8AMZ | pdb_00008amz

Spinach 19S proteasome

PDB DOI: https://doi.org/10.2210/pdb8AMZ/pdb
Entry: 8AMZ supersedes: 7QVG
EM Map EMD-14175: EMDB EMDataResource

Classification: PLANT PROTEIN
Organism(s): Spinacia oleracea
Mutation(s): No

Deposited: 2022-08-04 Released: 2022-08-24
Deposition Author(s): Kandolf, S., Grishkovskaya, I., Meinhart, A., Haselbach, D.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.30 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Cryo-EM structure of the plant 26S proteasome

Kandolf, S., Grishkovskaya, I., Belacic, K., Foster, B., Imre, R., Bolhuis, D.L., Mechtler, K., Schleiffer, A., Tagare, H., Zhong, E.D., Meinhart, A., Brown, N.G., Haselbach, D.

(2022) Plant Communications 3

Macromolecule Content

Total Structure Weight: 875.72 kDa
Atom Count: 34,609
Modeled Residue Count: 6,986
Deposited Residue Count: 7,818
Unique protein chains: 17

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome regulatory subunit 7	A [auth H]	426	Spinacia oleracea	Mutation(s): 0
UniProt
Find proteins for Q41365 (Spinacia oleracea) Explore Q41365 Go to UniProtKB: Q41365
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q41365
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
AAA domain-containing protein	B [auth I]	444	Spinacia oleracea	Mutation(s): 0
UniProt
Find proteins for A0A9R0HS13 (Spinacia oleracea) Explore A0A9R0HS13 Go to UniProtKB: A0A9R0HS13
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A9R0HS13
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
AAA domain-containing protein	C [auth J]	404	Spinacia oleracea	Mutation(s): 0
UniProt
Find proteins for A0A9R0HRN0 (Spinacia oleracea) Explore A0A9R0HRN0 Go to UniProtKB: A0A9R0HRN0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A9R0HRN0
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
AAA domain-containing protein	D [auth K]	420	Spinacia oleracea	Mutation(s): 0
UniProt
Find proteins for A0A9R0IXE2 (Spinacia oleracea) Explore A0A9R0IXE2 Go to UniProtKB: A0A9R0IXE2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A9R0IXE2
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
AAA domain-containing protein	E [auth L]	397	Spinacia oleracea	Mutation(s): 0
UniProt
Find proteins for A0A9R0IRU0 (Spinacia oleracea) Explore A0A9R0IRU0 Go to UniProtKB: A0A9R0IRU0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A9R0IRU0
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
AAA domain-containing protein	F [auth M]	427	Spinacia oleracea	Mutation(s): 0
UniProt
Find proteins for A0A9R0K0A4 (Spinacia oleracea) Explore A0A9R0K0A4 Go to UniProtKB: A0A9R0K0A4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A9R0K0A4
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome regulatory subunit RPN11	G [auth V]	309	Spinacia oleracea	Mutation(s): 0
UniProt
Find proteins for A0A9R0JDN1 (Spinacia oleracea) Explore A0A9R0JDN1 Go to UniProtKB: A0A9R0JDN1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A9R0JDN1
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
PCI domain-containing protein	H [auth S]	487	Spinacia oleracea	Mutation(s): 0
UniProt
Find proteins for A0A9R0HQR3 (Spinacia oleracea) Explore A0A9R0HQR3 Go to UniProtKB: A0A9R0HQR3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A9R0HQR3
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
PCI domain-containing protein	I [auth T]	267	Spinacia oleracea	Mutation(s): 0
UniProt
Find proteins for A0A9R0JCU5 (Spinacia oleracea) Explore A0A9R0JCU5 Go to UniProtKB: A0A9R0JCU5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A9R0JCU5
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
VWFA domain-containing protein	J [auth W]	403	Spinacia oleracea	Mutation(s): 0
UniProt
Find proteins for A0A9R0J6A8 (Spinacia oleracea) Explore A0A9R0J6A8 Go to UniProtKB: A0A9R0J6A8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A9R0J6A8
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
PCI domain-containing protein	K [auth O]	386	Spinacia oleracea	Mutation(s): 0
UniProt
Find proteins for A0A9R0J9C3 (Spinacia oleracea) Explore A0A9R0J9C3 Go to UniProtKB: A0A9R0J9C3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A9R0J9C3
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
MPN domain-containing protein	L [auth U]	304	Spinacia oleracea	Mutation(s): 0
UniProt
Find proteins for A0ABM3RJK3 (Spinacia oleracea) Explore A0ABM3RJK3 Go to UniProtKB: A0ABM3RJK3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0ABM3RJK3
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
PCI domain-containing protein	M [auth Q]	421	Spinacia oleracea	Mutation(s): 0
UniProt
Find proteins for A0A9R0JZ88 (Spinacia oleracea) Explore A0A9R0JZ88 Go to UniProtKB: A0A9R0JZ88
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A9R0JZ88
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
PCI domain-containing protein	N [auth P]	442	Spinacia oleracea	Mutation(s): 0
UniProt
Find proteins for A0ABF7PJD0 (Spinacia oleracea) Explore A0ABF7PJD0 Go to UniProtKB: A0ABF7PJD0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0ABF7PJD0
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome non-ATPase regulatory subunit 2 homolog	O [auth Z]	895	Spinacia oleracea	Mutation(s): 0
UniProt
Find proteins for A0A9R0JPV7 (Spinacia oleracea) Explore A0A9R0JPV7 Go to UniProtKB: A0A9R0JPV7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A9R0JPV7
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome non-ATPase regulatory subunit 1 homolog	P [auth N]	1,000	Spinacia oleracea	Mutation(s): 0
UniProt
Find proteins for A0A9R0HQY2 (Spinacia oleracea) Explore A0A9R0HQY2 Go to UniProtKB: A0A9R0HQY2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A9R0HQY2
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
PCI domain-containing protein	Q [auth R]	386	Spinacia oleracea	Mutation(s): 0
UniProt
Find proteins for A0A9R0ITF4 (Spinacia oleracea) Explore A0A9R0ITF4 Go to UniProtKB: A0A9R0ITF4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A9R0ITF4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP Query on ATP Download:Ideal Coordinates CCD File SDF format, chain R [auth H] MOL2 format, chain R [auth H] mmCIF format, chain R [auth H]	R [auth H]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain R [auth H] Interactions & Density Focus chain R [auth H]
ADP Query on ADP Download:Ideal Coordinates CCD File SDF format, chain S [auth I] MOL2 format, chain S [auth I] mmCIF format, chain S [auth I]	S [auth I]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain S [auth I] Interactions & Density Focus chain S [auth I]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.30 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.18.2
RECONSTRUCTION	cryoSPARC	3.0

