8FFV: GR-Hsp90-FKBP52 complex

Cryo-EM structure of the GR-Hsp90-FKBP52 complex. Determined by electron microscopy at 3.01 Å resolution. Released 1 Nov 2023.

Method: Electron microscopy
Resolution: 3.01 Å
Organism: Homo sapiens
Chains: 4
Atoms: 15,827
Mol. weight: 263.83 kDa
Ligands: DEX, MG, ATP
Released: 1 Nov 2023

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

Secondary structure: helices and β-sheets

8FFV contains 98 α-helices and 76 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: 32 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	18-21	4	1
β-strand	23	1	2
α-helix	26-35	10
α-helix	43-62	20
α-helix	67-70	4
β-strand	78-83	6	3
β-strand	88-92	5	3
α-helix	100-102	3
α-helix	103-107	5
β-strand	109-110	2	4
α-helix	114-120	7
α-helix	137-143	7
β-strand	145-153	9	3
β-strand	160-164	5	3
β-strand	170-174	5	3
β-strand	183-190	8	3
α-helix	196-198	3
α-helix	200-211	12
β-strand	218-224	7	3
β-strand	284-289	6	3
α-helix	296-298	3
α-helix	301-303	3
α-helix	306-317	12
β-strand	323-332	10	5
β-strand	336-344	9	5
β-strand	361-365	5	5
β-strand	368-371	4	5
α-helix	375-377	3
α-helix	380-382	3
β-strand	386-390	5	5
β-strand	396	1	6
β-strand	403	1	6
α-helix	407-427	21
α-helix	431-450	20
α-helix	453-455	3
α-helix	456-459	4
α-helix	460-462	3
β-strand	465-467	3	7
β-strand	474-475	2	7
α-helix	477-482	6
β-strand	490-495	6	7
α-helix	499-503	5
α-helix	506-508	3
α-helix	509-513	5
β-strand	518-521	4	7
α-helix	526-529	4
β-strand	535-536	2	7
β-strand	539-543	5	7
β-strand	546	1	8
α-helix	556-577	22
β-strand	585-588	4	8
β-strand	597-601	5	8
α-helix	608-614	7
α-helix	623-627	5
α-helix	629-631	3
β-strand	632-636	5	8
α-helix	641-652	12
α-helix	657-673	17
α-helix	676-678	3
α-helix	682-695	14

Chain B: 33 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	17-20	4	3
β-strand	23-24	2	4
α-helix	26-36	11
α-helix	41-43	3
α-helix	44-63	20
α-helix	67-70	4
β-strand	78-83	6	1
α-helix	84-86	3
β-strand	88-92	5	1
α-helix	100-107	8
β-strand	109	1	2
α-helix	114-121	8
α-helix	123	1
α-helix	138-143	6
β-strand	145-153	9	1
β-strand	160-164	5	1
β-strand	169-174	6	1
β-strand	183-190	8	1
α-helix	195-198	4
α-helix	200-210	11
β-strand	218-224	7	1
β-strand	284-290	7	1
α-helix	294-295	2
α-helix	301-303	3
α-helix	306-317	12
β-strand	323-331	9	9
β-strand	337-344	8	9
β-strand	361-365	5	9
β-strand	368-371	4	9
α-helix	380-382	3
β-strand	386-391	6	9
β-strand	396	1	10
β-strand	403	1	10
α-helix	407-427	21
α-helix	431-451	21
α-helix	456-459	4
α-helix	460-462	3
β-strand	465	1	11
β-strand	466-467	2	12
β-strand	475	1	11
α-helix	477-483	7
β-strand	490-495	6	12
α-helix	499-503	5
α-helix	506-508	3
α-helix	509-513	5
β-strand	518-521	4	12
α-helix	526-533	8
β-strand	535-536	2	12
β-strand	539-543	5	12
β-strand	546	1	13
α-helix	555-563	9
α-helix	564-566	3
α-helix	569-578	10
β-strand	585-588	4	13
β-strand	597-601	5	13
α-helix	610-615	6
α-helix	622-626	5
β-strand	632-636	5	13
α-helix	641-652	12
α-helix	657-673	17
α-helix	682-695	14
α-helix	727-729	3

