6FVU

26S proteasome, s2 state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Expanded Coverage of the 26S Proteasome Conformational Landscape Reveals Mechanisms of Peptidase Gating.

Eisele, M.R.Reed, R.G.Rudack, T.Schweitzer, A.Beck, F.Nagy, I.Pfeifer, G.Plitzko, J.M.Baumeister, W.Tomko Jr., R.J.Sakata, E.

(2018) Cell Rep 24: 1301-1315.e5

  • DOI: https://doi.org/10.1016/j.celrep.2018.07.004
  • Primary Citation of Related Structures:  
    6FVT, 6FVU, 6FVV, 6FVW, 6FVX, 6FVY

  • PubMed Abstract: 

    The proteasome is the central protease for intracellular protein breakdown. Coordinated binding and hydrolysis of ATP by the six proteasomal ATPase subunits induces conformational changes that drive the unfolding and translocation of substrates into the proteolytic 20S core particle for degradation. Here, we combine genetic and biochemical approaches with cryo-electron microscopy and integrative modeling to dissect the relationship between individual nucleotide binding events and proteasome conformational dynamics. We demonstrate unique impacts of ATP binding by individual ATPases on the proteasome conformational distribution and report two conformational states of the proteasome suggestive of a rotary ATP hydrolysis mechanism. These structures, coupled with functional analyses, reveal key roles for the ATPases Rpt1 and Rpt6 in gating substrate entry into the core particle. This deepened knowledge of proteasome conformational dynamics reveals key elements of intersubunit communication within the proteasome and clarifies the regulation of substrate entry into the proteolytic chamber.


  • Organizational Affiliation

    Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, FL 32306-4300, USA. Electronic address: robert.tomko@med.fsu.edu.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-1A [auth a],
O [auth A]
242Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.4.25.1
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-2B [auth b],
P [auth B]
249Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.4.25.1
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-3C [auth c],
Q [auth C]
244Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.4.25.1
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-4D [auth d],
R [auth D]
251Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.4.25.1
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-5E [auth e],
S [auth E]
249Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.4.25.1
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-6F [auth f],
T [auth F]
231Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.4.25.1
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Probable proteasome subunit alpha type-7G [auth g],
U [auth G]
242Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.4.25.1
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-1H [auth h],
V [auth 1]
196Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.4.25.1
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-2I [auth i],
W [auth 2]
226Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.4.25.1
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-3J [auth j],
X [auth 3]
204Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.4.25.1
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-4K [auth k],
Y [auth 4]
195Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.4.25.1
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-5L [auth l],
Z [auth 5]
212Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.4.25.1
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-6AA [auth 6],
M [auth m]
222Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.4.25.1
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-7BA [auth 7],
N [auth n]
232Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.4.25.1
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit RPN10CA [auth W]197Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin carboxyl-terminal hydrolase RPN11DA [auth V]289Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 3.4.19.12
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit RPN12EA [auth T]266Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit RPN13FA [auth X]127Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome complex subunit SEM1GA [auth Y]89Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit RPN1HA [auth Z]970Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit RPN2IA [auth N]922Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit RPN3JA [auth S]475Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit RPN5KA [auth P]440Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit RPN6LA [auth Q]434Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit RPN7MA [auth R]405Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit RPN8NA [auth U]304Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit RPN9OA [auth O]388Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 7 homologPA [auth H]426Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 4 homologQA [auth I]384Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 6B homologRA [auth K]394Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome subunit RPT4SA [auth L]388Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 6ATA [auth M]421Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 8 homologUA [auth J]405Saccharomyces cerevisiae S288CMutation(s): 0 
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
BB [auth L],
DB [auth M],
VA [auth H],
XA [auth I],
ZA [auth K]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP
Query on ADP

Download Ideal Coordinates CCD File 
FB [auth J]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AB [auth K]
CB [auth L]
EB [auth M]
GB [auth J]
WA [auth H]
AB [auth K],
CB [auth L],
EB [auth M],
GB [auth J],
WA [auth H],
YA [auth I]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-22
    Type: Initial release