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- PDB-7z3q: Crystal structure of the human leptin:LepR-CRH2 encounter complex... -

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Basic information

Entry
Database: PDB / ID: 7z3q
TitleCrystal structure of the human leptin:LepR-CRH2 encounter complex to 3.6 A resolution.
Components
  • Leptin receptor
  • Leptin
KeywordsCYTOKINE / leptin / obesity / leptin receptor / LepR / adipose tissue / hypothalamus / immune system
Function / homology
Function and homology information


regulation of lipoprotein lipid oxidation / cellular response to L-ascorbic acid / positive regulation of fat cell apoptotic process / negative regulation of glutamine transport / leptin receptor activity / regulation of transport / negative regulation of appetite by leptin-mediated signaling pathway / negative regulation of glucagon secretion / regulation of endothelial cell proliferation / regulation of natural killer cell proliferation ...regulation of lipoprotein lipid oxidation / cellular response to L-ascorbic acid / positive regulation of fat cell apoptotic process / negative regulation of glutamine transport / leptin receptor activity / regulation of transport / negative regulation of appetite by leptin-mediated signaling pathway / negative regulation of glucagon secretion / regulation of endothelial cell proliferation / regulation of natural killer cell proliferation / leptin receptor binding / positive regulation of luteinizing hormone secretion / regulation of natural killer cell mediated cytotoxicity / bone growth / regulation of natural killer cell activation / positive regulation of monoatomic ion transport / glycerol biosynthetic process / elastin metabolic process / leptin-mediated signaling pathway / positive regulation of follicle-stimulating hormone secretion / regulation of steroid biosynthetic process / regulation of intestinal cholesterol absorption / regulation of bone remodeling / regulation of brown fat cell differentiation / positive regulation of peroxisome proliferator activated receptor signaling pathway / adult feeding behavior / positive regulation of hepatic stellate cell activation / response to leptin / regulation of feeding behavior / bone mineralization involved in bone maturation / sexual reproduction / activation of protein kinase C activity / negative regulation of cartilage development / multicellular organism development / ovulation from ovarian follicle / negative regulation of appetite / positive regulation of developmental growth / leukocyte tethering or rolling / energy reserve metabolic process / prostaglandin secretion / bile acid metabolic process / negative regulation of glucose import / cellular response to leptin stimulus / hormone metabolic process / cardiac muscle hypertrophy / Signaling by Leptin / cytokine receptor activity / insulin secretion / intestinal absorption / aorta development / positive regulation of p38MAPK cascade / peptide hormone receptor binding / negative regulation of vasoconstriction / eating behavior / regulation of nitric-oxide synthase activity / regulation of gluconeogenesis / fatty acid beta-oxidation / glycogen metabolic process / central nervous system neuron development / cytokine binding / regulation of cytokine production involved in inflammatory response / response to dietary excess / regulation of insulin secretion / transport across blood-brain barrier / negative regulation of lipid storage / T cell differentiation / positive regulation of TOR signaling / response to vitamin E / Synthesis, secretion, and deacylation of Ghrelin / glial cell proliferation / adipose tissue development / regulation of angiogenesis / negative regulation of gluconeogenesis / phagocytosis / energy homeostasis / positive regulation of insulin receptor signaling pathway / cellular response to retinoic acid / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of T cell proliferation / cholesterol metabolic process / positive regulation of interleukin-12 production / negative regulation of autophagy / response to activity / placenta development / female pregnancy / gluconeogenesis / determination of adult lifespan / positive regulation of interleukin-8 production / positive regulation of receptor signaling pathway via JAK-STAT / response to insulin / lipid metabolic process / hormone activity / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / regulation of blood pressure / Transcriptional regulation of white adipocyte differentiation / cytokine-mediated signaling pathway / positive regulation of protein import into nucleus / positive regulation of interleukin-6 production / circadian rhythm / cellular response to insulin stimulus
Similarity search - Function
Leptin / Leptin / Leptin receptor, immunoglobulin-like domain / Obesity receptor immunoglobulin like domain / Immunoglobulin C2-set-like, ligand-binding / Ig-like C2-type domain / Short hematopoietin receptor, family 1, conserved site / Long hematopoietin receptor, Gp130 family 2, conserved site / Long hematopoietin receptor, gp130 family signature. / Four-helical cytokine-like, core ...Leptin / Leptin / Leptin receptor, immunoglobulin-like domain / Obesity receptor immunoglobulin like domain / Immunoglobulin C2-set-like, ligand-binding / Ig-like C2-type domain / Short hematopoietin receptor, family 1, conserved site / Long hematopoietin receptor, Gp130 family 2, conserved site / Long hematopoietin receptor, gp130 family signature. / Four-helical cytokine-like, core / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like fold
Similarity search - Domain/homology
Leptin / Leptin receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.617 Å
AuthorsVerstraete, K. / Verschueren, K. / Alexandra, T. / Savvides, S.N.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)G0G0619N Belgium
CitationJournal: Nat Struct Mol Biol / Year: 2023
Title: Mechanism of receptor assembly via the pleiotropic adipokine Leptin.
Authors: Alexandra Tsirigotaki / Ann Dansercoer / Koen H G Verschueren / Iva Marković / Christoph Pollmann / Maximillian Hafer / Jan Felix / Catherine Birck / Wouter Van Putte / Dominiek Catteeuw / ...Authors: Alexandra Tsirigotaki / Ann Dansercoer / Koen H G Verschueren / Iva Marković / Christoph Pollmann / Maximillian Hafer / Jan Felix / Catherine Birck / Wouter Van Putte / Dominiek Catteeuw / Jan Tavernier / J Fernando Bazan / Jacob Piehler / Savvas N Savvides / Kenneth Verstraete /
Abstract: The adipokine Leptin activates its receptor LEP-R in the hypothalamus to regulate body weight and exerts additional pleiotropic functions in immunity, fertility and cancer. However, the structure and ...The adipokine Leptin activates its receptor LEP-R in the hypothalamus to regulate body weight and exerts additional pleiotropic functions in immunity, fertility and cancer. However, the structure and mechanism of Leptin-mediated LEP-R assemblies has remained unclear. Intriguingly, the signaling-competent isoform of LEP-R is only lowly abundant amid several inactive short LEP-R isoforms contributing to a mechanistic conundrum. Here we show by X-ray crystallography and cryo-EM that, in contrast to long-standing paradigms, Leptin induces type I cytokine receptor assemblies featuring 3:3 stoichiometry and demonstrate such Leptin-induced trimerization of LEP-R on living cells via single-molecule microscopy. In mediating these assemblies, Leptin undergoes drastic restructuring that activates its site III for binding to the Ig domain of an adjacent LEP-R. These interactions are abolished by mutations linked to obesity. Collectively, our study provides the structural and mechanistic framework for how evolutionarily conserved Leptin:LEP-R assemblies with 3:3 stoichiometry can engage distinct LEP-R isoforms to achieve signaling.
History
DepositionMar 2, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 22, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 26, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Leptin
B: Leptin receptor
C: Leptin
D: Leptin receptor
E: Leptin
F: Leptin receptor


