8X80: Leptin-LepR trimer with a small gap

Structure of leptin-LepR trimer with a small gap. Determined by electron microscopy at 3.88 Å resolution. Released 7 Aug 2024.

Method: Electron microscopy
Resolution: 3.88 Å
Organism: Homo sapiens
Chains: 6
Atoms: 21,890
Mol. weight: 345.96 kDa
Ligands: NAG
Released: 7 Aug 2024

Explore 8X80 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8X80 contains 83 α-helices and 213 β-strands across 6 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: 21 helices, 77 β-strands

Element	Residues	Length	Sheet
β-strand	33-37	5	1
β-strand	86-88	3	2
β-strand	89-92	4	1
α-helix	106-108	3
α-helix	114-122	9
β-strand	126-130	5	1
β-strand	133	1	3
β-strand	139-141	3	3
β-strand	143-146	4	1
β-strand	157-164	8	2
α-helix	166-169	4
α-helix	175-177	3
β-strand	182-185	4	2
β-strand	186-188	3	1
β-strand	194-196	3	1
β-strand	197-199	3	3
β-strand	209-217	9	2
β-strand	220-223	4	2
β-strand	227-229	3	2
α-helix	231-233	3
β-strand	235	1	3
α-helix	237-240	4
β-strand	244-247	4	4
β-strand	253-256	4	4
β-strand	267-271	5	5
β-strand	274-276	3	6
β-strand	292-295	4	4
α-helix	298-299	2
β-strand	303-306	4	6
β-strand	308-312	5	5
α-helix	318-322	5
β-strand	326-329	4	6
β-strand	333-336	4	7
β-strand	339-343	5	8
β-strand	347-354	8	7
β-strand	355-356	2	9
β-strand	359-360	2	9
α-helix	361-362	2
α-helix	363-365	3
β-strand	367-370	4	8
β-strand	374-375	2	8
α-helix	376-377	2
α-helix	378-380	3
β-strand	382-383	2	7
β-strand	389-394	6	7
β-strand	402	1	10
β-strand	405	1	10
β-strand	408-413	6	8
β-strand	418	1	8
β-strand	423-428	6	8
β-strand	436	1	11
β-strand	438	1	12
β-strand	446-450	5	11
β-strand	462-465	4	13
β-strand	466	1	14
β-strand	484	1	14
β-strand	495-499	5	11
β-strand	509-511	3	15
β-strand	512-516	5	13
β-strand	521-523	3	13
α-helix	524-526	3
β-strand	527-529	3	15
α-helix	532-534	3
β-strand	535	1	12
α-helix	537-540	4
β-strand	544-547	4	16
α-helix	548	1
β-strand	553-557	5	16
β-strand	568-576	9	17
β-strand	584-588	5	17
β-strand	595-599	5	16
β-strand	607-615	9	17
α-helix	622-628	7
β-strand	629	1	17
β-strand	641	1	18
β-strand	645-649	5	19
β-strand	658-664	7	19
α-helix	665-667	3
α-helix	669-672	4
β-strand	678-685	8	20
β-strand	691-694	4	20
β-strand	700-705	6	19
β-strand	710-717	8	20
β-strand	722	1	20
β-strand	725	1	18
β-strand	729-731	3	20
α-helix	733-736	4
β-strand	741	1	21
β-strand	745	1	22
β-strand	748-750	3	22
β-strand	753-757	5	22
β-strand	760	1	21
β-strand	769-776	8	23
β-strand	784-789	6	23
β-strand	794-798	5	22
β-strand	807-813	7	23
α-helix	820-822	3
β-strand	823-825	3	23

