5FWK: Heat shock protein hsp 90 beta

Atomic cryoEM structure of Hsp90-Cdc37-Cdk4 complex. Determined by electron microscopy at 3.9 Å resolution. Released 6 Jul 2016.

Method: Electron microscopy
Resolution: 3.9 Å
Organism: HOMO SAPIENS
Chains: 4
Atoms: 13,112
Mol. weight: 247.5 kDa
Ligands: MG, ATP
Released: 6 Jul 2016

Explore 5FWK in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5FWK contains 82 α-helices and 69 β-strands across 4 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, 31 β-strands

Element	Residues	Length	Sheet
α-helix	11-12	2
β-strand	13-16	4	1
β-strand	18-19	2	2
α-helix	21-31	11
α-helix	38-60	23
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	110-116	7
α-helix	132-138	7
β-strand	140-147	8	3
β-strand	155-159	5	3
β-strand	164-169	6	3
β-strand	179-185	7	3
α-helix	190-193	4
α-helix	195-203	9
β-strand	213-215	3	3
β-strand	216-218	3	5
α-helix	219-220	2
β-strand	276-278	3	5
α-helix	280-283	4
α-helix	286-287	2
α-helix	293-295	3
α-helix	298-308	11
β-strand	317-323	7	6
β-strand	329-335	7	6
α-helix	349-350	2
β-strand	353-357	5	6
β-strand	360-363	4	6
α-helix	366-369	4
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
β-strand	456-459	4	8
β-strand	466-468	3	8
α-helix	469-474	6
β-strand	483-487	5	8
α-helix	491-495	5
α-helix	498-500	3
α-helix	501-505	5
β-strand	510-513	4	8
α-helix	516-521	6
β-strand	527-528	2	9
β-strand	531-532	2	9
β-strand	533-535	3	8
β-strand	538	1	10
α-helix	547-559	13
α-helix	561-570	10
β-strand	578-580	3	11
β-strand	589-592	4	11
β-strand	593	1	10
α-helix	600-609	10
α-helix	615-621	7
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: 32 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	12-16	5	3
β-strand	18-19	2	4
α-helix	21-28	8
α-helix	39-58	20
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	109-116	8
α-helix	117-119	3
α-helix	132-138	7
β-strand	140-148	9	1
β-strand	154-159	6	1
β-strand	164-169	6	1
β-strand	178-185	8	1
α-helix	187-193	7
α-helix	195-205	11
β-strand	213-219	7	1
β-strand	275-279	5	1
α-helix	280-283	4
α-helix	293-295	3
α-helix	298-309	12
β-strand	317-325	9	12
β-strand	329-335	7	12
β-strand	353-357	5	12
β-strand	360-363	4	12
α-helix	366-369	4
α-helix	372-374	3
β-strand	378-383	6	12
β-strand	388	1	13
β-strand	395	1	13
α-helix	399-421	23
α-helix	423-443	21
α-helix	448-452	5
β-strand	457	1	14
β-strand	458-459	2	15
β-strand	467	1	14
α-helix	469-474	6
β-strand	482-487	6	15
α-helix	491-495	5
α-helix	498-500	3
α-helix	501-505	5
β-strand	510-513	4	15
α-helix	518-524	7
β-strand	527-528	2	15
β-strand	531-535	5	15
β-strand	538	1	16
α-helix	547-559	13
α-helix	561-570	10
β-strand	577-580	4	16
β-strand	589-593	5	16
α-helix	600-606	7
α-helix	614-619	6
α-helix	622-623	2
β-strand	624-628	5	16
α-helix	633-645	13
α-helix	649-665	17
α-helix	668-670	3
α-helix	673-688	16

Chain E: 4 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	5-7	3
β-strand	10	1	17
β-strand	23	1	18
α-helix	25-73	49
α-helix	78-111	34
α-helix	112-113	2
β-strand	114	1	17
β-strand	120-129	10	12

Chain K: 12 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	94-96	3
β-strand	99	1	18
α-helix	100-106	7
α-helix	108	1
α-helix	114-133	20
α-helix	143-145	3
β-strand	146-148	3	18
β-strand	154-156	3	18
α-helix	161-163	3
α-helix	183-186	4
α-helix	193-209	17
α-helix	219-230	12
β-strand	231-232	2	19
β-strand	252-254	3	19
α-helix	257-260	4
α-helix	266-276	11
α-helix	286-290	5

