8EOB: Human HSP90B in the closed state

Name: PDB 8EOB: Cryo-EM structure of human HSP90B in the closed state
Published: 2023-01-25
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: chaperone

Cryo-EM structure of human HSP90B in the closed state. Determined by electron microscopy at 3.1 Å resolution. Released 25 Jan 2023.

Method: Electron microscopy
Resolution: 3.1 Å
Organism: Homo sapiens
Chains: 2
Atoms: 10,141
Mol. weight: 175.4 kDa
Ligands: MG, ANP
Released: 25 Jan 2023

Explore 8EOB in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8EOB contains 54 α-helices and 62 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 28 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	12-16	5	1
β-strand	18-19	2	2
α-helix	21-27	7
α-helix	28-32	5
α-helix	38-59	22
α-helix	62-65	4
β-strand	73-78	6	3
β-strand	83-88	6	3
α-helix	95-97	3
α-helix	98-102	5
β-strand	104-105	2	4
α-helix	109-116	8
α-helix	133-138	6
β-strand	140-148	9	3
β-strand	155-159	5	3
β-strand	164-169	6	3
β-strand	178-185	8	3
α-helix	190-193	4
α-helix	195-204	10
β-strand	213-215	3	3
β-strand	217-219	3	5
β-strand	276-278	3	5
β-strand	281	1	3
α-helix	288-290	3
α-helix	298-309	12
β-strand	315-323	9	6
β-strand	329-336	8	6
β-strand	353-357	5	6
β-strand	361-364	4	6
α-helix	372-374	3
β-strand	378-383	6	6
β-strand	388	1	7
β-strand	395	1	7
α-helix	398-419	22
α-helix	423-443	21
α-helix	448-453	6
β-strand	456-457	2	8
β-strand	458-459	2	9
β-strand	467-468	2	8
α-helix	469-475	7
β-strand	482-487	6	9
α-helix	491-495	5
α-helix	501-505	5
β-strand	510-513	4	9
α-helix	517-524	8
β-strand	527-528	2	9
β-strand	531-535	5	9
β-strand	538	1	10
α-helix	547-559	13
α-helix	561-570	10
β-strand	577-580	4	11
β-strand	589-592	4	11
β-strand	593	1	10
α-helix	600-606	7
α-helix	614-619	6
β-strand	625-628	4	11
α-helix	633-644	12
α-helix	649-665	17
α-helix	668-670	3
α-helix	673-688	16

