9SDR | pdb_00009sdr

CryoEM structure of human 20S proteasome in complex with proteasome inhibitor Carmaphycin B

PDB DOI: https://doi.org/10.2210/pdb9SDR/pdb
EM Map EMD-54791: EMDB EMDataResource

Classification: LYASE
Organism(s): Homo sapiens, synthetic construct
Expression System: Homo sapiens environmental sample
Mutation(s): No

Deposited: 2025-08-14 Released: 2026-11-04
Deposition Author(s): Havlikova, J., Sulzen, H., Boura, E., Fajtova, P., Silhan, J.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.78 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

CryoEM structure of human 20S proteasome in complex with proteasome inhibitors

Havlikova, J., Silhan, J., Benova, V., Fajtova, P., Boura, E.

To be published.

Macromolecule Content

Total Structure Weight: 720.11 kDa
Atom Count: 48,958
Modeled Residue Count: 6,280
Deposited Residue Count: 6,466
Unique protein chains: 15

Macromolecules

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| 3D Structure

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
UniProt & NIH Common Fund Data Resources
Find proteins for P60900 (Homo sapiens) Explore P60900 Go to UniProtKB: P60900
PHAROS: P60900 GTEx: ENSG00000100902
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P60900
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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
UniProt & NIH Common Fund Data Resources
Find proteins for P25787 (Homo sapiens) Explore P25787 Go to UniProtKB: P25787
PHAROS: P25787 GTEx: ENSG00000106588
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P25787
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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
UniProt & NIH Common Fund Data Resources
Find proteins for P25789 (Homo sapiens) Explore P25789 Go to UniProtKB: P25789
PHAROS: P25789 GTEx: ENSG00000041357
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P25789
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-5	D [auth E], R	241	Homo sapiens	Mutation(s): 0 Gene Names: PSMA5 EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for P28066 (Homo sapiens) Explore P28066 Go to UniProtKB: P28066
PHAROS: P28066 GTEx: ENSG00000143106
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P28066
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-1	E [auth F], S	263	Homo sapiens	Mutation(s): 0 Gene Names: PSMA1, HC2, NU, PROS30, PSC2
UniProt & NIH Common Fund Data Resources
Find proteins for P25786 (Homo sapiens) Explore P25786 Go to UniProtKB: P25786
PHAROS: P25786 GTEx: ENSG00000129084
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P25786
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-3	F [auth G], T	255	Homo sapiens	Mutation(s): 0 Gene Names: PSMA3, HC8, PSC8 EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for P25788 (Homo sapiens) Explore P25788 Go to UniProtKB: P25788
PHAROS: P25788 GTEx: ENSG00000100567
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P25788
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta type-3	G [auth J], U [auth V]	204	Homo sapiens	Mutation(s): 0 Gene Names: PSMB3 EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for P49720 (Homo sapiens) Explore P49720 Go to UniProtKB: P49720
PHAROS: P49720 GTEx: ENSG00000277791
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P49720
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Reference Sequence

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| 3D Structure

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta type-2	H [auth K], V [auth W]	201	Homo sapiens	Mutation(s): 0 Gene Names: PSMB2 EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for P49721 (Homo sapiens) Explore P49721 Go to UniProtKB: P49721
PHAROS: P49721 GTEx: ENSG00000126067
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P49721
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Reference Sequence

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| 3D Structure

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta type-1	I [auth M], W [auth X]	213	Homo sapiens	Mutation(s): 0 Gene Names: PSMB1, PSC5 EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for P20618 (Homo sapiens) Explore P20618 Go to UniProtKB: P20618
PHAROS: P20618 GTEx: ENSG00000008018
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P20618
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta type-4	J [auth N], X [auth Y]	219	Homo sapiens	Mutation(s): 0 Gene Names: PSMB4, PROS26 EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for P28070 (Homo sapiens) Explore P28070 Go to UniProtKB: P28070
PHAROS: P28070 GTEx: ENSG00000159377
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P28070
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-7	K [auth D], Y [auth Z]	248	Homo sapiens	Mutation(s): 0 Gene Names: PSMA7, HSPC
UniProt & NIH Common Fund Data Resources
Find proteins for O14818 (Homo sapiens) Explore O14818 Go to UniProtKB: O14818
PHAROS: O14818 GTEx: ENSG00000101182
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O14818
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Reference Sequence

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| 3D Structure

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta type-6	L [auth H], Z [auth a]	205	Homo sapiens	Mutation(s): 0 Gene Names: PSMB6, LMPY, Y EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for P28072 (Homo sapiens) Explore P28072 Go to UniProtKB: P28072
PHAROS: P28072 GTEx: ENSG00000142507
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P28072
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Reference Sequence

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| 3D Structure

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta type-7	AA [auth b], M [auth I]	234	Homo sapiens	Mutation(s): 0 Gene Names: PSMB7, Z EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q99436 (Homo sapiens) Explore Q99436 Go to UniProtKB: Q99436
PHAROS: Q99436 GTEx: ENSG00000136930
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q99436
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Reference Sequence

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| 3D Structure

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta type-5	BA [auth c], N [auth L]	200	Homo sapiens	Mutation(s): 0 Gene Names: PSMB5, LMPX, MB1, X EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for P28074 (Homo sapiens) Explore P28074 Go to UniProtKB: P28074
PHAROS: P28074 GTEx: ENSG00000100804
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P28074
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
Carmaphycin B, bound form	CA [auth U] DA [auth d] EA [auth e] FA [auth f] GA [auth g] CA [auth U], DA [auth d], EA [auth e], FA [auth f], GA [auth g], HA [auth h]	3	synthetic construct	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
6NA (Subject of Investigation/LOI) Query on 6NA Download:Ideal Coordinates CCD File SDF format, chain IA [auth U] SDF format, chain JA [auth d] SDF format, chain KA [auth e] SDF format, chain LA [auth f] SDF format, chain MA [auth g] SDF format, chain NA [auth h] MOL2 format, chain IA [auth U] MOL2 format, chain JA [auth d] MOL2 format, chain KA [auth e] MOL2 format, chain LA [auth f] MOL2 format, chain MA [auth g] MOL2 format, chain NA [auth h] mmCIF format, chain IA [auth U] mmCIF format, chain JA [auth d] mmCIF format, chain KA [auth e] mmCIF format, chain LA [auth f] mmCIF format, chain MA [auth g] mmCIF format, chain NA [auth h]	IA [auth U] JA [auth d] KA [auth e] LA [auth f] MA [auth g] IA [auth U], JA [auth d], KA [auth e], LA [auth f], MA [auth g], NA [auth h]	HEXANOIC ACID C₆ H₁₂ O₂ FUZZWVXGSFPDMH-UHFFFAOYSA-N		Interactions Focus chain IA [auth U] Focus chain JA [auth d] Focus chain KA [auth e] Focus chain LA [auth f] Focus chain MA [auth g] Focus chain NA [auth h] Interactions & Density Focus chain IA [auth U] Focus chain JA [auth d] Focus chain KA [auth e] Focus chain LA [auth f] Focus chain MA [auth g] Focus chain NA [auth h]

Modified Residues 1 Unique
ID	Chains	Modified Residue	Modification Type	Formula	2D Diagram
OMT Query on OMT	CA [auth U], DA [auth d], EA [auth e], FA [auth f], GA [auth g] CA [auth U], DA [auth d], EA [auth e], FA [auth f], GA [auth g], HA [auth h]	MET	Oxidation	C₅ H₁₁ N O₄ S

Non-standard Monomers 1 Unique
ID	Chains	Type	Formula	2D Diagram
A1KN4 Query on A1KN4	CA [auth U], DA [auth d], EA [auth e], FA [auth f], GA [auth g] CA [auth U], DA [auth d], EA [auth e], FA [auth f], GA [auth g], HA [auth h]	L-PEPTIDE LINKING	C₉ H₁₉ N O₂

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 15
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002605 Query on PRD_002605	CA [auth U] DA [auth d] EA [auth e] FA [auth f] GA [auth g] CA [auth U], DA [auth d], EA [auth e], FA [auth f], GA [auth g], HA [auth h]	Carmaphycin B, bound form	Peptide-like / Inhibitor		Interactions Focus chain CA [auth U] Focus chain DA [auth d] Focus chain EA [auth e] Focus chain FA [auth f] Focus chain GA [auth g] Focus chain HA [auth h] Interactions & Density Focus chain CA [auth U] Focus chain DA [auth d] Focus chain EA [auth e] Focus chain FA [auth f] Focus chain GA [auth g] Focus chain HA [auth h]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.78 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-11-04

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2026-11-04
Type: Initial release

9SDR | pdb_00009sdr

CryoEM structure of human 20S proteasome in complex with proteasome inhibitor Carmaphycin B

Literature

CryoEM structure of human 20S proteasome in complex with proteasome inhibitors

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 2

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 3

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 4

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 5

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 6

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 7

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 8

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 9

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 10

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 11

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 12

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 13

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 14

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 15

Sequence Annotations

Small Molecules

Biologically Interesting Molecules (External Reference)

Experimental Data & Validation

Experimental Data

Structure Validation

Entry History

Deposition Data

Revision History (Full details and data files)