6MSB

Cryo-EM structures and dynamics of substrate-engaged human 26S proteasome

  • Classification: HYDROLASE
  • Organism(s): Homo sapiens
  • Expression System: Homo sapiens
  • Mutation(s): No 

  • Deposited: 2018-10-16 Released: 2018-12-05 
  • Deposition Author(s): Mao, Y.D.
  • Funding Organization(s): National Natural Science Foundation of China (NSFC), National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Cryo-EM structures and dynamics of substrate-engaged human 26S proteasome.

Dong, Y.Zhang, S.Wu, Z.Li, X.Wang, W.L.Zhu, Y.Stoilova-McPhie, S.Lu, Y.Finley, D.Mao, Y.

(2019) Nature 565: 49-55

  • DOI: 10.1038/s41586-018-0736-4
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The proteasome is an ATP-dependent, 2.5-megadalton molecular machine that is responsible for selective protein degradation in eukaryotic cells. Here we present cryo-electron microscopy structures of the substrate-engaged human proteasome in seven con ...

    The proteasome is an ATP-dependent, 2.5-megadalton molecular machine that is responsible for selective protein degradation in eukaryotic cells. Here we present cryo-electron microscopy structures of the substrate-engaged human proteasome in seven conformational states at 2.8-3.6 Å resolution, captured during breakdown of a polyubiquitylated protein. These structures illuminate a spatiotemporal continuum of dynamic substrate-proteasome interactions from ubiquitin recognition to substrate translocation, during which ATP hydrolysis sequentially navigates through all six ATPases. There are three principal modes of coordinated hydrolysis, featuring hydrolytic events in two oppositely positioned ATPases, in two adjacent ATPases and in one ATPase at a time. These hydrolytic modes regulate deubiquitylation, initiation of translocation and processive unfolding of substrates, respectively. Hydrolysis of ATP powers a hinge-like motion in each ATPase that regulates its substrate interaction. Synchronization of ATP binding, ADP release and ATP hydrolysis in three adjacent ATPases drives rigid-body rotations of substrate-bound ATPases that are propagated unidirectionally in the ATPase ring and unfold the substrate.


    Organizational Affiliation

    Electron Microscopy Laboratory, School of Physics, Peking University, Beijing, China. youdong_mao@dfci.harvard.edu.



Macromolecules

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
26S proteasome non-ATPase regulatory subunit 11
X
422Homo sapiensMutation(s): 0 
Gene Names: PSMD11
Find proteins for O00231 (Homo sapiens)
Go to UniProtKB:  O00231
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PHAROS  O00231

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
26S proteasome non-ATPase regulatory subunit 6
Y
389Homo sapiensMutation(s): 0 
Gene Names: PSMD6KIAA0107PFAAP4
Find proteins for Q15008 (Homo sapiens)
Go to UniProtKB:  Q15008
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PHAROS  Q15008

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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
26S proteasome non-ATPase regulatory subunit 13
a
376Homo sapiensMutation(s): 0 
Gene Names: PSMD13
Find proteins for Q9UNM6 (Homo sapiens)
Go to UniProtKB:  Q9UNM6
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PHAROS  Q9UNM6

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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
26S proteasome complex subunit SEM1
e
70Homo sapiensMutation(s): 0 
Gene Names: SEM1C7orf76DSS1SHFDG1SHFM1
Find proteins for P60896 (Homo sapiens)
Go to UniProtKB:  P60896
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PHAROS  P60896

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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
26S proteasome regulatory subunit 8
C
398Homo sapiensMutation(s): 0 
Gene Names: PSMC5SUG1
Find proteins for P62195 (Homo sapiens)
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PHAROS  P62195

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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
26S proteasome regulatory subunit 6B
D
418Homo sapiensMutation(s): 0 
Gene Names: PSMC4MIP224TBP7
Find proteins for P43686 (Homo sapiens)
Go to UniProtKB:  P43686
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PHAROS  P43686

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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
26S proteasome regulatory subunit 6A
F
439Homo sapiensMutation(s): 0 
Gene Names: PSMC3TBP1
Find proteins for P17980 (Homo sapiens)
Go to UniProtKB:  P17980
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PHAROS  P17980

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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-2
H, h
233Homo sapiensMutation(s): 0 
Gene Names: PSMA2HC3PSC3
EC: 3.4.25.1
Find proteins for P25787 (Homo sapiens)
Go to UniProtKB:  P25787
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PHAROS  P25787

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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-1
L, l
268Homo sapiensMutation(s): 0 
Gene Names: PSMA1HC2NUPROS30PSC2
EC: 3.4.25.1
Find proteins for P25786 (Homo sapiens)
Go to UniProtKB:  P25786
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PHAROS  P25786

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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-3
M, m
254Homo sapiensMutation(s): 0 
Gene Names: PSMA3HC8PSC8
EC: 3.4.25.1
Find proteins for P25788 (Homo sapiens)
Go to UniProtKB:  P25788
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PHAROS  P25788

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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-6
N, n
238Homo sapiensMutation(s): 0 
Gene Names: PSMB6LMPYY
EC: 3.4.25.1
Find proteins for P28072 (Homo sapiens)
Go to UniProtKB:  P28072
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PHAROS  P28072

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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-2
Q, q
201Homo sapiensMutation(s): 0 
Gene Names: PSMB2
EC: 3.4.25.1
Find proteins for P49721 (Homo sapiens)
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PHAROS  P49721

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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-1
S, s
240Homo sapiensMutation(s): 0 
Gene Names: PSMB1PSC5
EC: 3.4.25.1
Find proteins for P20618 (Homo sapiens)
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PHAROS  P20618