Chain B: 26 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	13-16	4	3
β-strand	18-19	2	4
α-helix	21-30	10
α-helix	36-38	3
α-helix	39-59	21
α-helix	62-65	4
β-strand	73-78	6	1
β-strand	83-88	6	1
α-helix	95-97	3
α-helix	98-102	5
β-strand	104-105	2	2
α-helix	109-115	7
α-helix	133-138	6
β-strand	140-148	9	1
β-strand	155-159	5	1
β-strand	164-169	6	1
β-strand	178-185	8	1
α-helix	191-193	3
α-helix	195-204	10
β-strand	213-218	6	1
β-strand	277-281	5	1
α-helix	288-290	3
α-helix	298-309	12
β-strand	315-323	9	12
β-strand	329-336	8	12
β-strand	353-357	5	12
β-strand	361-364	4	12
β-strand	378-383	6	12
α-helix	399-419	21
α-helix	423-443	21
α-helix	448-451	4
α-helix	452-454	3
β-strand	456-457	2	13
β-strand	458-459	2	14
β-strand	467-468	2	13
α-helix	469-475	7
β-strand	482-487	6	14
α-helix	491-495	5
α-helix	500-506	7
β-strand	510-513	4	14
α-helix	516-524	9
β-strand	527-528	2	14
β-strand	531-535	5	14
β-strand	538	1	15
α-helix	547-570	24
β-strand	577-580	4	16
β-strand	589-592	4	16
β-strand	593	1	15
β-strand	598	1	17
α-helix	600-607	8
α-helix	617-620	4
β-strand	621	1	17
β-strand	625-628	4	16
α-helix	633-644	12
α-helix	649-666	18
α-helix	673-688	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Heat shock protein HSP 90-beta	A, B	protein	756	Homo sapiens	P08238 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8EOB_1 Heat shock protein HSP 90-beta (chains A, B)
MHHHHHHDYDIPTTGYPYDVPDYAENLYFQGASPEEVHHGEEEVETFAFQAEIAQLMSLI
INTFYSNKEIFLRELISNASDALDKIRYESLTDPSKLDSGKELKIDIIPNPQERTLTLVD
TGIGMTKADLINNLGTIAKSGTKAFMEALQAGADISMIGQFGVGFYSAYLVAEKVVVITK
HNDDEQYAWESSAGGSFTVRADHGEPIGRGTKVILHLKEDQTEYLEERRVKEVVKKHSQF
IGYPITLYLEKEREKEISDDEAEEEKGEKEEEDKDDEEKPKIEDVGSDEEDDSGKDKKKK
TKKIKEKYIDQEELNKTKPIWTRNPDDITQEEYGEFYKSLTNDWEDHLAVKHFSVEGQLE
FRALLFIPRRAPFDLFENKKKKNNIKLYVRRVFIMDSCDELIPEYLNFIRGVVDSEDLPL
NISREMLQQSKILKVIRKNIVKKCLELFSELAEDKENYKKFYEAFSKNLKLGIHEDSTNR
RRLSELLRYHTSQSGDEMTSLSEYVSRMKETQKSIYYITGESKEQVANSAFVERVRKRGF
EVVYMTEPIDEYCVQQLKEFDGKSLVSVTKEGLELPEDEEEKKKMEESKAKFENLCKLMK
EILDKKVEKVTISNRLVSSPCCIVTSTYGWTANMERIMKAQALRDNSTMGYMMAKKHLEI
NPDHPIVETLRQKAEADKNDKAVKDLVVLLFETALLSSGFSLEDPQTHSNRIYRMIKLGL
GIDEDEVAAEEPNAAVPDEIPPLEGDEDASRMEEVD

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2
ANP	Phosphoaminophosphonic acid-adenylate ester	C10 H17 N6 O12 P3	2

Primary citation

Unique interface and dynamics of the complex of HSP90 with a specialized cochaperone AIPL1. Srivastava, D., Yadav, R.P., Singh, S. et al. Structure (2023) 31:309. DOI 10.1016/j.str.2022.12.014 · PubMed

Other PDB entries of the same protein (UniProt P08238 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9D9I 1.5 Å, Human Hsp90b nucleotide binding domain in complex with BRI2312
6N8Y 1.55 Å, Hsp90-beta bound to PU-11-trans
5UCJ 1.69 Å, Hsp90b N-terminal domain with inhibitors
7ULJ 1.82 Å, Hsp90b N-terminal domain in complex with 42C
9D9H 1.96 Å, Human Hsp90b nucleotide binding domain in complex with BRI2311
5UC4 2.05 Å, Hsp90b N-terminal domain with inhibitors
3FWV 2.2 Å, Crystal Structure of a Redesigned TPR Protein, T-MOD(VMY), in Complex with MEEVF Peptide
3NMQ 2.2 Å, Hsp90b N-terminal domain in complex with EC44, a pyrrolo-pyrimidine methoxypyridine…
3PRY 2.28 Å, Crystal structure of the middle domain of human HSP90-beta refined at 2.3 A resolution
1UYM 2.45 Å, Human Hsp90-beta with PU3 (9-Butyl-8(3,4,5-trimethoxy-benzyl)-9H-purin-6-ylamine)
3UQ3 2.6 Å, TPR2AB-domain:pHSP90-complex of yeast Sti1
9W5I 2.63 Å, AGO maturation complex (AMC): AGO2-miRNA duplex in complex with Hsp90 beta and…

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