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-08-24

Deposition Author(s):

This entry supersedes: 7QVG

Funding Organization	Location	Grant Number
Other private		--

Revision History (Full details and data files)

Version 1.0: 2022-08-24
Type: Initial release
Version 1.1: 2024-07-24
Changes: Data collection, Refinement description

8AMZ | pdb_00008amz

Spinach 19S proteasome

Literature

Cryo-EM structure of the plant 26S proteasome

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Entity ID: 2

UniProt

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Sequence Annotations

Entity ID: 3

UniProt

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Sequence Annotations

Entity ID: 4

UniProt

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Entity ID: 5

UniProt

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Sequence Annotations

Entity ID: 6

UniProt

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Sequence Annotations

Entity ID: 7

UniProt

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Sequence Annotations

Entity ID: 8

UniProt

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Sequence Annotations

Entity ID: 9

UniProt

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Sequence Annotations

Entity ID: 10

UniProt

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Sequence Annotations

Entity ID: 11

UniProt

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Sequence Annotations

Entity ID: 12

UniProt

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Sequence Annotations

Entity ID: 13

UniProt

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Sequence Annotations

Entity ID: 14

UniProt

Entity Groups

Sequence Annotations

Entity ID: 15

UniProt

Entity Groups

Sequence Annotations

Entity ID: 16

UniProt

Entity Groups

Sequence Annotations

Entity ID: 17

UniProt

Entity Groups

Sequence Annotations

Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Entry History

Deposition Data