1G0U | pdb_00001g0u

A GATED CHANNEL INTO THE PROTEASOME CORE PARTICLE

PDB DOI: https://doi.org/10.2210/pdb1G0U/pdb

Classification: HYDROLASE
Organism(s): Saccharomyces cerevisiae
Mutation(s): No

Deposited: 2000-10-09 Released: 2000-11-06
Deposition Author(s): Groll, M., Bajorek, M., Kohler, A., Moroder, L., Rubin, D.M., Huber, R., Glickman, M.H., Finley, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.303 (Depositor)
R-Value Work:
0.250 (Depositor)
R-Value Observed:
0.260 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

A gated channel into the proteasome core particle.

Groll, M., Bajorek, M., Kohler, A., Moroder, L., Rubin, D.M., Huber, R., Glickman, M.H., Finley, D.

(2000) Nat Struct Biol 7: 1062-1067

PubMed: 11062564 Search on PubMed
DOI: https://doi.org/10.1038/80992
Primary Citation Related Structures:
1G0U

PubMed Abstract:
The core particle (CP) of the yeast proteasome is composed of four heptameric rings of subunits arranged in a hollow, barrel-like structure. We report that the CP is autoinhibited by the N-terminal tails of the outer (alpha) ring subunits. Crystallographic analysis showed that deletion of the tail of the alpha 3-subunit opens a channel into the proteolytically active interior chamber of the CP, thus derepressing peptide hydrolysis. In the latent state of the particle, the tails prevent substrate entry by imposing topological closure on the CP. Inhibition by the alpha-subunit tails is relieved upon binding of the regulatory particle to the CP to form the proteasome holoenzyme.

Organizational Affiliation

Max-Planck-Institut für Biochemie, D-82152 Martinsried, Germany. groll@biochem.mdg.de

Macromolecule Content

Total Structure Weight: 718.94 kDa
Atom Count: 51,834
Modeled Residue Count: 6,296
Deposited Residue Count: 6,506
Unique protein chains: 14

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEASOME COMPONENT Y7	A, O	250	Saccharomyces cerevisiae	Mutation(s): 0 EC: 3.4.99.46
UniProt
Find proteins for P23639 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P23639 Go to UniProtKB: P23639
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P23639
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEASOME COMPONENT Y13	B, P	245	Saccharomyces cerevisiae	Mutation(s): 0 EC: 3.4.99.46
UniProt
Find proteins for P23638 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P23638 Go to UniProtKB: P23638
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P23638
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEASOME COMPONENT PRE6	C, Q	243	Saccharomyces cerevisiae	Mutation(s): 0 EC: 3.4.99.46
UniProt
Find proteins for P40303 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40303 Go to UniProtKB: P40303
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P40303
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEASOME COMPONENT PUP2	D, R	241	Saccharomyces cerevisiae	Mutation(s): 0 EC: 3.4.99.46
UniProt
Find proteins for P32379 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32379 Go to UniProtKB: P32379
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P32379
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEASOME COMPONENT PRE5	E, S	234	Saccharomyces cerevisiae	Mutation(s): 0 EC: 3.4.99.46
UniProt
Find proteins for P40302 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40302 Go to UniProtKB: P40302
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P40302
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEASOME COMPONENT C1	F, T	248	Saccharomyces cerevisiae	Mutation(s): 0 EC: 3.4.99.46
UniProt
Find proteins for P21242 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P21242 Go to UniProtKB: P21242
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P21242
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEASOME COMPONENT C7-ALPHA	G, U	252	Saccharomyces cerevisiae	Mutation(s): 0 EC: 3.4.99.46
UniProt
Find proteins for P21243 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P21243 Go to UniProtKB: P21243
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P21243
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEASOME COMPONENT PUP1	H, V	222	Saccharomyces cerevisiae	Mutation(s): 0 EC: 3.4.99.46 (PDB Primary Data), 3.4.25.1 (UniProt)
UniProt
Find proteins for P25043 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P25043 Go to UniProtKB: P25043
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P25043
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEASOME COMPONENT PUP3	I, W	205	Saccharomyces cerevisiae	Mutation(s): 0 EC: 3.4.99.46
UniProt
Find proteins for P25451 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P25451 Go to UniProtKB: P25451
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P25451
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEASOME COMPONENT C11	J, X	198	Saccharomyces cerevisiae	Mutation(s): 0 EC: 3.4.99.46
UniProt
Find proteins for P22141 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P22141 Go to UniProtKB: P22141
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P22141
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEASOME COMPONENT PRE2	K, Y	212	Saccharomyces cerevisiae	Mutation(s): 0 EC: 3.4.99.46 (PDB Primary Data), 3.4.25.1 (UniProt)
UniProt
Find proteins for P30656 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P30656 Go to UniProtKB: P30656
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P30656
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEASOME COMPONENT C5	L, Z	241	Saccharomyces cerevisiae	Mutation(s): 0 EC: 3.4.99.46
UniProt
Find proteins for P23724 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P23724 Go to UniProtKB: P23724
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P23724
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Reference Sequence

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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEASOME COMPONENT PRE4	AA [auth 1], M	266	Saccharomyces cerevisiae	Mutation(s): 0 EC: 3.4.99.46
UniProt
Find proteins for P30657 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P30657 Go to UniProtKB: P30657
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P30657
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Reference Sequence