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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-4
T, t
263Homo sapiensMutation(s): 0 
Gene Names: PSMB4PROS26
EC: 3.4.25.1
Find proteins for P28070 (Homo sapiens)
Go to UniProtKB:  P28070
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PHAROS  P28070

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
26S proteasome non-ATPase regulatory subunit 1
U
953Homo sapiensMutation(s): 0 
Gene Names: PSMD1
Find proteins for Q99460 (Homo sapiens)
Go to UniProtKB:  Q99460
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PHAROS  Q99460

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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
26S proteasome non-ATPase regulatory subunit 8
d
349Homo sapiensMutation(s): 0 
Gene Names: PSMD8
Find proteins for P48556 (Homo sapiens)
Go to UniProtKB:  P48556
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PHAROS  P48556

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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
26S proteasome non-ATPase regulatory subunit 2
f
908Homo sapiensMutation(s): 0 
Gene Names: PSMD2TRAP2
Find proteins for Q13200 (Homo sapiens)
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PHAROS  Q13200

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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
26S proteasome regulatory subunit 7
A
433Homo sapiensMutation(s): 0 
Gene Names: PSMC2MSS1
Find proteins for P35998 (Homo sapiens)
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PHAROS  P35998

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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
26S proteasome regulatory subunit 4
B
440Homo sapiensMutation(s): 0 
Gene Names: PSMC1
Find proteins for P62191 (Homo sapiens)
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PHAROS  P62191

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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
26S proteasome regulatory subunit 10B
E
403Homo sapiensMutation(s): 0 
Gene Names: PSMC6
Find proteins for A0A087X2I1 (Homo sapiens)
Go to UniProtKB:  A0A087X2I1
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin
u, w
76Homo sapiensMutation(s): 0 
Gene Names: UBB
Find proteins for P0CG47 (Homo sapiens)
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PHAROS  P0CG47

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
26S proteasome non-ATPase regulatory subunit 3
V
534Homo sapiensMutation(s): 0 
Gene Names: PSMD3
Find proteins for O43242 (Homo sapiens)
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PHAROS  O43242

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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-6
G, g
245Homo sapiensMutation(s): 0 
Gene Names: PSMA6PROS27
EC: 3.4.25.1
Find proteins for P60900 (Homo sapiens)
Go to UniProtKB:  P60900
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PHAROS  P60900

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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-4
I, i
260Homo sapiensMutation(s): 0 
Gene Names: PSMA4HC9PSC9
EC: 3.4.25.1
Find proteins for P25789 (Homo sapiens)
Go to UniProtKB:  P25789
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PHAROS  P25789

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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-7
J, j
247Homo sapiensMutation(s): 0 
Gene Names: PSMA7HSPC
EC: 3.4.25.1
Find proteins for O14818 (Homo sapiens)
Go to UniProtKB:  O14818
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PHAROS  O14818

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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-5
K, k
240Homo sapiensMutation(s): 0 
Gene Names: PSMA5
EC: 3.4.25.1
Find proteins for P28066 (Homo sapiens)
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PHAROS  P28066

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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-7
O, o
276Homo sapiensMutation(s): 0 
Gene Names: PSMB7Z
EC: 3.4.25.1
Find proteins for Q99436 (Homo sapiens)
Go to UniProtKB:  Q99436
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PHAROS  Q99436

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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-3
P, p
204Homo sapiensMutation(s): 0 
Gene Names: PSMB3
EC: 3.4.25.1
Find proteins for P49720 (Homo sapiens)
Go to UniProtKB:  P49720
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PHAROS  P49720

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
26S proteasome non-ATPase regulatory subunit 12
W
456Homo sapiensMutation(s): 0 
Gene Names: PSMD12
Find proteins for O00232 (Homo sapiens)
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PHAROS  O00232

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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-5
R, r
262Homo sapiensMutation(s): 0 
Gene Names: PSMB5LMPXMB1X
EC: 3.4.25.1
Find proteins for P28074 (Homo sapiens)
Go to UniProtKB:  P28074
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PHAROS  P28074

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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
26S proteasome non-ATPase regulatory subunit 7
Z
324Homo sapiensMutation(s): 0 
Gene Names: PSMD7MOV34L
Find proteins for P51665 (Homo sapiens)
Go to UniProtKB:  P51665
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PHAROS  P51665

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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
26S proteasome non-ATPase regulatory subunit 4
b
377Homo sapiensMutation(s): 0 
Gene Names: PSMD4MCB1
Find proteins for P55036 (Homo sapiens)
Go to UniProtKB:  P55036
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PHAROS  P55036

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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
26S proteasome non-ATPase regulatory subunit 14
c
309Homo sapiensMutation(s): 0 
Gene Names: PSMD14POH1
EC: 3.4.19
Find proteins for O00487 (Homo sapiens)
Go to UniProtKB:  O00487
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PHAROS  O00487
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download CCD File 
A, B, D, E
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
ADP
Query on ADP

Download CCD File 
C, F
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
c
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A, B, D, E, F
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-10-16 
  • Released Date: 2018-12-05 
  • Deposition Author(s): Mao, Y.D.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China11774012
National Natural Science Foundation of China (NSFC)China91530321
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesGM43601

Revision History 

  • Version 1.0: 2018-12-05
    Type: Initial release
  • Version 1.1: 2018-12-12
    Changes: Data collection, Database references
  • Version 1.2: 2019-01-16
    Changes: Data collection, Database references
  • Version 1.3: 2019-12-18
    Changes: Author supporting evidence, Other