8GAE: Heat shock protein HSP 90-beta

Hsp90 provides platform for CRaf dephosphorylation by PP5. Determined by electron microscopy at 3.3 Å resolution. Released 26 Apr 2023.

Method: Electron microscopy
Resolution: 3.3 Å
Organism: Homo sapiens
Chains: 5
Atoms: 17,748
Mol. weight: 294.74 kDa
Ligands: MN, ATP, ADP, MG
Released: 26 Apr 2023

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

Secondary structure: helices and β-sheets

8GAE contains 114 α-helices and 84 β-strands across 5 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: 36 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	13-16	4	1
β-strand	18	1	2
α-helix	21-30	10
α-helix	38-58	21
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	118	1
α-helix	132-138	7
β-strand	140-148	9	3
β-strand	154-159	6	3
β-strand	165-169	5	3
β-strand	178-185	8	3
α-helix	190-193	4
α-helix	195-206	12
β-strand	213-215	3	3
β-strand	279	1	3
α-helix	281-283	3
α-helix	288-290	3
α-helix	293-295	3
α-helix	298-309	12
α-helix	314-315	2
β-strand	317-322	6	5
β-strand	330-335	6	5
β-strand	353-357	5	5
β-strand	360-363	4	5
α-helix	366-369	4
α-helix	372-376	5
β-strand	378-383	6	5
β-strand	388	1	6
β-strand	395	1	6
α-helix	398-421	24
α-helix	423-443	21
α-helix	448-451	4
α-helix	452-454	3
β-strand	456-457	2	7
β-strand	458-459	2	8
α-helix	460-462	3
β-strand	467-468	2	7
α-helix	469-474	6
β-strand	482-487	6	8
α-helix	491-495	5
α-helix	498-500	3
α-helix	501-505	5
β-strand	511-513	3	8
α-helix	518-524	7
β-strand	527-528	2	8
β-strand	531-535	5	8
β-strand	538	1	9
α-helix	547-559	13
α-helix	561-570	10
β-strand	577-580	4	9
β-strand	589-593	5	9
α-helix	600-608	9
α-helix	614-620	7
α-helix	621-623	3
β-strand	624-628	5	9
α-helix	633-644	12
α-helix	649-665	17
α-helix	668-670	3
α-helix	673-687	15

Chain B: 29 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	13-15	3	3
β-strand	18-19	2	4
α-helix	21-31	11
α-helix	38-60	23
α-helix	62-64	3
β-strand	73-78	6	1
β-strand	83-87	5	1
α-helix	95-103	9
β-strand	104	1	2
α-helix	109-114	6
α-helix	118	1
α-helix	132-138	7
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	186	1
α-helix	187-193	7
α-helix	195-205	11
β-strand	213-217	5	1
β-strand	277-279	3	1
α-helix	288-290	3
α-helix	293-295	3
α-helix	298-309	12
β-strand	317-324	8	10
β-strand	329-335	7	10
β-strand	353-357	5	10
β-strand	360-364	5	10
α-helix	372-374	3
β-strand	378-383	6	10
β-strand	388	1	11
β-strand	395	1	11
α-helix	400-419	20
α-helix	423-441	19
α-helix	448-452	5
β-strand	456-457	2	12
β-strand	459	1	13
β-strand	467-468	2	12
α-helix	469-475	7
β-strand	482-487	6	13
α-helix	491-495	5
α-helix	501-505	5
β-strand	510-513	4	13
α-helix	516-522	7
β-strand	527-528	2	13
β-strand	531-535	5	13
β-strand	538	1	14
α-helix	544-546	3
α-helix	547-571	25
β-strand	577-580	4	14
β-strand	589-593	5	14
β-strand	598	1	15
α-helix	600-607	8
α-helix	614-619	6
β-strand	621	1	15
β-strand	624-628	5	14
α-helix	633-644	12
α-helix	649-666	18
α-helix	668-670	3
α-helix	673-687	15

