6MSJ

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

  • Classification: HYDROLASE
  • Organism(s): Homo sapiens
  • Expression System: Homo sapiens, Escherichia coli K-12

  • Deposited: 2018-10-16 Released: 2018-11-21 
  • Deposition Author(s): Mao, Y.D.
  • Funding Organization(s): National Natural Science Foundation of China; National Institutes of Health/National Human Genome Research Institute 

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.3 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 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


Macromolecules

Find similar proteins by: Sequence  |  Structure

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 Gene View: PSMD1
Go to UniProtKB:  Q99460
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
26S proteasome non-ATPase regulatory subunit 3
V
533Homo sapiensMutation(s): 0 
Gene Names: PSMD3
Find proteins for O43242 (Homo sapiens)
Go to Gene View: PSMD3
Go to UniProtKB:  O43242
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)
Go to Gene View: PSMD12
Go to UniProtKB:  O00232
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 Gene View: PSMD11
Go to UniProtKB:  O00231
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
26S proteasome non-ATPase regulatory subunit 6
Y
389Homo sapiensMutation(s): 0 
Gene Names: PSMD6 (KIAA0107, PFAAP4)
Find proteins for Q15008 (Homo sapiens)
Go to Gene View: PSMD6
Go to UniProtKB:  Q15008
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
26S proteasome non-ATPase regulatory subunit 7
Z
324Homo sapiensMutation(s): 0 
Gene Names: PSMD7 (MOV34L)
Find proteins for P51665 (Homo sapiens)
Go to Gene View: PSMD7
Go to UniProtKB:  P51665
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 Gene View: PSMD13
Go to UniProtKB:  Q9UNM6
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
26S proteasome non-ATPase regulatory subunit 4
b
377Homo sapiensMutation(s): 0 
Gene Names: PSMD4 (MCB1)
Find proteins for P55036 (Homo sapiens)
Go to Gene View: PSMD4
Go to UniProtKB:  P55036
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
26S proteasome non-ATPase regulatory subunit 14
c
309Homo sapiensMutation(s): 0 
Gene Names: PSMD14 (POH1)
EC: 3.4.19.-
Find proteins for O00487 (Homo sapiens)
Go to Gene View: PSMD14
Go to UniProtKB:  O00487
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 Gene View: PSMD8
Go to UniProtKB:  P48556
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
26S proteasome complex subunit SEM1
e
70Homo sapiensMutation(s): 0 
Gene Names: SEM1 (C7orf76, DSS1, SHFDG1, SHFM1)
Find proteins for P60896 (Homo sapiens)
Go to Gene View: SEM1
Go to UniProtKB:  P60896
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
26S proteasome non-ATPase regulatory subunit 2
f
892Homo sapiensMutation(s): 0 
Gene Names: PSMD2 (TRAP2)
Find proteins for Q13200 (Homo sapiens)
Go to Gene View: PSMD2
Go to UniProtKB:  Q13200
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
26S proteasome regulatory subunit 7
A
433Homo sapiensMutation(s): 0 
Gene Names: PSMC2 (MSS1)
Find proteins for P35998 (Homo sapiens)
Go to Gene View: PSMC2
Go to UniProtKB:  P35998
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Rpt2, NP_002793.2 (26SHA chain B)
B
440Homo sapiensMutation(s): 0 
Gene Names: PSMC1
Find proteins for P62191 (Homo sapiens)
Go to Gene View: PSMC1
Go to UniProtKB:  P62191
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
26S proteasome regulatory subunit 8
C
398Homo sapiensMutation(s): 0 
Gene Names: PSMC5 (SUG1)
Find proteins for P62195 (Homo sapiens)
Go to Gene View: PSMC5
Go to UniProtKB:  P62195
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
26S proteasome regulatory subunit 6B
D
418Homo sapiensMutation(s): 0 
Gene Names: PSMC4 (MIP224, TBP7)
Find proteins for P43686 (Homo sapiens)
Go to Gene View: PSMC4
Go to UniProtKB:  P43686
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 Gene View: PSMC6
Go to UniProtKB:  A0A087X2I1
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
26S proteasome regulatory subunit 6A
F
439Homo sapiensMutation(s): 0 
Gene Names: PSMC3 (TBP1)
Find proteins for P17980 (Homo sapiens)
Go to Gene View: PSMC3
Go to UniProtKB:  P17980
