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- PDB-8av2: Crystal structure for the FnIII module of mouse LEP-R in complex ... -

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Basic information

Entry
Database: PDB / ID: 8av2
TitleCrystal structure for the FnIII module of mouse LEP-R in complex with the anti-LEP-R nanobody VHH-4.80
Components
  • Leptin receptor
  • anti-mLEPR VHH 4-80
KeywordsCYTOKINE / leptin / LEP-R / obesity / metabolism / energy balance
Function / homology
Function and homology information


negative regulation of locomotor rhythm / negative regulation of eating behavior / leptin receptor activity / regulation of transport / protein-hormone receptor activity / bone growth / leptin-mediated signaling pathway / regulation of bone remodeling / response to leptin / regulation of feeding behavior ...negative regulation of locomotor rhythm / negative regulation of eating behavior / leptin receptor activity / regulation of transport / protein-hormone receptor activity / bone growth / leptin-mediated signaling pathway / regulation of bone remodeling / response to leptin / regulation of feeding behavior / sexual reproduction / regulation of metabolic process / cytokine receptor activity / eating behavior / glycogen metabolic process / cytokine binding / positive regulation of insulin secretion involved in cellular response to glucose stimulus / peptide hormone binding / T cell differentiation / glial cell proliferation / negative regulation of gluconeogenesis / phagocytosis / energy homeostasis / cholesterol metabolic process / negative regulation of autophagy / gluconeogenesis / cytokine-mediated signaling pathway / transmembrane signaling receptor activity / glucose homeostasis / positive regulation of cold-induced thermogenesis / basolateral plasma membrane / angiogenesis / positive regulation of MAPK cascade / receptor complex / positive regulation of protein phosphorylation / external side of plasma membrane / signal transduction / extracellular space / identical protein binding / plasma membrane
Similarity search - Function
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. / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III ...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. / 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
Biological speciesMus musculus (house mouse)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsVerstraete, K. / Savvides, S.N. / Verschueren, K.G. / Tsirigotaki, A.
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
DepositionAug 26, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 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 1.2Feb 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

Downloads & links

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Assembly

Deposited unit
A: Leptin receptor
B: Leptin receptor
C: anti-mLEPR VHH 4-80
D: anti-mLEPR VHH 4-80
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,57018
Polymers76,7254
Non-polymers1,84514
Water9,260514
1
A: Leptin receptor
C: anti-mLEPR VHH 4-80
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,38110
Polymers38,3622
Non-polymers1,0198
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint-66 kcal/mol
Surface area15730 Å2
MethodPISA
2
B: Leptin receptor
D: anti-mLEPR VHH 4-80
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1898
Polymers38,3622
Non-polymers8276
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-40 kcal/mol
Surface area16080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.192, 85.876, 144.689
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Leptin receptor / / LEP-R / B219 / OB receptor / OB-R


Mass: 22779.152 Da / Num. of mol.: 2 / Mutation: N668Q, N698Q, N726Q
Source method: isolated from a genetically manipulated source
Details: This sequence corresponds to the membrane proximal FnIII module of the mouse leptin receptor (mLEP-R, residues 633 to 827). To facilitate crystallization, three Asn residues were mutated ...Details: This sequence corresponds to the membrane proximal FnIII module of the mouse leptin receptor (mLEP-R, residues 633 to 827). To facilitate crystallization, three Asn residues were mutated (N668Q, N698Q, N726Q). This FnIII module was co-expressed and co-purified with a His-tagged anti-mLEP-R nanobody (VHH 4.11). Prior to crystallisation experiments, the protein complex was deglycosylated with EndoH. Cys751 of mLEP-R was found to be oxidized and modelled as hydroxycysteine residue (CSO).
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Lepr, Db, Obr / Plasmid: pHLsec
Details (production host): Aricescu et al., ActaCrystD, 2006
Cell line (production host): HEK293 / Production host: Homo sapiens (human) / Variant (production host): FreeStyle cells / References: UniProt: P48356
#2: Antibody anti-mLEPR VHH 4-80


Mass: 15583.163 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: ETGQVQLQESGGGLVQPGGSLRLSCAASGFTLDDYGIAWFRQAPGKEREGVSCISTSDDSTYYADSVKGRFTISRDTAKNTVYLQMNSLKPEDTAVYYCAAERAPMCYSRSYYLVDYGMDYWGKGTQVTVSSGTKHHHHHH
Source: (gene. exp.) Lama glama (llama) / Plasmid: pHLsec / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / Variant (production host): FreeStyle
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 514 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.15 Å3/Da / Density % sol: 42.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2 M ammonium sulphate 0.1 M Na cacodylate pH 5.6 30% PEG Smear Medium
Temp details: Temperature-controlled cabinet