Chain C: 14 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	5-7	3
β-strand	10	1	16
α-helix	16-18	3
β-strand	23	1	17
α-helix	25-72	48
α-helix	78-111	34
α-helix	113	1
β-strand	114	1	16
β-strand	121-129	9	10
α-helix	131-134	4
α-helix	140-161	22
α-helix	169-177	9
α-helix	180-183	4
α-helix	186-188	3
α-helix	189-194	6
α-helix	203-225	23
α-helix	235-239	5
α-helix	243-258	16

Chain D: 12 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	421-424	4
α-helix	426	1
β-strand	427	1	17
α-helix	428	1
α-helix	429-430	2
α-helix	431-435	5
α-helix	442-460	19
β-strand	474-477	4	17
β-strand	481-484	4	17
α-helix	514-517	4
α-helix	528-543	16
α-helix	554-562	9
α-helix	579-590	12
α-helix	591-593	3
α-helix	599-609	11

Chain E: 23 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	24-39	16
α-helix	44-57	14
α-helix	62-74	13
α-helix	78-91	14
α-helix	96-109	14
α-helix	112-125	14
α-helix	130-152	23
α-helix	160-162	3
α-helix	163-169	7
α-helix	188-199	12
α-helix	206-222	17
β-strand	227-229	3	18
α-helix	235	1
β-strand	236-240	5	19
α-helix	247-256	10
β-strand	266-269	4	19
α-helix	279-292	14
α-helix	294-296	3
β-strand	297-300	4	19
α-helix	307-312	6
α-helix	315-322	8
α-helix	325-337	13
β-strand	342-344	3	18
β-strand	348-350	3	18
α-helix	363-366	4
α-helix	380-386	7
α-helix	387	1
β-strand	388-389	2	20
β-strand	396	1	20
β-strand	405-406	2	20
α-helix	408-417	10
β-strand	422-425	4	18
β-strand	432-433	2	19
β-strand	435-437	3	18
α-helix	438-440	3
β-strand	442-444	3	18
β-strand	450-452	3	21
β-strand	455-456	2	21
β-strand	458-465	8	19
β-strand	472-476	5	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Heat shock protein HSP 90-beta	A, B	protein	727	Homo sapiens	P08238 (AlphaFold model)
Hsp90 co-chaperone Cdc37	C	protein	384	Homo sapiens	Q16543 (AlphaFold model)
RAF proto-oncogene serine/threonine-protein kinase	D	protein	207	Homo sapiens	P04049 (AlphaFold model)
Serine/threonine-protein phosphatase 5	E	protein	503	Homo sapiens	P53041 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8GAE_1 Heat shock protein HSP 90-beta (chains A, B)
GPGMPEEVHHGEEEVETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNASDALDKIRYE
SLTDPSKLDSGKELKIDIIPNPQERTLTLVDTGIGMTKADLINNLGTIAKSGTKAFMEAL
QAGADISMIGQFGVGFYSAYLVAEKVVVITKHNDDEQYAWESSAGGSFTVRADHGEPIGR
GTKVILHLKEDQTEYLEERRVKEVVKKHSQFIGYPITLYLEKEREKEISDDEAEEEKGEK
EEEDKDDEEKPKIEDVGSDEEDDSGKDKKKKTKKIKEKYIDQEELNKTKPIWTRNPDDIT
QEEYGEFYKSLTNDWEDHLAVKHFSVEGQLEFRALLFIPRRAPFDLFENKKKKNNIKLYV
RRVFIMDSCDELIPEYLNFIRGVVDSEDLPLNISREMLQQSKILKVIRKNIVKKCLELFS
ELAEDKENYKKFYEAFSKNLKLGIHEDSTNRRRLSELLRYHTSQSGDEMTSLSEYVSRMK
ETQKSIYYITGESKEQVANSAFVERVRKRGFEVVYMTEPIDEYCVQQLKEFDGKSLVSVT
KEGLELPEDEEEKKKMEESKAKFENLCKLMKEILDKKVEKVTISNRLVSSPCCIVTSTYG
WTANMERIMKAQALRDNSTMGYMMAKKHLEINPDHPIVETLRQKAEADKNDKAVKDLVVL
LFETALLSSGFSLEDPQTHSNRIYRMIKLGLGIDEDEVAAEEPNAAVPDEIPPLEGDEDA
SRMEEVD