Chain B: 21 helices, 64 β-strands

Element	Residues	Length	Sheet
β-strand	32-37	6	24
β-strand	86-88	3	25
β-strand	89-92	4	24
β-strand	97	1	24
α-helix	114-122	9
β-strand	127-133	7	24
β-strand	139-146	8	24
β-strand	157-163	7	25
β-strand	164	1	26
α-helix	166-168	3
α-helix	173-177	5
β-strand	182-186	5	25
β-strand	187	1	24
α-helix	188	1
β-strand	193-199	7	24
α-helix	202-206	5
α-helix	208-209	2
β-strand	210	1	26
β-strand	213-217	5	25
β-strand	220-223	4	25
β-strand	235	1	24
α-helix	237-240	4
α-helix	258-260	3
β-strand	271-276	6	27
β-strand	282-286	5	27
α-helix	293-294	2
β-strand	303-305	3	27
α-helix	318-321	4
β-strand	327-329	3	27
β-strand	334	1	28
β-strand	341-343	3	29
β-strand	347-350	4	30
β-strand	353	1	28
β-strand	366-370	5	31
β-strand	373	1	31
α-helix	375-377	3
α-helix	378-380	3
β-strand	391-394	4	30
α-helix	398-401	4
β-strand	408-414	7	31
β-strand	417-418	2	31
β-strand	423-425	3	31
β-strand	426-428	3	29
β-strand	434-438	5	32
β-strand	445-449	5	32
β-strand	461-469	9	33
α-helix	472-474	3
β-strand	484-485	2	33
β-strand	498-500	3	32
β-strand	508-516	9	33
β-strand	522-523	2	33
β-strand	528-529	2	33
α-helix	535-540	6
β-strand	541-547	7	34
α-helix	548	1
β-strand	554-559	6	34
β-strand	568-576	9	35
β-strand	584-588	5	35
β-strand	595-598	4	34
β-strand	607-615	9	35
β-strand	629-630	2	35
β-strand	641	1	36
β-strand	645-649	5	37
β-strand	660-664	5	37
α-helix	665-667	3
β-strand	679-684	6	38
β-strand	700-703	4	37
β-strand	710-716	7	38
β-strand	717	1	39
β-strand	722	1	39
β-strand	725	1	36
β-strand	728-731	4	38
α-helix	733-736	4
β-strand	741-750	10	40
β-strand	753-760	8	40
α-helix	761-762	2
β-strand	769-776	8	41
α-helix	781-783	3
β-strand	784-789	6	41
β-strand	798	1	40
β-strand	807-813	7	41
β-strand	814	1	42
β-strand	819	1	42
α-helix	820-822	3
β-strand	823-825	3	41

Chain C: 22 helices, 71 β-strands

Element	Residues	Length	Sheet
β-strand	26	1	43
β-strand	32-34	3	44
β-strand	35-37	3	45
β-strand	86-88	3	43
β-strand	89-92	4	45
β-strand	97-98	2	45
α-helix	114-122	9
β-strand	127-133	7	44
β-strand	139-146	8	44
β-strand	158-164	7	43
α-helix	166-168	3
α-helix	173-177	5
β-strand	182-186	5	43
β-strand	187	1	44
β-strand	194-199	6	44
β-strand	209-217	9	43
β-strand	220-223	4	43
α-helix	224-226	3
β-strand	227-229	3	43
β-strand	235	1	44
α-helix	236-240	5
β-strand	243	1	46
α-helix	256	1
β-strand	257	1	46
α-helix	258-260	3
β-strand	268	1	47
β-strand	271-273	3	48
β-strand	275-276	2	49
β-strand	281	1	49
β-strand	284-286	3	48
α-helix	298-299	2
β-strand	303-304	2	49
β-strand	306	1	50
β-strand	311	1	47
α-helix	318-322	5
β-strand	326	1	50
β-strand	333-335	3	51
β-strand	342-343	2	52
β-strand	347-350	4	53
β-strand	352-354	3	51
β-strand	366-370	5	54
β-strand	373	1	54
α-helix	375-377	3
α-helix	378-380	3
β-strand	381-383	3	53
β-strand	389-394	6	53
α-helix	396-399	4
β-strand	410-414	5	54
β-strand	423	1	54
β-strand	427-428	2	52
β-strand	435-438	4	55
β-strand	445-448	4	55
α-helix	451-454	4
β-strand	461-469	9	56
α-helix	473-474	2
β-strand	484-486	3	56
β-strand	489	1	57
β-strand	497	1	57
β-strand	498-500	3	55
β-strand	508-516	9	56
β-strand	521-523	3	56
α-helix	524-526	3
β-strand	527-529	3	56
α-helix	532-534	3
β-strand	535	1	55
α-helix	537-540	4
β-strand	544-547	4	58
β-strand	554-557	4	58
β-strand	568-576	9	59
β-strand	584-588	5	59
β-strand	595-598	4	58
β-strand	607-615	9	59
α-helix	624-628	5
β-strand	629	1	59
β-strand	646-649	4	60
β-strand	660-663	4	60
α-helix	665-668	4
α-helix	669-671	3
β-strand	678-685	8	61
β-strand	700-703	4	60
β-strand	710-717	8	61
β-strand	722	1	61
β-strand	729-731	3	61
α-helix	734-736	3
β-strand	741-747	7	62
β-strand	753-760	8	62
α-helix	761-762	2
β-strand	769-776	8	63
β-strand	784-789	6	63
β-strand	796-798	3	62
β-strand	807-814	8	63
β-strand	819	1	63
β-strand	825	1	63

