8GFT: Heat shock protein HSP 90-beta

Hsp90 provides platform for CRaf dephosphorylation by PP5. Determined by electron microscopy at 3.8 Å resolution. Released 3 May 2023.

Method: Electron microscopy
Resolution: 3.8 Å
Organism: Homo sapiens
Chains: 5
Atoms: 17,797
Mol. weight: 305.83 kDa
Ligands: MN, ATP, MG, ADP
Released: 3 May 2023

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

Secondary structure: helices and β-sheets

8GFT contains 116 α-helices and 81 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: 34 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	13-16	4	1
β-strand	18-19	2	2
α-helix	21-31	11
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	132-138	7
β-strand	140-148	9	3
β-strand	154-159	6	3
β-strand	164-169	6	3
α-helix	174-175	2
β-strand	178-185	8	3
α-helix	190-193	4
α-helix	195-205	11
β-strand	213-217	5	3
β-strand	220-222	3	5
β-strand	271-273	3	5
β-strand	277-279	3	3
α-helix	280-281	2
α-helix	288-290	3
α-helix	293-295	3
α-helix	298-309	12
α-helix	314	1
β-strand	315-323	9	6
β-strand	329-336	8	6
β-strand	353-357	5	6
β-strand	360-363	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	399-419	21
α-helix	423-443	21
α-helix	448-451	4
α-helix	452-454	3
β-strand	456-459	4	8
β-strand	466-468	3	8
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	510-513	4	8
α-helix	518-522	5
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	600-607	8
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	673-688	16

Chain B: 32 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	13-17	5	3
β-strand	19-20	2	4
α-helix	22-31	10
α-helix	39-58	20
α-helix	63-68	6
β-strand	74-79	6	1
β-strand	84-89	6	1
α-helix	96-98	3
α-helix	99-103	5
β-strand	105-106	2	2
α-helix	110-117	8
α-helix	133-139	7
β-strand	141-149	9	1
β-strand	156-160	5	1
β-strand	165-170	6	1
β-strand	179-186	8	1
α-helix	188-194	7
α-helix	196-206	11
β-strand	214-218	5	1
β-strand	277-279	3	1
α-helix	280-283	4
α-helix	288-290	3
α-helix	293-295	3
α-helix	298-309	12
β-strand	315-325	11	10
β-strand	329-336	8	10
β-strand	353-357	5	10
β-strand	360-363	4	10
α-helix	372-374	3
β-strand	378-383	6	10
β-strand	388	1	11
β-strand	395	1	11
α-helix	399-419	21
α-helix	423-443	21
α-helix	448-454	7
β-strand	457	1	12
β-strand	458-459	2	13
β-strand	467	1	12
α-helix	469-474	6
β-strand	482-487	6	13
α-helix	491-495	5
α-helix	498-500	3
α-helix	501-505	5
β-strand	510-513	4	13
α-helix	518-524	7
β-strand	527-528	2	13
β-strand	531-535	5	13
β-strand	538	1	14
α-helix	543-545	3
α-helix	547-570	24
α-helix	572-574	3
β-strand	577-580	4	14
β-strand	589-593	5	14
β-strand	598	1	15
α-helix	600-606	7
α-helix	617-620	4
β-strand	621	1	15
α-helix	622-623	2
β-strand	624-628	5	14
α-helix	633-644	12
α-helix	649-665	17
α-helix	668-670	3
α-helix	673-688	16

Chain C: 16 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	5-7	3
β-strand	10	1	16
β-strand	23	1	17
α-helix	25-72	48
α-helix	77-109	33
α-helix	113	1
β-strand	114	1	16
β-strand	120-129	10	10
α-helix	140-147	8
α-helix	148-152	5
α-helix	153-155	3
α-helix	156-160	5
α-helix	174-177	4
α-helix	179-181	3
α-helix	184-192	9
α-helix	195-199	5
α-helix	203-226	24
α-helix	230-232	3
α-helix	235-242	8
α-helix	252-258	7

Chain D: 12 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	426-427	2
β-strand	428	1	17
α-helix	429-430	2
α-helix	431-435	5
α-helix	442-461	20
β-strand	474-476	3	17
α-helix	478-480	3
β-strand	482-484	3	17
α-helix	514-517	4
α-helix	527-541	15
α-helix	554-562	9
α-helix	570-572	3
α-helix	579-588	10
α-helix	593-595	3
α-helix	599-610	12

Chain E: 22 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	25-40	16
α-helix	44-57	14
α-helix	62-74	13
α-helix	78-91	14
α-helix	96-108	13
α-helix	112-125	14
α-helix	132-152	21
α-helix	166-169	4
α-helix	178-180	3
α-helix	185-187	3
α-helix	188-199	12
α-helix	206-220	15
β-strand	226-229	4	18
β-strand	236-240	5	19
α-helix	248-256	9
β-strand	267-268	2	19
α-helix	279-292	14
β-strand	298-299	2	19
α-helix	300-302	3
α-helix	307-312	6
α-helix	315-322	8
α-helix	326-336	11
β-strand	341-344	4	18
β-strand	348-350	3	18
α-helix	363-367	5
α-helix	374-376	3
α-helix	380-386	7
β-strand	395	1	20
β-strand	406	1	20
α-helix	408-418	11
β-strand	422-425	4	18
β-strand	436-437	2	18
β-strand	442-444	3	18
β-strand	459-465	7	19
β-strand	468-476	9	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, N-terminally processed	C	protein	384	Homo sapiens	Q16543 (AlphaFold model)
RAF proto-oncogene serine/threonine-protein kinase	D	protein	304	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

>8GFT_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

>8GFT_2 Hsp90 co-chaperone Cdc37, N-terminally processed (chains C)
MVDYSVWDHIEVSDDEDETHPNIDTASLFRWRHQARVERMEQFQKEKEELDRGCRECKRK
VAECQRKLKELEVAEGGKAELERLQAEAQQLRKEERSWEQKLEEMRKKEKSMPWNVDTLS
KDGFSKSMVNTKPEKTEEDSEEVREQKHKTFVEKYEKQIKHFGMLRRWDDSQKYLSDNVH
LVCEETANYLVIWCIDLEVEEKCALMEQVAHQTIVMQFILELAKSLKVDPRACFRQFFTK
IKTADRQYMEGFNDELEAFKERVRGRAKLRIEKAMKEYEEEERKKRLGPGGLDPVEVYES
LPEELQKCFDVKDVQMLQDAISKMDPTDAKYHMQRCIDSGLWVPNSKASEAKEGEEAGPG
DPLLEAVPKTGDEKDVSVLEVLFQ

Sequence of entity 3 (D), FASTA

>8GFT_3 RAF proto-oncogene serine/threonine-protein kinase (chains D)
GGRDSSYYWEIEASEVMLSTRIGSGSFGTVYKGKWHGDVAVKILKVVDPTPEQFQAFRNE
VAVLRKTRHVNILLFMGYMTKDNLAIVTQWCEGSSLYKHLHVQETKFQMFQLIDIARQTA
QGMDYLHAKNIIHRDMKSNNIFLHEGLTVKIGDFGLATVKSRWSGSQQVEQPTGSVLWMA
PEVIRMQDNNPFSFQSDVYSYGIVLYELMTGELPYSHINNRDQIIFMVGRGYASPDLSKL
YKNCPKAMKRLVADCVKKVKEERPLFPQILSSIELLQHSLPKINRLPESGWSHPQFEKLE
VLFQ

Sequence of entity 4 (E), FASTA

>8GFT_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
MG	Magnesium ion	Mg	2
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	1

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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