Theoretical massNumber of molelcules
Total (without water)134,1656
Polymers134,1656
Non-polymers00
Water362
1
A: Leptin
D: Leptin receptor


Theoretical massNumber of molelcules
Total (without water)44,7222
Polymers44,7222
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-9 kcal/mol
Surface area15900 Å2
2
B: Leptin receptor
C: Leptin


Theoretical massNumber of molelcules
Total (without water)44,7222
Polymers44,7222
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-8 kcal/mol
Surface area16830 Å2
3
E: Leptin
F: Leptin receptor


Theoretical massNumber of molelcules
Total (without water)44,7222
Polymers44,7222
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-6 kcal/mol
Surface area16110 Å2
Unit cell
Length a, b, c (Å)156.197, 156.644, 95.55
Angle α, β, γ (deg.)90, 90, 90
Int Tables number21
Space group name H-MC222

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Components

#1: Protein Leptin / / Obese protein / Obesity factor


Mass: 18605.061 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: The human leptin:LepR-CRH2 complex was produced by transient co-transfection in HEK293 FreeStyle cells in the presence of kifunensine. Prior to crystallisation, the N-terminal His-tags were ...Details: The human leptin:LepR-CRH2 complex was produced by transient co-transfection in HEK293 FreeStyle cells in the presence of kifunensine. Prior to crystallisation, the N-terminal His-tags were removed by a TEV-digest and the N-linked glycans were minimized by EndoH treatment.
Source: (gene. exp.) Homo sapiens (human) / Gene: LEP, OB, OBS / Plasmid: pTwist CMV BetaGlobin / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / Variant (production host): FreeStyle / References: UniProt: P41159
#2: Protein Leptin receptor / / LEP-R / HuB219 / OB receptor / OB-R


