4X6Z

Yeast 20S proteasome in complex with PR-VI modulator


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.180 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal structures revealed the common place of binding of low-molecular mass activators with the 20S proteasome

Witkowska, J.Rostankowski, R.Dubin, G.Grudnik, P.Golik, P.Gaczynska, M.Osmulski, P.Borek, D.Otwinowski, Z.Jankowska, E.

To be published.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-6A [auth 1],
O [auth M]
241Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.4.25.1
UniProt
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-7B [auth 2],
P [auth N]
266Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.4.25.1
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-1C [auth A],
Q [auth O]
252Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.4.25.1
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-2D [auth B],
R [auth P]
250Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.4.25.1
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-3E [auth C],
S [auth Q]
258Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.4.25.1
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-4F [auth D],
T [auth R]
254Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.4.25.1
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-5G [auth E],
U [auth S]
260Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.4.25.1
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-6H [auth F],
V [auth T]
234Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.4.25.1
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Probable proteasome subunit alpha type-7I [auth G],
W [auth U]
288Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.4.25.1
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-1J [auth H],
X [auth V]
215Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.4.25.1
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-2K [auth I],
Y [auth W]
261Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.4.25.1
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-3L [auth J],
Z [auth X]
205Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.4.25.1
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-4AA [auth Y],
M [auth K]
198Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.4.25.1
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-5BA [auth Z],
N [auth L]
287Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.4.25.1
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
synthetic peptide (polymer)CA [auth a],
DA [auth e]
13synthetic constructMutation(s): 0 
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MPD
Query on MPD

Download Ideal Coordinates CCD File 
DC [auth M]
DD [auth T]
EA [auth 1]
HD [auth V]
IA [auth 2]
DC [auth M],
DD [auth T],
EA [auth 1],
HD [auth V],
IA [auth 2],
KC [auth N],
QD [auth X],
XD [auth Z],
YB [auth L]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AB [auth F]
AC [auth L]
AD [auth S]
AE [auth Z]
BB [auth F]
AB [auth F],
AC [auth L],
AD [auth S],
AE [auth Z],
BB [auth F],
CB [auth F],
DB [auth F],
EC [auth M],
ED [auth T],
FA [auth 1],
FB [auth G],
FC [auth M],
GA [auth 1],
GB [auth G],
HB [auth H],
ID [auth V],
JA [auth 2],
JD [auth V],
KA [auth 2],
LC [auth N],
MB [auth I],
MC [auth N],
NB [auth I],
OD [auth W],
PB [auth J],
QA [auth A],
RA [auth A],
RC [auth O],
RD [auth X],
SA [auth A],
SC [auth O],
TA [auth A],
VB [auth K],
XA [auth D],
YD [auth Z],
ZA [auth E],
ZB [auth L],
ZD [auth Z]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
BC [auth L]
BD [auth S]
BE [auth Z]
CC [auth L]
CD [auth S]
BC [auth L],
BD [auth S],
BE [auth Z],
CC [auth L],
CD [auth S],
CE [auth Z],
EB [auth F],
FD [auth T],
GC [auth M],
GD [auth T],
HA [auth 1],
HC [auth M],
IB [auth H],
IC [auth M],
JB [auth H],
JC [auth M],
KB [auth H],
KD [auth V],
LA [auth 2],
LB [auth H],
LD [auth V],
MA [auth 2],
MD [auth V],
NA [auth 2],
NC [auth N],
ND [auth V],
OA [auth 2],
OB [auth J],
OC [auth N],
PA [auth 2],
PC [auth N],
PD [auth W],
QB [auth J],
QC [auth N],
RB [auth J],
SB [auth J],
SD [auth X],
TB [auth J],
TC [auth O],
TD [auth X],
UA [auth B],
UB [auth J],
UC [auth P],
UD [auth X],
VA [auth C],
VC [auth Q],
VD [auth Y],
WA [auth C],
WB [auth K],
WC [auth Q],
WD [auth Y],
XB [auth K],
XC [auth R],
YA [auth D],
YC [auth R],
ZC [auth R]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.180 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 133.35α = 90
b = 300.79β = 112.11
c = 144.58γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
Cootmodel building
MOLREPphasing
HKL-3000data scaling

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science CentrePolandNCN 2011/01/B/ST5/06616

Revision History  (Full details and data files)

  • Version 1.0: 2015-12-23
    Type: Initial release
  • Version 1.1: 2024-01-10
    Changes: Data collection, Database references, Refinement description