Chain C: 13 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	522-524	3
α-helix	526-530	5
α-helix	532-539	8
α-helix	540-545	6
α-helix	556-579	24
α-helix	584-586	3
α-helix	589-615	27
β-strand	621-624	4	14
β-strand	627-629	3	14
α-helix	631-633	3
α-helix	637-655	19
α-helix	660-671	12
β-strand	674-676	3	15
α-helix	683-705	23
α-helix	710-741	32
α-helix	751-765	15
β-strand	769-771	3	15

Chain D: 20 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	20-22	3
β-strand	25	1	16
α-helix	26	1
β-strand	34	1	16
β-strand	39	1	17
β-strand	49	1	18
β-strand	52-61	10	17
β-strand	65-66	2	17
α-helix	70-73	4
β-strand	77-80	4	17
α-helix	88-95	8
β-strand	102-107	6	17
α-helix	109-111	3
α-helix	114-116	3
β-strand	128-138	11	17
β-strand	140-141	2	18
β-strand	150-159	10	18
β-strand	169-178	10	18
β-strand	181-191	11	18
α-helix	195-197	3
α-helix	203-208	6
α-helix	211-212	2
β-strand	213-221	9	18
α-helix	233-235	3
β-strand	243-253	11	18
α-helix	254-257	4
α-helix	258-260	3
α-helix	263-282	20
α-helix	286-301	16
α-helix	308-331	24
α-helix	335-348	14
α-helix	353-364	12
α-helix	369-382	14
α-helix	387-410	24
α-helix	414-421	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Heat shock protein HSP 90-alpha	A, B	protein	731	Homo sapiens	P07900 (AlphaFold model)
Glucocorticoid receptor	C	protein	360	Homo sapiens	P04150 (AlphaFold model)
Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed	D	protein	459	Homo sapiens	Q02790 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8FFV_1 Heat shock protein HSP 90-alpha (chains A, B)
PEETQTQDQPMEEEEVETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNSSDALDKIRY
ESLTDPSKLDSGKELHINLIPNKQDRTLTIVDTGIGMTKADLINNLGTIAKSGTKAFMEA
LQAGADISMIGQFGVGFYSAYLVAEKVTVITKHNDDEQYAWESSAGGSFTVRTDTGEPMG
RGTKVILHLKEDQTEYLEERRIKEIVKKHSQFIGYPITLFVEKERDKEVSDDEAEEKEDK
EEEKEKEEKESEDKPEIEDVGSDEEEEKKDGDKKKKKKIKEKYIDQEELNKTKPIWTRNP
DDITNEEYGEFYKSLTNDWEDHLAVKHFSVEGQLEFRALLFVPRRAPFDLFENRKKKNNI
KLYVRRVFIMDNCEELIPEYLNFIRGVVDSEDLPLNISREMLQQSKILKVIRKNLVKKCL
ELFTELAEDKENYKKFYEQFSKNIKLGIHEDSQNRKKLSELLRYYTSASGDEMVSLKDYC
TRMKENQKHIYYITGETKDQVANSAFVERLRKHGLEVIYMIEPIDEYCVQQLKEFEGKTL
VSVTKEGLELPEDEEEKKKQEEKKTKFENLCKIMKDILEKKVEKVVVSNRLVTSPCCIVT
STYGWTANMERIMKAQALRDNSTMGYMAAKKHLEINPDHSIIETLRQKAEADKNDKSVKD
LVILLYETALLSSGFSLEDPQTHANRIYRMIKLGLGIDEDDPTADDTSAAVTEEMPPLEG
DDDTSRMEEVD

