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
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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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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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q41365
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
AAA domain-containing protein	B [auth I]	444	Spinacia oleracea	Mutation(s): 0
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
AAA domain-containing protein	C [auth J]	404	Spinacia oleracea	Mutation(s): 0
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
AAA domain-containing protein	D [auth K]	420	Spinacia oleracea	Mutation(s): 0
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
AAA domain-containing protein	E [auth L]	397	Spinacia oleracea	Mutation(s): 0
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
AAA domain-containing protein	F [auth M]	427	Spinacia oleracea	Mutation(s): 0
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome regulatory subunit RPN11	G [auth V]	309	Spinacia oleracea	Mutation(s): 0
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
PCI domain-containing protein	H [auth S]	487	Spinacia oleracea	Mutation(s): 0
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
PCI domain-containing protein	I [auth T]	267	Spinacia oleracea	Mutation(s): 0
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
VWFA domain-containing protein	J [auth W]	403	Spinacia oleracea	Mutation(s): 0
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
PCI domain-containing protein	K [auth O]	386	Spinacia oleracea	Mutation(s): 0
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
MPN domain-containing protein	L [auth U]	304	Spinacia oleracea	Mutation(s): 0
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Reference Sequence

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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
PCI domain-containing protein	M [auth Q]	421	Spinacia oleracea	Mutation(s): 0
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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
PCI domain-containing protein	N [auth P]	442	Spinacia oleracea	Mutation(s): 0
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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
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Reference Sequence

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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
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Reference Sequence

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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
PCI domain-containing protein	Q [auth R]	386	Spinacia oleracea	Mutation(s): 0
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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]