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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEASOME COMPONENT PRE3	BA [auth 2], N	196	Saccharomyces cerevisiae	Mutation(s): 0 EC: 3.4.99.46 (PDB Primary Data), 3.4.25.1 (UniProt)
UniProt
Find proteins for P38624 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38624 Go to UniProtKB: P38624
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P38624
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Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain CA [auth F] SDF format, chain DA [auth G] SDF format, chain EA [auth G] SDF format, chain FA [auth H] SDF format, chain GA [auth I] SDF format, chain HA [auth I] SDF format, chain IA [auth K] SDF format, chain JA [auth L] SDF format, chain KA [auth L] SDF format, chain LA [auth N] SDF format, chain MA [auth T] SDF format, chain NA [auth U] SDF format, chain OA [auth U] SDF format, chain PA [auth V] SDF format, chain QA [auth W] SDF format, chain RA [auth W] SDF format, chain SA [auth Y] SDF format, chain TA [auth Z] SDF format, chain UA [auth Z] SDF format, chain VA [auth 2] MOL2 format, chain CA [auth F] MOL2 format, chain DA [auth G] MOL2 format, chain EA [auth G] MOL2 format, chain FA [auth H] MOL2 format, chain GA [auth I] MOL2 format, chain HA [auth I] MOL2 format, chain IA [auth K] MOL2 format, chain JA [auth L] MOL2 format, chain KA [auth L] MOL2 format, chain LA [auth N] MOL2 format, chain MA [auth T] MOL2 format, chain NA [auth U] MOL2 format, chain OA [auth U] MOL2 format, chain PA [auth V] MOL2 format, chain QA [auth W] MOL2 format, chain RA [auth W] MOL2 format, chain SA [auth Y] MOL2 format, chain TA [auth Z] MOL2 format, chain UA [auth Z] MOL2 format, chain VA [auth 2] mmCIF format, chain CA [auth F] mmCIF format, chain DA [auth G] mmCIF format, chain EA [auth G] mmCIF format, chain FA [auth H] mmCIF format, chain GA [auth I] mmCIF format, chain HA [auth I] mmCIF format, chain IA [auth K] mmCIF format, chain JA [auth L] mmCIF format, chain KA [auth L] mmCIF format, chain LA [auth N] mmCIF format, chain MA [auth T] mmCIF format, chain NA [auth U] mmCIF format, chain OA [auth U] mmCIF format, chain PA [auth V] mmCIF format, chain QA [auth W] mmCIF format, chain RA [auth W] mmCIF format, chain SA [auth Y] mmCIF format, chain TA [auth Z] mmCIF format, chain UA [auth Z] mmCIF format, chain VA [auth 2]	CA [auth F] DA [auth G] EA [auth G] FA [auth H] GA [auth I] CA [auth F], DA [auth G], EA [auth G], FA [auth H], GA [auth I], HA [auth I], IA [auth K], JA [auth L], KA [auth L], LA [auth N], MA [auth T], NA [auth U], OA [auth U], PA [auth V], QA [auth W], RA [auth W], SA [auth Y], TA [auth Z], UA [auth Z], VA [auth 2]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain CA [auth F] Focus chain DA [auth G] Focus chain EA [auth G] Focus chain FA [auth H] Focus chain GA [auth I] Focus chain HA [auth I] Focus chain IA [auth K] Focus chain JA [auth L] Focus chain KA [auth L] Focus chain LA [auth N] Focus chain MA [auth T] Focus chain NA [auth U] Focus chain OA [auth U] Focus chain PA [auth V] Focus chain QA [auth W] Focus chain RA [auth W] Focus chain SA [auth Y] Focus chain TA [auth Z] Focus chain UA [auth Z] Focus chain VA [auth 2]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.303 (Depositor)
R-Value Work: 0.250 (Depositor)
R-Value Observed: 0.260 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.18	α = 90
b = 301.1	β = 113
c = 144.1	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2000-11-06

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2000-11-06
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2024-02-07
Changes: Data collection, Database references, Derived calculations

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

1G0U | pdb_00001g0u

A GATED CHANNEL INTO THE PROTEASOME CORE PARTICLE

Literature

A gated channel into the proteasome core particle.

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

Entity ID: 4

UniProt

Entity Groups

Sequence Annotations

Entity ID: 5

UniProt

Entity Groups

Sequence Annotations

Entity ID: 6

UniProt

Entity Groups

Sequence Annotations

Entity ID: 7

UniProt

Entity Groups

Sequence Annotations

Entity ID: 8

UniProt

Entity Groups

Sequence Annotations

Entity ID: 9

UniProt

Entity Groups

Sequence Annotations

Entity ID: 10

UniProt

Entity Groups

Sequence Annotations

Entity ID: 11

UniProt

Entity Groups

Sequence Annotations

Entity ID: 12

UniProt

Entity Groups

Sequence Annotations

Entity ID: 13

UniProt

Entity Groups

Sequence Annotations

Entity ID: 14

UniProt

Entity Groups

Sequence Annotations

Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Entry History

Deposition Data

Revision History (Full details and data files)