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Cryostream 800 series / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.972418 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 12, 2022 / Details: adaptive KB-mirrors
RadiationMonochromator: Si(111) or Si(311); both crystals LN2 cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972418 Å / Relative weight: 1
ReflectionResolution: 1.75→90 Å / Num. obs: 67680 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 11.9 % / Biso Wilson estimate: 32.147 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.164 / Net I/av σ(I): 10.48 / Net I/σ(I): 10.48
Reflection shellResolution: 1.75→1.86 Å / Redundancy: 11.5 % / Mean I/σ(I) obs: 0.86 / Num. unique obs: 10778 / CC1/2: 0.326 / Rrim(I) all: 2.066 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (3-FEB-2022)refinement
XDSVERSION Jan 10, 2022 BUILT=20220220data reduction
Aimlessversion 0.7.7data scaling
PHASERversion 2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OHQ, AF-P48356-F1-model_v1

1ohq


Resolution: 1.75→25.42 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.943 / SU R Cruickshank DPI: 0.123 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.131 / SU Rfree Blow DPI: 0.124 / SU Rfree Cruickshank DPI: 0.12
RfactorNum. reflection% reflectionSelection details
Rfree0.2333 3373 5 %RANDOM
Rwork0.1934 ---
obs0.1953 67651 100 %-
Displacement parametersBiso mean: 38.46 Å2
Baniso -1Baniso -2Baniso -3
1-1.6091 Å20 Å20 Å2
2---2.2495 Å20 Å2
3---0.6404 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: LAST / Resolution: 1.75→25.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5131 0 106 514 5751
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0085531HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.937546HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1885SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes922HARMONIC5
X-RAY DIFFRACTIONt_it5531HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion705SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies16HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact5000SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.71
X-RAY DIFFRACTIONt_other_torsion15.69
LS refinement shellResolution: 1.75→1.76 Å
RfactorNum. reflection% reflection
Rfree0.4167 58 -
Rwork0.4067 --
obs0.4071 1354 99.26 %
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)
11.0965-0.4741-0.26231.3821-0.06265.8203-0.1970.2620.24490.2620.03770.40120.24490.40120.15920.02980.0253-0.0066-0.03310.0158-0.035122.483716.722328.4817
22.5127-0.2894-1.12773.2939-2.06573.6902-0.12530.6989-0.19630.6989-0.05430.4859-0.19630.48590.17960.10990.0281-0.0803-0.00350.0259-0.019926.483113.061935.9606
32.3625-0.5637-0.3592.6877-0.14753.5714-0.19810.28510.37610.28510.08930.0450.37610.0450.10880.03820.03260.0266-0.10020.0293-0.041221.57458.511731.2949
41.302-0.35941.13123.90351.70832.0667-0.1201-0.0737-0.2123-0.07370.1118-0.0575-0.2123-0.05750.0083-0.0229-0.00210.0193-0.0195-0.02390.020418.344731.682925.6701
55.60712.811.29296.50750.31263.63760.05190.0666-0.10810.0666-0.045-0.0838-0.1081-0.0838-0.007-0.0597-0.0048-0.0321-0.10770.012-0.04121.532229.631828.7778
62.30911.37220.45915.4037-0.17472.6771-0.0918-0.0836-0.2924-0.08360.03310.2743-0.29240.27430.0587-0.0003-0.0202-0.0047-0.0154-0.00340.045824.922432.358623.4904
71.1987-0.1188-0.83760.0189-0.4319.0641-0.26560.00750.44630.0075-0.0646-0.33220.4463-0.33220.33010.0349-0.06410.0568-0.0314-0.0511-0.02830.871614.656540.3619
83.8592-0.084-1.03893.9430.96678.4769-0.3936-0.37930.9417-0.3793-0.1016-0.70110.9417-0.70110.49520.0692-0.13060.1732-0.1592-0.093-0.0642-1.02818.708339.5006
90.77-0.4832-0.75221.51190.6031.5793-0.0228-0.1591-0.0127-0.1591-0.0435-0.0823-0.0127-0.08230.0663-0.03080.01330.0555-0.0516-0.0023-0.0233.278924.787742.1938
