8X85: Leptin-LepR dimer

Structure of leptin-LepR dimer. Determined by electron microscopy at 3.58 Å resolution. Released 7 Aug 2024.

Method: Electron microscopy
Resolution: 3.58 Å
Organism: Homo sapiens
Chains: 4
Atoms: 14,490
Mol. weight: 230.71 kDa
Ligands: NAG
Released: 7 Aug 2024

Explore 8X85 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8X85 contains 42 α-helices and 160 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: 17 helices, 85 β-strands

Element	Residues	Length	Sheet
β-strand	26-27	2	1
β-strand	34-37	4	2
β-strand	85-88	4	1
β-strand	89-91	3	2
α-helix	117-122	6
β-strand	126-131	6	2
β-strand	134	1	3
β-strand	139	1	4
β-strand	142-146	5	2
β-strand	158-164	7	1
α-helix	174-176	3
β-strand	182-186	5	1
β-strand	187-188	2	2
β-strand	194-196	3	2
β-strand	199	1	4
α-helix	202-204	3
β-strand	209-217	9	1
β-strand	220-223	4	1
β-strand	227-229	3	1
α-helix	232-234	3
β-strand	236	1	3
α-helix	238-240	3
β-strand	241	1	5
β-strand	247	1	6
β-strand	253	1	6
β-strand	254-256	3	7
β-strand	258	1	5
β-strand	267-272	6	8
β-strand	274-276	3	9
β-strand	281-283	3	9
β-strand	286-288	3	8
β-strand	292-294	3	7
β-strand	303-306	4	9
β-strand	307-312	6	8
α-helix	321-325	5
β-strand	326-329	4	9
β-strand	333-334	2	10
β-strand	341-343	3	11
β-strand	353-354	2	10
β-strand	355	1	12
β-strand	360	1	12
α-helix	361-362	2
α-helix	363-365	3
β-strand	366-368	3	13
β-strand	369-370	2	14
β-strand	374-375	2	14
α-helix	376-377	2
α-helix	378-380	3
β-strand	381-383	3	15
β-strand	389-391	3	15
β-strand	402	1	16
β-strand	405	1	16
β-strand	408-410	3	17
β-strand	412-414	3	13
β-strand	417	1	13
β-strand	423-425	3	17
β-strand	426-428	3	11
β-strand	438	1	18
β-strand	445-447	3	19
β-strand	450	1	20
β-strand	462-466	5	21
β-strand	484-486	3	21
β-strand	489-490	2	22
β-strand	495	1	20
β-strand	496-497	2	22
β-strand	498-500	3	19
β-strand	509-511	3	23
β-strand	512-516	5	21
β-strand	521-523	3	21
β-strand	527-529	3	23
α-helix	531-533	3
β-strand	535	1	18
α-helix	537-540	4
β-strand	541-547	7	24
β-strand	554-559	6	24
β-strand	568-576	9	25
β-strand	584-588	5	25
β-strand	595-598	4	24
β-strand	607-615	9	25
α-helix	624-628	5
β-strand	641	1	26
β-strand	645-649	5	27
β-strand	658-664	7	27
α-helix	665-668	4
α-helix	669-672	4
β-strand	678-684	7	28
β-strand	692-696	5	28
β-strand	700-705	6	27
β-strand	709-717	9	28
β-strand	722	1	28
β-strand	725	1	26
β-strand	728-732	5	28
α-helix	734-737	4
β-strand	741-750	10	29
β-strand	753-760	8	29
β-strand	767-776	10	30
α-helix	781-783	3
β-strand	784-789	6	30
β-strand	794-797	4	29
β-strand	807-815	9	30
β-strand	818-819	2	30
β-strand	823-825	3	30