Mass: 26116.633 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: The human leptin:LepR-CRH2 complex was produced by transient co-transfection in HEK293 FreeStyle cells in the presence of kifunensine. Prior to crystallisation, the N-terminal His-tags were ...Details: The human leptin:LepR-CRH2 complex was produced by transient co-transfection in HEK293 FreeStyle cells in the presence of kifunensine. Prior to crystallisation, the N-terminal His-tags were removed by a TEV-digest and the N-linked glycans were minimized by EndoH treatment.
Source: (gene. exp.) Homo sapiens (human) / Gene: LEPR, DB, OBR / Plasmid: pTwist CMV BetaGlobin / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / Variant (production host): FreeStyle / References: UniProt: P48357
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Index screen HT #F1 0.2 M L-proline 0.1 M HEPES pH 7.5 10% PEG 3350 cryo: 25% PEG400
Temp details: Temperature-controlled cabinet

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Cold nitrogen stream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jun 6, 2020
RadiationMonochromator: Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.6→78.32 Å / Num. obs: 13958 / % possible obs: 100 % / Redundancy: 9.8 % / Biso Wilson estimate: 94.5 Å2 / CC1/2: 0.994 / Rrim(I) all: 0.334 / Net I/σ(I): 6
Reflection shellResolution: 3.6→3.94 Å / Redundancy: 10.1 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3298 / CC1/2: 0.584 / Rrim(I) all: 2.085 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (3-FEB-2022)refinement
XDSVERSION Feb 5, 2021 BUILT=20210205data reduction
Aimless0.7.3data scaling
PHASER2.7.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ax8, 3v6o

