5MP9

26S proteasome in presence of ATP (s1)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural insights into the functional cycle of the ATPase module of the 26S proteasome.

Wehmer, M.Rudack, T.Beck, F.Aufderheide, A.Pfeifer, G.Plitzko, J.M.Forster, F.Schulten, K.Baumeister, W.Sakata, E.

(2017) Proc Natl Acad Sci U S A 114: 1305-1310

  • DOI: 10.1073/pnas.1621129114
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • In eukaryotic cells, the ubiquitin-proteasome system (UPS) is responsible for the regulated degradation of intracellular proteins. The 26S holocomplex comprises the core particle (CP), where proteolysis takes place, and one or two regulatory particle ...

    In eukaryotic cells, the ubiquitin-proteasome system (UPS) is responsible for the regulated degradation of intracellular proteins. The 26S holocomplex comprises the core particle (CP), where proteolysis takes place, and one or two regulatory particles (RPs). The base of the RP is formed by a heterohexameric AAA + ATPase module, which unfolds and translocates substrates into the CP. Applying single-particle cryo-electron microscopy (cryo-EM) and image classification to samples in the presence of different nucleotides and nucleotide analogs, we were able to observe four distinct conformational states (s1 to s4). The resolution of the four conformers allowed for the construction of atomic models of the AAA + ATPase module as it progresses through the functional cycle. In a hitherto unobserved state (s4), the gate controlling access to the CP is open. The structures described in this study allow us to put forward a model for the 26S functional cycle driven by ATP hydrolysis.


    Organizational Affiliation

    Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany; baumeist@biochem.mpg.de sakata@biochem.mpg.de.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-1
A, a
252Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SCL1PRC2PRS2YGL011C
EC: 3.4.25.1
Find proteins for P21243 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P21243

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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-3
3, j
205Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PUP3YER094C
EC: 3.4.25.1
Find proteins for P25451 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P25451

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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-4
4, k
198Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE1YER012W
EC: 3.4.25.1
Find proteins for P22141 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P22141

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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-5
5, l
287Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE2DOA3PRG1YPR103WP8283.10
EC: 3.4.25.1
Find proteins for P30656 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P30656

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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-6
6, m
241Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE7PRS3PTS1YBL041WYBL0407
EC: 3.4.25.1
Find proteins for P23724 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P23724

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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-7
7, n
266Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE4YFR050C
EC: 3.4.25.1
Find proteins for P30657 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
26S protease regulatory subunit 7 homolog
H
467Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPT1CIM5YTA3YKL145W
Find proteins for P33299 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
26S protease regulatory subunit 4 homolog
I
437Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPT2YHS4YTA5YDL007WD2920
Find proteins for P40327 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
26S protease regulatory subunit 6B homolog
K
428Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPT3YNT1YTA2YDR394WD9509.14
Find proteins for P33298 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
26S protease subunit RPT4
L
437Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPT4CRL13PCS1SUG2YOR259C
Find proteins for P53549 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P53549

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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
26S protease regulatory subunit 6A
M
434Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPT5YTA1YOR117WO3258YOR3258W
Find proteins for P33297 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-2
B, b
250Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE8PRS4YML092C
EC: 3.4.25.1
Find proteins for P23639 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P23639

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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
26S protease regulatory subunit 8 homolog
J
405Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPT6CIM3CRL3SUG1TBPYTBY1YGL048C
Find proteins for Q01939 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q01939

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-3
C, c
258Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE9PRS5YGR135W
EC: 3.4.25.1
Find proteins for P23638 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P23638

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-4
D, d
254Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE6YOL038W
EC: 3.4.25.1
Find proteins for P40303 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P40303

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-5
E, e
260Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PUP2DOA5YGR253CG9155
EC: 3.4.25.1
Find proteins for P32379 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32379

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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-6
F, f
234Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE5YMR314WYM9924.06
EC: 3.4.25.1
Find proteins for P40302 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Probable proteasome subunit alpha type-7
G, g
288Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE10PRC1PRS1YOR362CO6650
EC: 3.4.25.1
Find proteins for P21242 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P21242

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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-1
1, h
215Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE3YJL001WJ1407
EC: 3.4.25.1
Find proteins for P38624 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P38624

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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-2
2, i
261Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PUP1YOR157C
EC: 3.4.25.1
Find proteins for P25043 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P25043
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download CCD File 
H, I, K, L, M
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
ADP
Query on ADP

Download CCD File 
J
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
H, I, J, K, L, M
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanySFB-1035
National Science FoundationUnited StatesPHY1430124
National Institutes of HealthUnited States9P41GM104601

Revision History 

  • Version 1.0: 2017-03-08
    Type: Initial release
  • Version 1.1: 2017-08-02
    Changes: Data collection, Derived calculations