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
substrate
v
36N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-6
G
245Homo sapiensMutation(s): 0 
Gene Names: PSMA6 (PROS27)
EC: 3.4.25.1
Find proteins for P60900 (Homo sapiens)
Go to Gene View: PSMA6
Go to UniProtKB:  P60900
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-2
H, h
233Homo sapiensMutation(s): 0 
Gene Names: PSMA2 (HC3, PSC3)
EC: 3.4.25.1
Find proteins for P25787 (Homo sapiens)
Go to Gene View: PSMA2
Go to UniProtKB:  P25787
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-4
I, i
260Homo sapiensMutation(s): 0 
Gene Names: PSMA4 (HC9, PSC9)
EC: 3.4.25.1
Find proteins for P25789 (Homo sapiens)
Go to Gene View: PSMA4
Go to UniProtKB:  P25789
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-7
J, j
247Homo sapiensMutation(s): 0 
Gene Names: PSMA7 (HSPC)
EC: 3.4.25.1
Find proteins for O14818 (Homo sapiens)
Go to Gene View: PSMA7
Go to UniProtKB:  O14818
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)
Go to Gene View: PSMA5
Go to UniProtKB:  P28066
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-1
L, l
268Homo sapiensMutation(s): 0 
Gene Names: PSMA1 (HC2, NU, PROS30, PSC2)
EC: 3.4.25.1
Find proteins for P25786 (Homo sapiens)
Go to Gene View: PSMA1
Go to UniProtKB:  P25786
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-3
M, m
254Homo sapiensMutation(s): 0 
Gene Names: PSMA3 (HC8, PSC8)
EC: 3.4.25.1
Find proteins for P25788 (Homo sapiens)
Go to Gene View: PSMA3
Go to UniProtKB:  P25788
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-6
N, n
238Homo sapiensMutation(s): 0 
Gene Names: PSMB6 (LMPY, Y)
EC: 3.4.25.1
Find proteins for P28072 (Homo sapiens)
Go to Gene View: PSMB6
Go to UniProtKB:  P28072
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-7
O, o
276Homo sapiensMutation(s): 0 
Gene Names: PSMB7 (Z)
EC: 3.4.25.1
Find proteins for Q99436 (Homo sapiens)
Go to Gene View: PSMB7
Go to UniProtKB:  Q99436
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 Gene View: PSMB3
Go to UniProtKB:  P49720
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)
Go to Gene View: PSMB2
Go to UniProtKB:  P49721
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-5
R, r
262Homo sapiensMutation(s): 0 
Gene Names: PSMB5 (LMPX, MB1, X)
EC: 3.4.25.1
Find proteins for P28074 (Homo sapiens)
Go to Gene View: PSMB5
Go to UniProtKB:  P28074
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-1
S, s
240Homo sapiensMutation(s): 0 
Gene Names: PSMB1 (PSC5)
EC: 3.4.25.1
Find proteins for P20618 (Homo sapiens)
Go to Gene View: PSMB1
Go to UniProtKB:  P20618
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-4
T, t
263Homo sapiensMutation(s): 0 
Gene Names: PSMB4 (PROS26)
EC: 3.4.25.1
Find proteins for P28070 (Homo sapiens)
Go to Gene View: PSMB4
Go to UniProtKB:  P28070
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-6
g
240Homo sapiensMutation(s): 0 
Gene Names: PSMA6 (PROS27)
EC: 3.4.25.1
Find proteins for P60900 (Homo sapiens)
Go to Gene View: PSMA6
Go to UniProtKB:  P60900
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP
Download SDF File 
Download CCD File 
A, B, C, D
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
ZN
Query on ZN
Download SDF File 
Download CCD File 
c
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ADP
Query on ADP
Download SDF File 
Download CCD File 
E
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG
Download SDF File 
Download CCD File 
A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
v
L-PEPTIDE LINKINGC4 H9 N O2

--

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.3 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-10-16 
  • Released Date: 2018-11-21 
  • Deposition Author(s): Mao, Y.D.
Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina11774012
National Natural Science Foundation of ChinaChina91530321
National Institutes of Health/National Human Genome Research InstituteUnited StatesGM43601

Revision History 

  • Version 1.0: 2018-11-21
    Type: Initial release
  • Version 1.1: 2018-12-12
    Type: Data collection, Database references
  • Version 1.2: 2019-01-16
    Type: Data collection, Database references