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	E	protein	378	HOMO SAPIENS	Q16543 (AlphaFold model)
Cyclin-dependent kinase 4	K	protein	310	HOMO SAPIENS	P11802 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5FWK_1 HEAT SHOCK PROTEIN HSP 90 BETA (chains A, B)
GGFMPEEVHHGEEEVETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNASDALDKIRYE
SLTDPSKLDSGKELKIDIIPNPQERTLTLVDTGIGMTKADLINNLGTIAKSGTKAFMEAL
QAGADISMIGQFGVGFYSAYLVAEKVVVITKHNDDEQYAWESSAGGSFTVRADHGEPIGR
GTKVILHLKEDQTEYLEERRVKEVVKKHSQFIGYPITLYLEKEREKEISDDEAEEEKGEK
EEEDKDDEEKPKIEDVGSDEEDDSGKDKKKKTKKIKEKYIDQEELNKTKPIWTRNPDDIT
QEEYGEFYKSLTNDWEDHLAVKHFSVEGQLEFRALLFIPRRAPFDLFENKKKKNNIKLYV
RRVFIMDSCDELIPEYLNFIRGVVDSEDLPLNISREMLQQSKILKVIRKNIVKKCLELFS
ELAEDKENYKKFYEAFSKNLKLGIHEDSTNRRRLSELLRYHTSQSGDEMTSLSEYVSRMK
ETQKSIYYITGESKEQVANSAFVERVRKRGFEVVYMTEPIDEYCVQQLKEFDGKSLVSVT
KEGLELPEDEEEKKKMEESKAKFENLCKLMKEILDKKVEKVTISNRLVSSPCCIVTSTYG
WTANMERIMKAQALRDNSTMGYMMAKKHLEINPDHPIVETLRQKAEADKNDKAVKDLVVL
LFETALLSSGFSLEDPQTHSNRIYRMIKLGLGIDEDEVAAEEPNAAVPDEIPPLEGDEDA
SRMEEVD

Sequence of entity 2 (E), FASTA

>5FWK_2 HSP90 CO-CHAPERONE CDC37 (chains E)
MVDYSVWDHIEVSDDEDETHPNIDTASLFRWRHQARVERMEQFQKEKEELDRGCRECKRK
VAECQRKLKELEVAEGGKAELERLQAEAQQLRKEERSWEQKLEEMRKKEKSMPWNVDTLS
KDGFSKSMVNTKPEKTEEDSEEVREQKHKTFVEKYEKQIKHFGMLRRWDDSQKYLSDNVH
LVCEETANYLVIWCIDLEVEEKCALMEQVAHQTIVMQFILELAKSLKVDPRACFRQFFTK
IKTADRQYMEGFNDELEAFKERVRGRAKLRIEKAMKEYEEEERKKRLGPGGLDPVEVYES
LPEELQKCFDVKDVQMLQDAISKMDPTDAKYHMQRCIDSGLWVPNSKASEAKEGEEAGPG
DPLLEAVPKTGDEKDVSV

Sequence of entity 3 (K), FASTA

>5FWK_3 CYCLIN-DEPENDENT KINASE 4 (chains K)
GAMDPEFMATSRYEPVAEIGVGAYGTVYKARDPHSGHFVALKSVRVPNGGGGGGGLPIST
VREVALLRRLEAFEHPNVVRLMDVCATSRTDREIKVTLVFEHVDQDLRTYLDKAPPPGLP
AETIKDLMRQFLRGLDFLHANCIVHRDLKPENILVTSGGTVKLADFGLARIYSYQMALTP
VVVTLWYRAPEVLLQSTYATPVDMWSVGCIFAEMFRRKPLFCGNSEADQLGKIFDLIGLP
PEDDWPRDVSLPRGAFPPRGPRPVQSVVPEMEESGAQLLLEMLTFNPHKRISAFRALQHS
YLHKDEGNPE

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	2

Primary citation

Atomic Structure of Hsp90-Cdc37-Cdk4 Reveals that Hsp90 Traps and Stabilizes an Unfolded Kinase. Verba, K.A., Wang, R.Y., Arakawa, A. et al. Science (2016) 352:1542. DOI 10.1126/SCIENCE.AAF5023 · 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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