8QMO: Benzo[a]pyrene-bound Hsp90-XAP2-AHR complex

Cryo-EM structure of the benzo[a]pyrene-bound Hsp90-XAP2-AHR complex. Determined by electron microscopy at 2.76 Å resolution. Released 10 Jan 2024.

Method: Electron microscopy
Resolution: 2.76 Å
Organism: Homo sapiens
Chains: 4
Atoms: 14,052
Mol. weight: 257.09 kDa
Ligands: W62, MG, ADP, MOO
Released: 10 Jan 2024

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

Secondary structure: helices and β-sheets

8QMO contains 78 α-helices and 79 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: 28 helices, 31 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	38-60	23
α-helix	62-66	5
β-strand	73-78	6	3
β-strand	83-88	6	3
α-helix	95-97	3
α-helix	98-102	5
α-helix	103	1
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
β-strand	178-185	8	3
α-helix	190-193	4
α-helix	195-205	11
β-strand	213-218	6	3
β-strand	277-281	5	3
α-helix	288-290	3
α-helix	293-295	3
α-helix	298-309	12
β-strand	315-323	9	5
β-strand	329-336	8	5
β-strand	353-357	5	5
β-strand	360-364	5	5
α-helix	372-374	3
β-strand	378-383	6	5
β-strand	388	1	6
β-strand	395	1	6
α-helix	400-420	21
α-helix	423-443	21
α-helix	448-452	5
β-strand	457	1	7
β-strand	458-459	2	8
β-strand	467	1	7
α-helix	469-474	6
β-strand	482-487	6	8
α-helix	491-495	5
α-helix	501-505	5
β-strand	510-513	4	8
α-helix	516-522	7
β-strand	527-528	2	8
β-strand	531-535	5	8
β-strand	538	1	9
α-helix	547-570	24
β-strand	577-580	4	9
β-strand	589-593	5	9
β-strand	598	1	10
α-helix	600-607	8
α-helix	617-619	3
β-strand	621	1	10
α-helix	622-623	2
β-strand	624-628	5	9
α-helix	633-644	12
α-helix	649-665	17
α-helix	673-688	16

Chain B: 30 helices, 33 β-strands

Element	Residues	Length	Sheet
β-strand	12-16	5	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	83-88	6	1
α-helix	95-97	3
α-helix	98-102	5
α-helix	103	1
β-strand	104-105	2	2
α-helix	109-116	8
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	190-193	4
α-helix	195-205	11
β-strand	213-215	3	1
β-strand	216	1	11
β-strand	279	1	11
α-helix	288-290	3
α-helix	293-295	3
α-helix	298-309	12
β-strand	317-323	7	12
β-strand	329-335	7	12
β-strand	353-357	5	12
β-strand	360-364	5	12
α-helix	372-374	3
β-strand	378-383	6	12
β-strand	388	1	13
β-strand	395	1	13
α-helix	400-419	20
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	483-487	5	15
α-helix	491-495	5
α-helix	501-505	5
β-strand	510-513	4	15
α-helix	516-522	7
β-strand	527-528	2	16
β-strand	531-532	2	16
β-strand	533-535	3	15
β-strand	538	1	17
α-helix	547-559	13
α-helix	561-570	10
β-strand	577-580	4	17
β-strand	589-593	5	17
β-strand	598	1	18
α-helix	600-607	8
α-helix	614-619	6
β-strand	621	1	18
α-helix	622-623	2
β-strand	624-628	5	17
α-helix	633-644	12
α-helix	649-665	17
α-helix	673-688	16
α-helix	715-720	6

Chain C: 13 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	4-11	8
β-strand	15-19	5	19
β-strand	33-42	10	19
β-strand	49	1	19
β-strand	60	1	19
β-strand	63	1	19
α-helix	72-78	7
β-strand	85-88	4	19
α-helix	98-100	3
α-helix	140-142	3
β-strand	148-158	11	19
β-strand	160	1	20
β-strand	163	1	20
α-helix	167-169	3
α-helix	172-192	21
α-helix	196-213	18
α-helix	221-228	8
α-helix	230-243	14
α-helix	247-261	15
α-helix	265-277	13
α-helix	281-294	14
α-helix	299-323	25

