Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 28-mer - A2B2C2D2E2F2G2H2I2J2K2L2M2N2 Pseudo Symmetry: Dihedral - D7  (3D View)
Pseudo Stoichiometry: Homo 28-mer - A28 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 723.19 kDa 
• Atom Count: 43448 
• Residue Count: 5582 
• Unique protein chains: 14

5A0Q

Cryo-EM reveals the conformation of a substrate analogue in the human 20S proteasome core

• DOI: 10.2210/pdb5A0Q/pdb
• EMDataResource: EMD-2981

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


• Deposited: 2015-04-22 Released: 2015-12-30 
• Deposition Author(s): daFonseca, P.C.A., Morris, E.P.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-Em Reveals the Conformation of a Substrate Analogue in the Human 20S Proteasome Core.

Da Fonseca, P.C.A., Morris, E.P.

(2015) Nat Commun 6: 7573

• PubMed: 26133119 
• DOI: 10.1038/ncomms8573
• Primary Citation of Related Structures:  
  5A0Q


• PubMed Abstract: 
  

The proteasome is a highly regulated protease complex fundamental for cell homeostasis and controlled cell cycle progression. It functions by removing a wide range of specifically tagged proteins, including key cellular regulators. Here we present the structure of the human 20S proteasome core bound to a substrate analogue inhibitor molecule, determined by electron cryo-microscopy (cryo-EM) and single-particle analysis at a resolution of around 3.5 Å. Our map allows the building of protein coordinates as well as defining the location and conformation of the inhibitor at the different active sites. These results open new prospects to tackle the proteasome functional mechanisms. Moreover, they also further demonstrate that cryo-EM is emerging as a realistic approach for general structural studies of protein-ligand interactions.

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Organizational Affiliation: 

Division of Structural Biology, The Institute of Cancer Research, London SW3 3RP, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEASOME SUBUNIT ALPHA TYPE-6	A, O	246	Homo sapiens	Mutation(s): 0  Gene Names: PSMA6, PROS27 EC: 3.4.25.1
Find proteins for P60900 (Homo sapiens) Explore P60900  Go to UniProtKB:  P60900
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PHAROS:  P60900 GTEx:  ENSG00000100902

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEASOME SUBUNIT ALPHA TYPE-2	B, P	234	Homo sapiens	Mutation(s): 0  Gene Names: PSMA2, HC3, PSC3 EC: 3.4.25.1
Find proteins for P25787 (Homo sapiens) Explore P25787  Go to UniProtKB:  P25787
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PHAROS:  P25787 GTEx:  ENSG00000106588

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEASOME SUBUNIT ALPHA TYPE-4	C, Q	261	Homo sapiens	Mutation(s): 0  Gene Names: PSMA4, HC9, PSC9 EC: 3.4.25.1
Find proteins for P25789 (Homo sapiens) Explore P25789  Go to UniProtKB:  P25789
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PHAROS:  P25789 GTEx:  ENSG00000041357

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEASOME SUBUNIT ALPHA TYPE-7	D, R	248	Homo sapiens	Mutation(s): 0  Gene Names: PSMA7, HSPC EC: 3.4.25.1
Find proteins for O14818 (Homo sapiens) Explore O14818  Go to UniProtKB:  O14818
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PHAROS:  O14818 GTEx:  ENSG00000101182

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEASOME SUBUNIT ALPHA TYPE-5	E, S	241	Homo sapiens	Mutation(s): 0  Gene Names: PSMA5 EC: 3.4.25.1
Find proteins for P28066 (Homo sapiens) Explore P28066  Go to UniProtKB:  P28066
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PHAROS:  P28066 GTEx:  ENSG00000143106

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEASOME SUBUNIT ALPHA TYPE-1	F, T	263	Homo sapiens	Mutation(s): 0  Gene Names: PSMA1, HC2, NU, PROS30, PSC2 EC: 3.4.25.1
Find proteins for P25786 (Homo sapiens) Explore P25786  Go to UniProtKB:  P25786
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PHAROS:  P25786 GTEx:  ENSG00000129084

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEASOME SUBUNIT ALPHA TYPE-3	G, U	255	Homo sapiens	Mutation(s): 0  Gene Names: PSMA3, HC8, PSC8 EC: 3.4.25.1
Find proteins for P25788 (Homo sapiens) Explore P25788  Go to UniProtKB:  P25788
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PHAROS:  P25788 GTEx:  ENSG00000100567

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEASOME SUBUNIT BETA TYPE-6	H, V	205	Homo sapiens	Mutation(s): 0  Gene Names: PSMB6, LMPY, Y EC: 3.4.25.1
Find proteins for P28072 (Homo sapiens) Explore P28072  Go to UniProtKB:  P28072
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PHAROS:  P28072 GTEx:  ENSG00000142507

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEASOME SUBUNIT BETA TYPE-7	I, W	234	Homo sapiens	Mutation(s): 0  Gene Names: PSMB7, Z EC: 3.4.25.1
Find proteins for Q99436 (Homo sapiens) Explore Q99436  Go to UniProtKB:  Q99436
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PHAROS:  Q99436 GTEx:  ENSG00000136930

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEASOME SUBUNIT BETA TYPE-3	J, X	204	Homo sapiens	Mutation(s): 0  Gene Names: PSMB3 EC: 3.4.25.1
Find proteins for P49720 (Homo sapiens) Explore P49720  Go to UniProtKB:  P49720
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PHAROS:  P49720 GTEx:  ENSG00000277791

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEASOME SUBUNIT BETA TYPE-2	K, Y	201	Homo sapiens	Mutation(s): 0  Gene Names: PSMB2 EC: 3.4.25.1
Find proteins for P49721 (Homo sapiens) Explore P49721  Go to UniProtKB:  P49721
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PHAROS:  P49721 GTEx:  ENSG00000126067

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEASOME SUBUNIT BETA TYPE-5	L, Z	204	Homo sapiens	Mutation(s): 0  Gene Names: PSMB5, LMPX, MB1, X EC: 3.4.25.1
Find proteins for P28074 (Homo sapiens) Explore P28074  Go to UniProtKB:  P28074
NIH Common Fund Data Resources
PHAROS:  P28074 GTEx:  ENSG00000100804

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEASOME SUBUNIT BETA TYPE-1	M, a	213	Homo sapiens	Mutation(s): 0  Gene Names: PSMB1, PSC5 EC: 3.4.25.1
Find proteins for P20618 (Homo sapiens) Explore P20618  Go to UniProtKB:  P20618
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PHAROS:  P20618 GTEx:  ENSG00000008018

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEASOME SUBUNIT BETA TYPE-4	N, b	219	Homo sapiens	Mutation(s): 0  Gene Names: PSMB4, PROS26 EC: 3.4.25.1
Find proteins for P28070 (Homo sapiens) Explore P28070  Go to UniProtKB:  P28070
NIH Common Fund Data Resources
PHAROS:  P28070 GTEx:  ENSG00000159377

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
KNM	H, I, L, V, W, Z	ADA-(AHX)3-(LEU)3-VINYL SULFONE C51 H92 N6 O8 S BVBBFBDIMMETKA-GNKIUVBNSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-04-22 
• Released Date: 2015-12-30 
Deposition Author(s): daFonseca, P.C.A., Morris, E.P.

Revision History 

• Version 1.0: 2015-12-30
  Type: Initial release
  
• Version 1.1: 2017-08-02
  Changes: Data collection