1ax8

3v6o


Resolution: 3.617→60.57 Å / Cor.coef. Fo:Fc: 0.876 / Cor.coef. Fo:Fc free: 0.87 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.782
RfactorNum. reflection% reflectionSelection details
Rfree0.3053 1050 -RANDOM
Rwork0.275 ---
obs0.2774 13623 98.9 %-
Displacement parametersBiso mean: 185.02 Å2
Baniso -1Baniso -2Baniso -3
1--53.7964 Å20 Å20 Å2
2--46.1946 Å20 Å2
3---7.6018 Å2
Refinement stepCycle: LAST / Resolution: 3.617→60.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7100 0 0 2 7102
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0057263HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.749886HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2486SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1173HARMONIC5
X-RAY DIFFRACTIONt_it7263HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion984SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact4876SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.34
X-RAY DIFFRACTIONt_other_torsion15.76
LS refinement shellResolution: 3.62→3.65 Å
RfactorNum. reflection% reflection
Rfree1.2157 19 -
Rwork1.0294 --
obs1.0415 273 64.17 %
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
114.42198.43745.60630-1.76719.8980.02810.5315-0.28330.53150.25840.4422-0.28330.4422-0.2865-0.2674-0.0688-0.04170.0136-0.089-0.0275-21.0349-49.2814-4.2632
23.9069-1.45493.909404.81335.89260.39380.37340.33030.37340.08720.69780.33030.6978-0.4810.1193-0.2299-0.1097-0.0523-0.1921-0.1185-27.2448-60.28876.2123
30-0.61412.34363.36667.29510-0.1819-1.0377-0.2298-1.03770.12920.435-0.22980.4350.0527-0.0872-0.0954-0.06240.2153-0.0992-0.1329-21.6792-58.957-0.9571
48.0952-0.5793.86540.5414-0.50760-0.0754-0.0911-0.2316-0.09110.58020.6156-0.23160.6156-0.5047-0.05750.02250.1055-0.0572-0.1492-0.0118-30.5512-51.62223.8026
50.85468.5839-4.970-7.72110-0.0179-0.2331-0.0788-0.23310.3389-0.0821-0.0788-0.0821-0.3210.4236-0.45590.2241-0.3656-0.1263-0.1572-18.0785-42.40076.4367
60.13560.7299-0.27611.01561.01400.0648-0.2398-0.0007-0.2398-0.08230.0704-0.00070.07040.0175-0.2155-0.0381-0.04980.24710.0128-0.0537-25.374-37.268829.7122
700.21766.41778.00077.38934.81490.6379-1.0617-1.3012-1.06170.2028-0.0613-1.3012-0.0613-0.84080.33950.0736-0.2623-0.2773-0.3355-0.15-15.4857-51.095543.4204
83.0392-0.0761-2.35145.76512.29151.10530.43880.84550.15360.8455-0.6920.34780.15360.34780.2532-0.1036-0.1743-0.21190.31710.0342-0.2232-9.4306-39.849852.2068
90.8708-0.40773.54170-0.03210-0.53940.9460.31670.9460.0168-0.34860.3167-0.34860.5226-0.43260.0523-0.27850.39120.0175-0.0021-17.1082-57.330531.4186
101.7853-3.4588-3.88111.8875-1.48850.29280.412-0.679-0.2172-0.6790.12710.1605-0.21720.1605-0.5391-0.1830.0811-0.07040.1497-0.1803-0.0077-25.6422-62.44225.5035
112.59913.0477-2.8831.88890.558200.3855-0.06560.5836-0.06560.14440.14250.58360.1425-0.53-0.47730.1437-0.13240.16-0.07840.2162-19.9433-67.723329.451
1202.22870.20540.3983-1.40781.9152-0.3545-0.40250.4012-0.40250.61210.48260.40120.4826-0.2577-0.0737-0.27990.06030.2289-0.1659-0.1054-16.7042-60.7785-21.606
138.2288.7312-8.73127.4096-8.731200.07420.0221-1.63270.02210.9139-0.4989-1.6327-0.4989-0.98810.4518-0.0261-0.2526-0.16110.0281-0.3892-27.4142-42.9436-14.4717
145.91940.7284-4.10855.91934.04183.27360.2253-0.24840.0581-0.2484-0.4008-0.65240.0581-0.65240.1755-0.2008-0.1953-0.22020.00360.1953-0.2119-25.2432-35.1979-26.9196
152.3309-3.7096-2.983302.230600.4345-0.7059-0.0689-0.70590.75680.936-0.06890.936-1.1912-0.26370.0192-0.2379-0.0166-0.08340.1541-44.5635-82.419119.3184
160-1.18772.770101.05695.50060.2289-0.6102-0.6797-0.61020.25080.0929-0.67970.0929-0.4797-0.3173-0.0121-0.0314-0.127-0.14860.235-40.3307-71.805415.2297
1702.18321.96173.7193.65250-0.8542-1.3217-0.3563-1.32170.5457-0.3663-0.3563-0.36630.30860.02810.12710.0634-0.3286-0.11740.2062-37.4622-78.609311.065
187.6873-2.6713.68560-2.08453.85790.50370.4706-0.24330.47060.07050.6038-0.24330.6038-0.5742-0.3401-0.2580.1275-0.36080.06610.6427-59.7565-74.490830.539
1908.73128.731212.271-4.82724.9119-0.1133-1.59340.43-1.5934-0.33121.40050.431.40050.4445-0.43750.0323-0.1432-0.5217-0.15890.9119-56.2929-88.878315.4317
200.06740.3975-5.85297.4475-1.16618.11690.2554-0.15950.5618-0.1595-0.2138-0.04190.5618-0.0419-0.0416-0.5326-0.0783-0.1665-0.3603-0.1030.8387-66.9725-98.806920.4901
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|22 - A|44 }A22 - 44
2X-RAY DIFFRACTION2{ A|67 - A|91 }A71 - 91
3X-RAY DIFFRACTION3{ A|92 - A|113 }A92 - 113
4X-RAY DIFFRACTION4{ A|114 - A|160 }A114 - 160
5X-RAY DIFFRACTION5{ A|161 - A|164 }A161 - 164
6X-RAY DIFFRACTION6{ B|429 - B|557 }B429 - 557
7X-RAY DIFFRACTION7{ B|558 - B|567 }B558 - 567
8X-RAY DIFFRACTION8{ B|568 - B|632 }B568 - 632
9X-RAY DIFFRACTION9{ C|24 - C|44 }C24 - 44
10X-RAY DIFFRACTION10{ C|45 - C|114 }C45 - 114
11X-RAY DIFFRACTION11{ C|115 - C|167 }C115 - 167
12X-RAY DIFFRACTION12{ D|430 - D|557 }D430 - 557
13X-RAY DIFFRACTION13{ D|558 - D|567 }D558 - 567
14X-RAY DIFFRACTION14{ D|568 - D|631 }D568 - 631
15X-RAY DIFFRACTION15{ E|22 - E|43 }E22 - 43
16X-RAY DIFFRACTION16{ E|44 - E|114 }E44 - 114
17X-RAY DIFFRACTION17{ E|115 - E|167 }E115 - 167
18X-RAY DIFFRACTION18{ F|430 - F|557 }F430 - 557
19X-RAY DIFFRACTION19{ F|558 - F|567 }F558 - 567
20X-RAY DIFFRACTION20{ F|568 - F|631 }F568 - 631

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