Chain B: 16 helices, 74 β-strands

Element	Residues	Length	Sheet
β-strand	26-27	2	31
β-strand	33-38	6	31
β-strand	85-92	8	31
β-strand	97-98	2	31
α-helix	117-122	6
β-strand	126-131	6	31
β-strand	133	1	32
β-strand	139-146	8	31
β-strand	158-164	7	31
α-helix	174-176	3
β-strand	182-185	4	31
β-strand	187-188	2	31
β-strand	193-199	7	31
α-helix	202-204	3
β-strand	209-217	9	31
β-strand	220-223	4	31
α-helix	224-226	3
β-strand	227-229	3	31
β-strand	235	1	32
α-helix	238-240	3
β-strand	241	1	33
β-strand	246	1	34
β-strand	254	1	34
β-strand	258	1	33
α-helix	259-260	2
β-strand	267-268	2	35
β-strand	271-272	2	36
β-strand	285-286	2	36
β-strand	294	1	34
β-strand	304-306	3	37
β-strand	311-312	2	35
β-strand	317	1	32
α-helix	319-322	4
β-strand	326-328	3	37
β-strand	333-335	3	38
β-strand	341-343	3	39
β-strand	348	1	40
β-strand	352-354	3	38
α-helix	363-365	3
β-strand	369-370	2	41
β-strand	373	1	41
α-helix	375-377	3
β-strand	381-383	3	42
β-strand	389-391	3	42
β-strand	393	1	40
α-helix	396-398	3
β-strand	402	1	43
β-strand	405	1	43
β-strand	410-411	2	41
β-strand	423	1	41
β-strand	426-428	3	39
β-strand	435-438	4	44
β-strand	445-450	6	44
β-strand	461-469	9	45
α-helix	473-474	2
β-strand	484-486	3	45
β-strand	489-490	2	44
β-strand	495-500	6	44
β-strand	508-517	10	45
β-strand	520-523	4	45
α-helix	524-526	3
β-strand	527-529	3	45
β-strand	535	1	44
α-helix	537-540	4
β-strand	541-547	7	46
α-helix	548	1
β-strand	553-559	7	46
β-strand	568-576	9	47
β-strand	584-588	5	47
β-strand	595-599	5	46
β-strand	607-615	9	47
β-strand	646-647	2	48
β-strand	660-663	4	48
α-helix	665-667	3
β-strand	678-685	8	49
β-strand	700-703	4	48
β-strand	710-717	8	49
β-strand	729-730	2	49
α-helix	734-737	4
β-strand	744-747	4	50
β-strand	753-758	6	50
β-strand	767-768	2	51
β-strand	769	1	52
β-strand	770-776	7	51
β-strand	784-786	3	51
β-strand	789	1	52
β-strand	796-798	3	50
β-strand	807-815	9	51
β-strand	818	1	51
β-strand	823-825	3	51

Chain C: 4 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	24-44	21
β-strand	56	1	13
α-helix	72-86	15
α-helix	92-114	23
α-helix	131-161	31

Chain D: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	27-44	18
α-helix	72-87	16
α-helix	92-114	23
α-helix	119-121	3
α-helix	142-163	22

Molecules and chains

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

Sequence of entity 1 (A, B), FASTA

>8X85_1 Leptin receptor (chains A, B)
AFNLSYPITPWRFKLSCMPPNSTYDYFLLPAGLSKNTSNSNGHYETAVEPKFNSSGTHFS
NLSKTTFHCCFRSEQDRNCSLCADNIEGKTFVSTVNSLVFQQIDANWNIQCWLKGDLKLF
ICYVESLFKNLFRNYNYKVHLLYVLPEVLEDSPLVPQKGSFQMVHCNCSVHECCECLVPV
PTAKLNDTLLMCLKITSGGVIFQSPLMSVQPINMVKPDPPLGLHMEITDDGNLKISWSSP
PLVPFPLQYQVKYSENSTTVIREADKIVSATSLLVDSILPGSSYEVQVRGKRLDGPGIWS
DWSTPRVFTTQDVIYFPPKILTSVGSNVSFHCIYKKENKIVPSKEIVWWMNLAEKIPQSQ
YDVVSDHVSKVTFFNLNETKPRGKFTYDAVYCCNEHECHHRYAELYVIDVNINISCETDG
YLTKMTCRWSTSTIQSLAESTLQLRYHRSSLYCSDIPSIHPISEPKDCYLQSDGFYECIF
QPIFLLSGYTMWIRINHSLGSLDSPPTCVLPDSVVKPLPPSSVKAEITINIGLLKISWEK
PVFPENNLQFQIRYGLSGKEVQWKMYEVYDAKSKSVSLPVPDLCAVYAVQVRCKRLDGLG
YWSNWSNPAYTVVMDIKVPMRGPEFWRIINGDTMKKEKNVTLLWKPLMKNDSLCSVQRYV
INHHTSCNGTWSEDVGNHTKFTFLWTEQAHTVTVLAINSIGASVANFNLTFSWPMSKVNI
VQSLSAYPLNSSCVIVSWILSPSDYKLMYFIIEWKNLNEDGEIKWLRISSSVKKYYIHDH
FIPIEKYQFSLYPIFMEGVGKPKIINSFTQDDIEKHQSDGTHHHHHHHH

Sequence of entity 2 (C, D), FASTA

>8X85_2 Leptin (chains C, D)
MHWGTLCGFLWLWPYLFYVQAVPIQKVQDDTKTLIKTIVTRINDISHTQSVSSKQKVTGL
DFIPGLHPILTLSKMDQTLAVYQQILTSMPSRNVIQISNDLENLRDLLHVLAFSKSCHLP
WASGLETLDSLGGVLEASGYSTEVVALSRLQGSLQDMLWQLDLSPGC

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	11

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
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
8X80 3.88 Å, Structure of leptin-LepR trimer with a small 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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