Chain D: 7 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	287-291	5	21
β-strand	297-300	4	21
α-helix	302-307	6
α-helix	312-316	5
α-helix	322-324	3
β-strand	325	1	21
α-helix	327-329	3
α-helix	330-343	14
β-strand	345-354	10	21
β-strand	360-371	12	21
β-strand	376-386	11	21
α-helix	388-396	9
α-helix	422-424	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Heat shock protein HSP 90-beta	A, B	protein	730	Homo sapiens	P08238 (AlphaFold model)
AH receptor-interacting protein	C	protein	330	Homo sapiens	O00170 (AlphaFold model)
Aryl hydrocarbon receptor	D	protein	439	Homo sapiens	P35869 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8QMO_1 Heat shock protein HSP 90-beta (chains A, B)
MHHHHHHPEEVHHGEEEVETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNASDALDKI
RYESLTDPSKLDSGKELKIDIIPNPQERTLTLVDTGIGMTKADLINNLGTIAKSGTKAFM
EALQAGADISMIGQFGVGFYSAYLVAEKVVVITKHNDDEQYAWESSAGGSFTVRADHGEP
IGRGTKVILHLKEDQTEYLEERRVKEVVKKHSQFIGYPITLYLEKEREKEISDDEAEEEK
GEKEEEDKDDEEKPKIEDVGSDEEDDSGKDKKKKTKKIKEKYIDQEELNKTKPIWTRNPD
DITQEEYGEFYKSLTNDWEDHLAVKHFSVEGQLEFRALLFIPRRAPFDLFENKKKKNNIK
LYVRRVFIMDSCDELIPEYLNFIRGVVDSEDLPLNISREMLQQSKILKVIRKNIVKKCLE
LFSELAEDKENYKKFYEAFSKNLKLGIHEDSTNRRRLSELLRYHTSQSGDEMTSLSEYVS
RMKETQKSIYYITGESKEQVANSAFVERVRKRGFEVVYMTEPIDEYCVQQLKEFDGKSLV
SVTKEGLELPEDEEEKKKMEESKAKFENLCKLMKEILDKKVEKVTISNRLVSSPCCIVTS
TYGWTANMERIMKAQALRDNSTMGYMMAKKHLEINPDHPIVETLRQKAEADKNDKAVKDL
VVLLFETALLSSGFSLEDPQTHSNRIYRMIKLGLGIDEDEVAAEEPNAAVPDEIPPLEGD
EDASRMEEVD

Sequence of entity 2 (C), FASTA

>8QMO_2 AH receptor-interacting protein (chains C)
MADIIARLREDGIQKRVIQEGRGELPDFQDGTKATFHYRTLHSDDEGTVLDDSRARGKPM
ELIIGKKFKLPVWETIVCTMREGEIAQFLCDIKHVVLYPLVAKSLRNIAVGKDPLEGQRH
CCGVAQMREHSSLGHADLDALQQNPQPLIFHMEMLKVESPGTYQQDPWAMTDEEKAKAVP
LIHQEGNRLYREGHVKEAAAKYYDAIACLKNLQMKEQPGSPEWIQLDQQITPLLLNYCQC
KLVVEEYYEVLDHCSSILNKYDDNVKAYFKRGKAHAAVWNAQEAQADFAKVLELDPALAP
VVSRELQALEARIRQKDEEDKARFRGIFSH

Sequence of entity 3 (D), FASTA

>8QMO_3 Aryl hydrocarbon receptor (chains D)
GAPNSSSANITYASRKRRKPVQKTVKPIPAEGIKSNPSKRHRDRLNTELDRLASLLPFPQ
DVINKLDKLSVLRLSVSYLRAKSFFDVALKSSPTERNGGQDNCRAANFREGLNLQEGEFL
LQALNGFVLVVTTDALVFYASSTIQDYLGFQQSDVIHQSVYELIHTEDRAEFQRQLHWAL
NPSQCTESGQGIEEATGLPQTVVCYNPDQIPPENSPLMERCFICRLRCLLDNSSGFLAMN
FQGKLKYLHGQKKKGKDGSILPPQLALFAIATPLQPPSILEIRTKNFIFRTKHKLDFTPI
GCDAKGRIVLGYTEAELCTRGSGYQFIHAADMLYCAESHIRMIKTGESGMIVFRLLTKNN
RWTWVQSNARLLYKNGRPDYIIVTQRPLTDEEGTEHLRKRNTKLPFMFTTGEAVLYEATN
PFPAIMDPLPLRTKNGTSG

Ligands and cofactors

ID	Name	Formula	Copies
W62	benzo[a]pyrene	C20 H12	1
MG	Magnesium ion	Mg	2
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	2
MOO	Molybdate ion	Mo O4	2

Primary citation

Structural Insights into the Activation of Human Aryl Hydrocarbon Receptor by the Environmental Contaminant Benzo[a]pyrene and Structurally Related Compounds. Kwong, H.S., Paloni, M., Grandvuillemin, L. et al. J Mol Biol (2024) 436:168411-168411. DOI 10.1016/j.jmb.2023.168411 · 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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