8BZL

Human 20S Proteasome in complex with peptide activator peptide BLM42

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.196 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history. 


Literature

Peptidic, Blm10-based activators of human 20S proteasome in vitro and in cellulo enhance degradation of proteins connected with neurodegeneration.

Gizynska, M., Karpowicz, P., Sowik, D., Trepczyk, K., Witkowska, J., Hennenberg, F., Chari, A., Gieldon, A., Pierzynowska, K., Gaffke, L., Wegrzyn, G., Jankowska, E.

To be published.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-3A [auth 3],
J [auth I]		205Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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PHAROS:  P49720
GTEx:  ENSG00000277791 
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UniProt GroupP49720
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-2B [auth A],
P [auth O]		234Homo sapiensMutation(s): 0 
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PHAROS:  P25787
GTEx:  ENSG00000106588 
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UniProt GroupP25787
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-4C [auth B],
Q [auth P]		261Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000041357 
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UniProt GroupP25789
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-7D [auth C],
R [auth Q]		248Homo sapiensMutation(s): 0 
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PHAROS:  O14818
GTEx:  ENSG00000101182 
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UniProt GroupO14818
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-5E [auth D],
S [auth R]		241Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000143106 
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UniProt GroupP28066
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-1F [auth E],
T [auth S]		263Homo sapiensMutation(s): 0 
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PHAROS:  P25786
GTEx:  ENSG00000129084 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-3G [auth F],
U [auth T]		255Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100567 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-6H [auth G],
V [auth U]		246Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100902 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-7I [auth H],
W [auth V]		277Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000136930 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-2K [auth J],
X		201Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000126067 
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UniProt GroupP49721
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-5L [auth K],
Y		263Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000100804 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-1M [auth L],
Z		241Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000008018 
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UniProt GroupP20618
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-4AA [auth a],
N [auth M]		264Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000159377 
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UniProt GroupP28070
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-6BA [auth b],
O [auth N]		239Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000142507 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
ARG-SER-TYR-TYR-SER14synthetic constructMutation(s): 0 
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1PE
Query on 1PE
Download Ideal Coordinates CCD File 
BB [auth G]
FD [auth a]
IB [auth I]
JB [auth I]
KA [auth 3]
BB [auth G],
FD [auth a],
IB [auth I],
JB [auth I],
KA [auth 3],
NC [auth U],
QB [auth K],
WB [auth M],
ZC [auth Y]
PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
K
Query on K
Download Ideal Coordinates CCD File 
AB [auth G]
AC [auth N]
AD [auth Z]
ID [auth b]
MC [auth U]
AB [auth G],
AC [auth N],
AD [auth Z],
ID [auth b],
MC [auth U],
RB [auth L]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL
Query on CL
Download Ideal Coordinates CCD File 
BC [auth O]
BD [auth a]
CB [auth H]
CC [auth O]
CD [auth a]
BC [auth O],
BD [auth a],
CB [auth H],
CC [auth O],
CD [auth a],
DB [auth H],
DC [auth O],
DD [auth a],
EC [auth O],
ED [auth a],
FC [auth P],
GB [auth I],
GC [auth Q],
GD [auth b],
HC [auth Q],
HD [auth b],
IA [auth 3],
IC [auth R],
JC [auth S],
KC [auth S],
LA [auth A],
LB [auth K],
LC [auth U],
MA [auth A],
MB [auth K],
NA [auth A],
NB [auth K],
OA [auth A],
OB [auth K],
OC [auth V],
PA [auth B],
PC [auth V],
QA [auth B],
RA [auth C],
SA [auth C],
SB [auth M],
TA [auth D],
TB [auth M],
TC [auth Y],
UA [auth E],
UB [auth M],
UC [auth Y],
VA [auth E],
VB [auth M],
VC [auth Y],
WA [auth E],
WC [auth Y],
XA [auth F],
XB [auth N],
XC [auth Y],
YA [auth G],
YB [auth N],
ZA [auth G],
ZB [auth N]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG
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EB [auth H]
FB [auth H]
HB [auth I]
JA [auth 3]
KB [auth J]
EB [auth H],
FB [auth H],
HB [auth I],
JA [auth 3],
KB [auth J],
PB [auth K],
QC [auth V],
RC [auth V],
SC [auth X],
YC [auth Y]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
YCM
Query on YCM		D [auth C],
R [auth Q]		L-PEPTIDE LINKINGC5 H10 N2 O3 SCYS
6V1
Query on 6V1		F [auth E],
T [auth S]		L-PEPTIDE LINKINGC9 H14 N2 O4 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.196 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.915α = 90
b = 203.262β = 90
c = 316.421γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
autoPROCdata processing
XDSdata reduction
Aimlessdata scaling
Cootmodel building
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-27
    Type: Initial release