Sequence of entity 2 (C), FASTA

>8FFV_2 Glucocorticoid receptor (chains C)
PKLCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACR
YRKCLQAGMNLEARKTKKKIKGIQQATTGVSQETSENPGNKTIVPATLPQLTPTLVSLLE
VIEPEVLYAGYDSSVPDSTWRIMTTLNMLGGRQVIAAVKWAKAIPGFRNLHLDDQMTLLQ
YSWMSLMAFALGWRSYRQSSANLLCFAPDLIINEQRMTLPCMYDQCKHMLYVSSELHRLQ
VSYEEYLCMKTLLLLSSVPKDGLKSQELFDEIRMTYIKELGKAIVKREGNSSQNWQRFYQ
LTKLLDSMHEVVENLLNYCFQTFLDKTMSIEFPEMLAEIITNQIPKYSNGNIKKLLFHQK

Sequence of entity 3 (D), FASTA

>8FFV_3 Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed (chains D)
MTAEEMKATESGAQSAPLPMEGVDISPKQDEGVLKVIKREGTGTEMPMIGDRVFVHYTGW
LLDGTKFDSSLDRKDKFSFDLGKGEVIKAWDIAIATMKVGEVCHITCKPEYAYGSAGSPP
KIPPNATLVFEVELFEFKGEDLTEEEDGGIIRRIQTRGEGYAKPNEGAIVEVALEGYYKD
KLFDQRELRFEIGEGENLDLPYGLERAIQRMEKGEHSIVYLKPSYAFGSVGKEKFQIPPN
AELKYELHLKSFEKAKESWEMNSEEKLEQSTIVKERGTVYFKEGKYKQALLQYKKIVSWL
EYESSFSNEEAQKAQALRLASHLNLAMCHLKLQAFSAAIESCNKALELDSNNEKGLFRRG
EAHLAVNDFELARADFQKVLQLYPNNKAAKTQLAVCQQRIRRQLAREKKLYANMFERLAE
EENKAKAEASSGDHPTDTEMKEEQKSNTAGSQSQVETEA

Ligands and cofactors

ID	Name	Formula	Copies
DEX	Dexamethasone	C22 H29 F O5	1
MG	Magnesium ion	Mg	2
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	2

Primary citation

Cryo-EM reveals how Hsp90 and FKBP immunophilins co-regulate the glucocorticoid receptor. Noddings, C.M., Johnson, J.L., Agard, D.A. Nat Struct Mol Biol (2023) 30:1867-1877. DOI 10.1038/s41594-023-01128-y · PubMed

Other PDB entries of the same protein (UniProt P07900 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6TN5 1.17 Å, Rapid optimisation of fragments and hits to lead compounds from screening of crude…
5J80 1.17 Å, Crystal Structure of Apo Hsp90-alpha N-domain L107A mutant
3T0H 1.2 Å, Structure insights into mechanisms of ATP hydrolysis and the activation of human Hsp90
5J2X 1.22 Å, Crystal Structure of Hsp90-alpha N-domain in complex with…
3T10 1.24 Å, HSP90 N-terminal domain bound to ACP
6TN4 1.27 Å, Rapid optimisation of fragments and hits to lead compounds from screening of crude…
3WHA 1.3 Å, Hsp90 alpha N-terminal domain in complex with a tricyclic inhibitor
5XRD 1.3 Å, Crystal Structure of the human Hsp90-alpha N-domain bound to the hsp90 inhibitor FS7
2YK9 1.32 Å, Tricyclic series of Hsp90 inhibitors
5LRL 1.33 Å, Crystal structure of HSP90 in complex with A003492875
6GR5 1.34 Å, Structure of human Heat shock protein 90-alpha N-terminal domain (Hsp90-NTD) variant…
3B28 1.35 Å, Hsp90 alpha N-terminal domain in complex with an inhibitor CH5015765

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