Sequence of entity 2 (C), FASTA

>8GAE_2 Hsp90 co-chaperone Cdc37 (chains C)
MVDYSVWDHIEVSDDEDETHPNIDTASLFRWRHQARVERMEQFQKEKEELDRGCRECKRK
VAECQRKLKELEVAEGGKAELERLQAEAQQLRKEERSWEQKLEEMRKKEKSMPWNVDTLS
KDGFSKSMVNTKPEKTEEDSEEVREQKHKTFVEKYEKQIKHFGMLRRWDDSQKYLSDNVH
LVCEETANYLVIWCIDLEVEEKCALMEQVAHQTIVMQFILELAKSLKVDPRACFRQFFTK
IKTADRQYMEGFNDELEAFKERVRGRAKLRIEKAMKEYEEEERKKRLGPGGLDPVEVYES
LPEELQKCFDVKDVQMLQDAISKMDPTDAKYHMQRCIDSGLWVPNSKASEAKEGEEAGPG
DPLLEAVPKTGDEKDVSVLEVLFQ

Sequence of entity 3 (D), FASTA

>8GAE_3 RAF proto-oncogene serine/threonine-protein kinase (chains D)
NILLFMGYMTKDNLAIVTQWCEGSSLYKHLHVQETKFQMFQLIDIARQTAQGMDYLHAKN
IIHRDMKSNNIFLHEGLTVKIGDFGLATVKSRWSGSQQVEQPTGSVLWMAPEVIRMQDNN
PFSFQSDVYSYGIVLYELMTGELPYSHINNRDQIIFMVGRGYASPDLSKLYKNCPKAMKR
LVADCVKKVKEERPLFPQILSSIELLQ

Sequence of entity 4 (E), FASTA

>8GAE_4 Serine/threonine-protein phosphatase 5 (chains E)
GPGSMAMAEGERTECAEPPRDEPPADGALKRAEELKTQANDYFKAKDYENAIKFYSQAIE
LNPSNAIYYGNRSLAYLRTECYGYALGDATRAIELDKKYIKGYYRRAASNMALGKFRAAL
RDYETVVKVKPHDKDAKMKYQECNKIVKQKAFERAIAGDEHKRSVVDSLDIESMTIEDEY
SGPKLEDGKVTISFMKELMQWYKDQKKLHRKCAYQILVQVKEVLSKLSTLVETTLKETEK
ITVCGDTHGQFYDLLNIFELNGLPSETNPYIFNGDFVDRGSFSVEVILTLFGFKLLYPDH
FHLLRGNAETDNMNQIYGFEGEVKAKYTAQMYELFSEVFEWLPLAQCINGKVLIMHGGLF
SEDGVTLDDIRKIERNRQPPDSGPMCDLLWSDPQPQNGRSISKRGVSCQFGPDVTKAFLE
ENNLDYIIRSHEVKAEGYEVAHGGRCVTVFSAPNYCDQMGNKASYIHLQGSDLRPQFHQF
TAVPHPNVKPMAYANTLLQLGMM

Ligands and cofactors

ID	Name	Formula	Copies
MN	Manganese (II) ion	Mn	2
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	1
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	1
MG	Magnesium ion	Mg	2

Water and common crystallization additives (K) are not listed.

Primary citation

Hsp90 provides a platform for kinase dephosphorylation by PP5. Jaime-Garza, M., Nowotny, C.A., Coutandin, D. et al. Nat Commun (2023) 14:2197-2197. DOI 10.1038/s41467-023-37659-7 · 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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