Chain D: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	24-44	21
α-helix	72-88	17
α-helix	92-98	7
α-helix	101-114	14
α-helix	118-121	4
α-helix	144-163	20

Chain E: 6 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	24-42	19
β-strand	57	1	8
α-helix	72-87	16
α-helix	92-114	23
α-helix	128-130	3
α-helix	131-137	7
α-helix	140-161	22

Chain F: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	24-44	21
α-helix	47-49	3
α-helix	72-88	17
α-helix	92-114	23
α-helix	120-125	6
α-helix	128-135	8
α-helix	140-163	24

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Leptin receptor	A, B, C	protein	829	Homo sapiens	P48357 (AlphaFold model)
Leptin	D, E, F	protein	167	Homo sapiens	P41159 (AlphaFold model)

Sequence of entity 1 (A, B, C), FASTA

>8X80_1 Leptin receptor (chains A, B, C)
AFNLSYPITPWRFKLSCMPPNSTYDYFLLPAGLSKNTSNSNGHYETAVEPKFNSSGTHFS
NLSKTTFHCCFRSEQDRNCSLCADNIEGKTFVSTVNSLVFQQIDANWNIQCWLKGDLKLF
ICYVESLFKNLFRNYNYKVHLLYVLPEVLEDSPLVPQKGSFQMVHCNCSVHECCECLVPV
PTAKLNDTLLMCLKITSGGVIFQSPLMSVQPINMVKPDPPLGLHMEITDDGNLKISWSSP
PLVPFPLQYQVKYSENSTTVIREADKIVSATSLLVDSILPGSSYEVQVRGKRLDGPGIWS
DWSTPRVFTTQDVIYFPPKILTSVGSNVSFHCIYKKENKIVPSKEIVWWMNLAEKIPQSQ
YDVVSDHVSKVTFFNLNETKPRGKFTYDAVYCCNEHECHHRYAELYVIDVNINISCETDG
YLTKMTCRWSTSTIQSLAESTLQLRYHRSSLYCSDIPSIHPISEPKDCYLQSDGFYECIF
QPIFLLSGYTMWIRINHSLGSLDSPPTCVLPDSVVKPLPPSSVKAEITINIGLLKISWEK
PVFPENNLQFQIRYGLSGKEVQWKMYEVYDAKSKSVSLPVPDLCAVYAVQVRCKRLDGLG
YWSNWSNPAYTVVMDIKVPMRGPEFWRIINGDTMKKEKNVTLLWKPLMKNDSLCSVQRYV
INHHTSCNGTWSEDVGNHTKFTFLWTEQAHTVTVLAINSIGASVANFNLTFSWPMSKVNI
VQSLSAYPLNSSCVIVSWILSPSDYKLMYFIIEWKNLNEDGEIKWLRISSSVKKYYIHDH
FIPIEKYQFSLYPIFMEGVGKPKIINSFTQDDIEKHQSDGTHHHHHHHH

Sequence of entity 2 (D, E, F), FASTA

>8X80_2 Leptin (chains D, E, F)
MHWGTLCGFLWLWPYLFYVQAVPIQKVQDDTKTLIKTIVTRINDISHTQSVSSKQKVTGL
DFIPGLHPILTLSKMDQTLAVYQQILTSMPSRNVIQISNDLENLRDLLHVLAFSKSCHLP
WASGLETLDSLGGVLEASGYSTEVVALSRLQGSLQDMLWQLDLSPGC

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	15

Primary citation

Structural plasticity of human leptin binding to its receptor LepR. Xie, Y.F., Li, X., Qi, J. et al. Hlife (2023) 1:115-123. DOI 10.1016/j.hlife.2023.10.010

Other PDB entries of the same protein (UniProt P48357 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3V6O 1.95 Å, Leptin Receptor-antibody complex
6E2P 2.83 Å, Structure of human JAK2 FERM/SH2 in complex with Leptin Receptor
8X85 3.58 Å, Structure of leptin-LepR dimer
7Z3Q 3.62 Å, Crystal structure of the human leptin:LepR-CRH2 encounter complex to 3.6 A resolution.
8X81 3.77 Å, Structure of leptin-LepR trimer with a large gap
8AVE 5.62 Å, Human leptin in complex with the human LEP-R ectodomain fused to a C-terminal trimeric…
8AVF 6.45 Å, Human leptin in complex with the human LEP-R ectodomain fused to a C-terminal trimeric…
8AVO 6.84 Å, Human leptin in complex with the human LEP-R ectodomain fused to a C-terminal trimeric…

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