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: PRE3
EC: 3.4.25.1
Find proteins for P38624 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P38624
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ESY
Query on ESY

Download SDF File 
Download CCD File 
K, Y
benzyl N-[(benzyloxy)carbonyl]-L-alanyl-N~6~-[(2R,3S,4S)-3-formyl-2-hydroxy-4-methylhexanoyl]-L-lysinate
C32 H43 N3 O8
ODPOWFGUTQNCGV-RIBUPYHESA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.218 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 135.490α = 90.00
b = 301.057β = 112.78
c = 144.453γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
CNSphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-09-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance