8BZL

Human 20S Proteasome in complex with peptide activator peptide BLM42

PDB DOI: https://doi.org/10.2210/pdb8BZL/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens, synthetic construct
Mutation(s): No

Deposited: 2022-12-15 Released: 2023-12-27
Deposition Author(s): Henneberg, F., Chari, A., Jankowska, E., Witkowska, J.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.14 Å
R-Value Free: 0.226
R-Value Work: 0.196

wwPDB Validation 3D Report Full Report

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

Literature

Peptidic, Blm10-based activators of human 20S proteasome in vitro and in cellulo enhance degradation of proteins connected with neurodegeneration.

Gizynska, M., Karpowicz, P., Sowik, D., Trepczyk, K., Witkowska, J., Hennenberg, F., Chari, A., Gieldon, A., Pierzynowska, K., Gaffke, L., Wegrzyn, G., Jankowska, E.

To be published.

Macromolecule Content

Total Structure Weight: 777.6 kDa
Atom Count: 50,949
Modelled Residue Count: 6,153
Deposited Residue Count: 6,960
Unique protein chains: 15

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta type-3	A [auth 3], J [auth I]	205	Homo sapiens	Mutation(s): 0 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P49720
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-2	B [auth A], P [auth O]	234	Homo sapiens	Mutation(s): 0
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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P25787
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-4	C [auth B], Q [auth P]	261	Homo sapiens	Mutation(s): 0
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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P25789
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-7	D [auth C], R [auth Q]	248	Homo sapiens	Mutation(s): 0
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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O14818
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-5	E [auth D], S [auth R]	241	Homo sapiens	Mutation(s): 0
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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P28066
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-1	F [auth E], T [auth S]	263	Homo sapiens	Mutation(s): 0
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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P25786
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-3	G [auth F], U [auth T]	255	Homo sapiens	Mutation(s): 0
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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P25788
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-6	H [auth G], V [auth U]	246	Homo sapiens	Mutation(s): 0
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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P60900
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta type-7	I [auth H], W [auth V]	277	Homo sapiens	Mutation(s): 0 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q99436
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta type-2	K [auth J], X	201	Homo sapiens	Mutation(s): 0 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P49721
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta type-5	L [auth K], Y	263	Homo sapiens	Mutation(s): 0 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P28074
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta type-1	M [auth L], Z	241	Homo sapiens	Mutation(s): 0 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P20618
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Reference Sequence

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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta type-4	AA [auth a], N [auth M]	264	Homo sapiens	Mutation(s): 0 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P28070
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Reference Sequence

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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta type-6	BA [auth b], O [auth N]	239	Homo sapiens	Mutation(s): 0 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P28072
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Reference Sequence

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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
ARG-SER-TYR-TYR-SER	CA [auth c] DA [auth d] EA [auth e] FA [auth f] GA [auth g] CA [auth c], DA [auth d], EA [auth e], FA [auth f], GA [auth g], HA [auth h]	14	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1PE Query on 1PE Download Ideal Coordinates CCD File SDF format, chain BB [auth G] SDF format, chain FD [auth a] SDF format, chain IB [auth I] SDF format, chain JB [auth I] SDF format, chain KA [auth 3] SDF format, chain NC [auth U] SDF format, chain QB [auth K] SDF format, chain WB [auth M] SDF format, chain ZC [auth Y] MOL2 format, chain BB [auth G] MOL2 format, chain FD [auth a] MOL2 format, chain IB [auth I] MOL2 format, chain JB [auth I] MOL2 format, chain KA [auth 3] MOL2 format, chain NC [auth U] MOL2 format, chain QB [auth K] MOL2 format, chain WB [auth M] MOL2 format, chain ZC [auth Y]	BB [auth G] FD [auth a] IB [auth I] JB [auth I] KA [auth 3] BB [auth G], FD [auth a], IB [auth I], JB [auth I], KA [auth 3], NC [auth U], QB [auth K], WB [auth M], ZC [auth Y]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain BB [auth G] Focus chain FD [auth a] Focus chain IB [auth I] Focus chain JB [auth I] Focus chain KA [auth 3] Focus chain NC [auth U] Focus chain QB [auth K] Focus chain WB [auth M] Focus chain ZC [auth Y] Interactions & Density Focus chain BB [auth G] Focus chain FD [auth a] Focus chain IB [auth I] Focus chain JB [auth I] Focus chain KA [auth 3] Focus chain NC [auth U] Focus chain QB [auth K] Focus chain WB [auth M] Focus chain ZC [auth Y]
K Query on K Download Ideal Coordinates CCD File SDF format, chain AB [auth G] SDF format, chain AC [auth N] SDF format, chain AD [auth Z] SDF format, chain ID [auth b] SDF format, chain MC [auth U] SDF format, chain RB [auth L] MOL2 format, chain AB [auth G] MOL2 format, chain AC [auth N] MOL2 format, chain AD [auth Z] MOL2 format, chain ID [auth b] MOL2 format, chain MC [auth U] MOL2 format, chain RB [auth L]	AB [auth G] AC [auth N] AD [auth Z] ID [auth b] MC [auth U] AB [auth G], AC [auth N], AD [auth Z], ID [auth b], MC [auth U], RB [auth L]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain AB [auth G] Focus chain AC [auth N] Focus chain AD [auth Z] Focus chain ID [auth b] Focus chain MC [auth U] Focus chain RB [auth L] Interactions & Density Focus chain AB [auth G] Focus chain AC [auth N] Focus chain AD [auth Z] Focus chain ID [auth b] Focus chain MC [auth U] Focus chain RB [auth L]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain BC [auth O] SDF format, chain BD [auth a] SDF format, chain CB [auth H] SDF format, chain CC [auth O] SDF format, chain CD [auth a] SDF format, chain DB [auth H] SDF format, chain DC [auth O] SDF format, chain DD [auth a] SDF format, chain EC [auth O] SDF format, chain ED [auth a] SDF format, chain FC [auth P] SDF format, chain GB [auth I] SDF format, chain GC [auth Q] SDF format, chain GD [auth b] SDF format, chain HC [auth Q] SDF format, chain HD [auth b] SDF format, chain IA [auth 3] SDF format, chain IC [auth R] SDF format, chain JC [auth S] SDF format, chain KC [auth S] SDF format, chain LA [auth A] SDF format, chain LB [auth K] SDF format, chain LC [auth U] SDF format, chain MA [auth A] SDF format, chain MB [auth K] SDF format, chain NA [auth A] SDF format, chain NB [auth K] SDF format, chain OA [auth A] SDF format, chain OB [auth K] SDF format, chain OC [auth V] SDF format, chain PA [auth B] SDF format, chain PC [auth V] SDF format, chain QA [auth B] SDF format, chain RA [auth C] SDF format, chain SA [auth C] SDF format, chain SB [auth M] SDF format, chain TA [auth D] SDF format, chain TB [auth M] SDF format, chain TC [auth Y] SDF format, chain UA [auth E] SDF format, chain UB [auth M] SDF format, chain UC [auth Y] SDF format, chain VA [auth E] SDF format, chain VB [auth M] SDF format, chain VC [auth Y] SDF format, chain WA [auth E] SDF format, chain WC [auth Y] SDF format, chain XA [auth F] SDF format, chain XB [auth N] SDF format, chain XC [auth Y] SDF format, chain YA [auth G] SDF format, chain YB [auth N] SDF format, chain ZA [auth G] SDF format, chain ZB [auth N] MOL2 format, chain BC [auth O] MOL2 format, chain BD [auth a] MOL2 format, chain CB [auth H] MOL2 format, chain CC [auth O] MOL2 format, chain CD [auth a] MOL2 format, chain DB [auth H] MOL2 format, chain DC [auth O] MOL2 format, chain DD [auth a] MOL2 format, chain EC [auth O] MOL2 format, chain ED [auth a] MOL2 format, chain FC [auth P] MOL2 format, chain GB [auth I] MOL2 format, chain GC [auth Q] MOL2 format, chain GD [auth b] MOL2 format, chain HC [auth Q] MOL2 format, chain HD [auth b] MOL2 format, chain IA [auth 3] MOL2 format, chain IC [auth R] MOL2 format, chain JC [auth S] MOL2 format, chain KC [auth S] MOL2 format, chain LA [auth A] MOL2 format, chain LB [auth K] MOL2 format, chain LC [auth U] MOL2 format, chain MA [auth A] MOL2 format, chain MB [auth K] MOL2 format, chain NA [auth A] MOL2 format, chain NB [auth K] MOL2 format, chain OA [auth A] MOL2 format, chain OB [auth K] MOL2 format, chain OC [auth V] MOL2 format, chain PA [auth B] MOL2 format, chain PC [auth V] MOL2 format, chain QA [auth B] MOL2 format, chain RA [auth C] MOL2 format, chain SA [auth C] MOL2 format, chain SB [auth M] MOL2 format, chain TA [auth D] MOL2 format, chain TB [auth M] MOL2 format, chain TC [auth Y] MOL2 format, chain UA [auth E] MOL2 format, chain UB [auth M] MOL2 format, chain UC [auth Y] MOL2 format, chain VA [auth E] MOL2 format, chain VB [auth M] MOL2 format, chain VC [auth Y] MOL2 format, chain WA [auth E] MOL2 format, chain WC [auth Y] MOL2 format, chain XA [auth F] MOL2 format, chain XB [auth N] MOL2 format, chain XC [auth Y] MOL2 format, chain YA [auth G] MOL2 format, chain YB [auth N] MOL2 format, chain ZA [auth G] MOL2 format, chain ZB [auth N]	BC [auth O] BD [auth a] CB [auth H] CC [auth O] CD [auth a] BC [auth O], BD [auth a], CB [auth H], CC [auth O], CD [auth a], DB [auth H], DC [auth O], DD [auth a], EC [auth O], ED [auth a], FC [auth P], GB [auth I], GC [auth Q], GD [auth b], HC [auth Q], HD [auth b], IA [auth 3], IC [auth R], JC [auth S], KC [auth S], LA [auth A], LB [auth K], LC [auth U], MA [auth A], MB [auth K], NA [auth A], NB [auth K], OA [auth A], OB [auth K], OC [auth V], PA [auth B], PC [auth V], QA [auth B], RA [auth C], SA [auth C], SB [auth M], TA [auth D], TB [auth M], TC [auth Y], UA [auth E], UB [auth M], UC [auth Y], VA [auth E], VB [auth M], VC [auth Y], WA [auth E], WC [auth Y], XA [auth F], XB [auth N], XC [auth Y], YA [auth G], YB [auth N], ZA [auth G], ZB [auth N]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain BC [auth O] Focus chain BD [auth a] Focus chain CB [auth H] Focus chain CC [auth O] Focus chain CD [auth a] Focus chain DB [auth H] Focus chain DC [auth O] Focus chain DD [auth a] Focus chain EC [auth O] Focus chain ED [auth a] Focus chain FC [auth P] Focus chain GB [auth I] Focus chain GC [auth Q] Focus chain GD [auth b] Focus chain HC [auth Q] Focus chain HD [auth b] Focus chain IA [auth 3] Focus chain IC [auth R] Focus chain JC [auth S] Focus chain KC [auth S] Focus chain LA [auth A] Focus chain LB [auth K] Focus chain LC [auth U] Focus chain MA [auth A] Focus chain MB [auth K] Focus chain NA [auth A] Focus chain NB [auth K] Focus chain OA [auth A] Focus chain OB [auth K] Focus chain OC [auth V] Focus chain PA [auth B] Focus chain PC [auth V] Focus chain QA [auth B] Focus chain RA [auth C] Focus chain SA [auth C] Focus chain SB [auth M] Focus chain TA [auth D] Focus chain TB [auth M] Focus chain TC [auth Y] Focus chain UA [auth E] Focus chain UB [auth M] Focus chain UC [auth Y] Focus chain VA [auth E] Focus chain VB [auth M] Focus chain VC [auth Y] Focus chain WA [auth E] Focus chain WC [auth Y] Focus chain XA [auth F] Focus chain XB [auth N] Focus chain XC [auth Y] Focus chain YA [auth G] Focus chain YB [auth N] Focus chain ZA [auth G] Focus chain ZB [auth N] Interactions & Density Focus chain BC [auth O] Focus chain BD [auth a] Focus chain CB [auth H] Focus chain CC [auth O] Focus chain CD [auth a] Focus chain DB [auth H] Focus chain DC [auth O] Focus chain DD [auth a] Focus chain EC [auth O] Focus chain ED [auth a] Focus chain FC [auth P] Focus chain GB [auth I] Focus chain GC [auth Q] Focus chain GD [auth b] Focus chain HC [auth Q] Focus chain HD [auth b] Focus chain IA [auth 3] Focus chain IC [auth R] Focus chain JC [auth S] Focus chain KC [auth S] Focus chain LA [auth A] Focus chain LB [auth K] Focus chain LC [auth U] Focus chain MA [auth A] Focus chain MB [auth K] Focus chain NA [auth A] Focus chain NB [auth K] Focus chain OA [auth A] Focus chain OB [auth K] Focus chain OC [auth V] Focus chain PA [auth B] Focus chain PC [auth V] Focus chain QA [auth B] Focus chain RA [auth C] Focus chain SA [auth C] Focus chain SB [auth M] Focus chain TA [auth D] Focus chain TB [auth M] Focus chain TC [auth Y] Focus chain UA [auth E] Focus chain UB [auth M] Focus chain UC [auth Y] Focus chain VA [auth E] Focus chain VB [auth M] Focus chain VC [auth Y] Focus chain WA [auth E] Focus chain WC [auth Y] Focus chain XA [auth F] Focus chain XB [auth N] Focus chain XC [auth Y] Focus chain YA [auth G] Focus chain YB [auth N] Focus chain ZA [auth G] Focus chain ZB [auth N]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain EB [auth H] SDF format, chain FB [auth H] SDF format, chain HB [auth I] SDF format, chain JA [auth 3] SDF format, chain KB [auth J] SDF format, chain PB [auth K] SDF format, chain QC [auth V] SDF format, chain RC [auth V] SDF format, chain SC [auth X] SDF format, chain YC [auth Y] MOL2 format, chain EB [auth H] MOL2 format, chain FB [auth H] MOL2 format, chain HB [auth I] MOL2 format, chain JA [auth 3] MOL2 format, chain KB [auth J] MOL2 format, chain PB [auth K] MOL2 format, chain QC [auth V] MOL2 format, chain RC [auth V] MOL2 format, chain SC [auth X] MOL2 format, chain YC [auth Y]	EB [auth H] FB [auth H] HB [auth I] JA [auth 3] KB [auth J] EB [auth H], FB [auth H], HB [auth I], JA [auth 3], KB [auth J], PB [auth K], QC [auth V], RC [auth V], SC [auth X], YC [auth Y]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain EB [auth H] Focus chain FB [auth H] Focus chain HB [auth I] Focus chain JA [auth 3] Focus chain KB [auth J] Focus chain PB [auth K] Focus chain QC [auth V] Focus chain RC [auth V] Focus chain SC [auth X] Focus chain YC [auth Y] Interactions & Density Focus chain EB [auth H] Focus chain FB [auth H] Focus chain HB [auth I] Focus chain JA [auth 3] Focus chain KB [auth J] Focus chain PB [auth K] Focus chain QC [auth V] Focus chain RC [auth V] Focus chain SC [auth X] Focus chain YC [auth Y]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
YCM Query on YCM	D [auth C], R [auth Q]	L-PEPTIDE LINKING	C₅ H₁₀ N₂ O₃ S		CYS
6V1 Query on 6V1	F [auth E], T [auth S]	L-PEPTIDE LINKING	C₉ H₁₄ N₂ O₄ S		CYS