103.4788-2.6122-0.66614.2542-0.35942.8719-0.00810.0621-0.11740.06210.0784-0.2991-0.1174-0.2991-0.0703-0.04980.01910.0402-0.0467-0.0022-0.0162-3.742330.402445.2413
116.892-3.769-3.34087.71642.63734.13330.1956-0.4049-0.2693-0.4049-0.1283-0.4693-0.2693-0.4693-0.0673-0.1352-0.0011-0.03710.13370.0765-0.177418.029226.5249-10.2313
122.4074-0.9334-4.93050.31123.591710.17640.1020.14570.1130.14570.085-0.24040.113-0.2404-0.187-0.08130.0014-0.00860.0870.1046-0.021220.545331.3087-7.1551
134.1315-1.8254-1.14245.00152.42293.1241-0.0172-0.3163-0.5884-0.31630.0286-0.1717-0.5884-0.1717-0.01140.01060.0291-0.02620.0350.05370.006415.622230.49343.0801
145.02210.89020.94241.35840.86963.52860.10920.14520.06410.14520.0648-0.07310.0641-0.0731-0.174-0.0566-0.0084-0.00030.02480.0364-0.064419.294322.47273.5217
153.0393-0.93170.09711.4304-0.58822.2533-0.01210.0728-0.17860.0728-0.02070.0325-0.17860.03250.0328-0.0386-0.0247-0.00580.02760.0426-0.01325.504927.424-0.9186
167.18750.9451-2.0272.0509-0.2682.7621-0.03360.13940.11330.1394-0.1211-0.26330.1133-0.26330.1547-0.0842-0.0243-0.00540.0958-0.0287-0.020125.747615.2254-9.4031
173.0377-1.4077-1.14112.43591.09864.0980.02520.0447-0.17130.0447-0.1029-0.371-0.1713-0.3710.0777-0.0823-0.0123-0.00580.06170.0305-0.039514.158225.4930.4699
181.8693-0.0237-0.41640.47160.27782.0138-0.00490.0536-0.0620.05360.0336-0.1902-0.062-0.1902-0.0287-0.0431-0.0057-0.00910.03740.0131-0.034315.715523.32543.1814
194.23222.3195-2.6127.5933-4.7667.16690.36090.5223-0.41870.5223-0.47260.8655-0.41870.86550.1117-0.184-0.0256-0.00390.2691-0.1051-0.27340.786124.527481.3147
207.12821.3463-1.58173.0157-3.20178.31-0.01540.8447-1.35230.8447-0.0610.4305-1.35230.43050.0764-0.0107-0.0201-0.03630.0646-0.0617-0.07354.256128.409769.0597
2113.0956-0.6213-0.92031.47761.66227.0034-0.41250.38530.47190.38530.33870.370.47190.370.0738-0.02230.04930.02820.13680.05360.03845.607515.310171.6789
224.50624.2145-3.16899.4899-6.39836.8836-0.1231-0.35210.1326-0.35210.096-0.44680.1326-0.44680.027-0.07270.04180.00640.0567-0.0738-0.0935-6.272920.090966.2053
236.91842.71430.636810.1437-0.05895.040.0878-0.1497-0.5331-0.1497-0.1757-0.1578-0.5331-0.15780.0879-0.07620.04190.03910.0748-0.1512-0.0647-4.706128.721374.1429
246.21473.4398-4.20372.6463-2.7847.4129-0.032-0.00930.0844-0.0093-0.32070.52770.08440.52770.3526-0.16870.1059-0.00530.12250.0391-0.11971.700517.818275.6793
253.19211.0586-1.50760.5828-0.47792.8127-0.0266-0.06760.0069-0.0676-0.08970.24690.00690.24690.1163-0.05790.04060.00080.10260.0193-0.04195.023721.139868.241
268.05676.096-4.05268.76885.03651.0176-0.2076-0.24480.4092-0.24480.55050.92710.40920.9271-0.34290.13140.15430.01230.0499-0.0431-0.02229.29478.639114.116
270.6804-1.29060.52840.36150.202400.0196-0.16930.1305-0.16930.00690.07280.13050.0728-0.02650.3044-0.01750.07961.00020.02710.784616.70311.257618.363
289.341-4.9127-5.06234.66444.2580.45560.0455-0.6120.3873-0.6120.1348-0.3250.3873-0.325-0.18030.4839-0.30160.28390.01580.0622-0.0476-5.20795.32456.6881
290-0.6738-0.02911.3253-0.84870-0.03640.04850.12760.04850.02030.22430.12760.22430.01610.1772-0.01330.2994-0.10540.23760.19945.5241.201452.2591
301.2826-0.5904-0.61621.8123-0.2853.4197-0.3587-0.12040.2907-0.12040.13660.1330.29070.1330.2221-0.3306-0.0488-0.266-0.3095-0.1252-0.189814.145916.405333.6679
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|636 - A|655 }A636 - 655
2X-RAY DIFFRACTION2{ A|656 - A|683 }A656 - 683
3X-RAY DIFFRACTION3{ A|684 - A|725 }A684 - 725
4X-RAY DIFFRACTION4{ A|726 - A|758 }A726 - 758
5X-RAY DIFFRACTION5{ A|759 - A|796 }A759 - 796
6X-RAY DIFFRACTION6{ A|797 - A|827 }A797 - 827
7X-RAY DIFFRACTION7{ B|632 - B|655 }B632 - 655
8X-RAY DIFFRACTION8{ B|656 - B|707 }B656 - 707
9X-RAY DIFFRACTION9{ B|708 - B|774 }B708 - 774
10X-RAY DIFFRACTION10{ B|775 - B|827 }B775 - 827
11X-RAY DIFFRACTION11{ C|4 - C|20 }C4 - 20
12X-RAY DIFFRACTION12{ C|21 - C|28 }C21 - 28
13X-RAY DIFFRACTION13{ C|29 - C|42 }C29 - 42
14X-RAY DIFFRACTION14{ C|43 - C|60 }C43 - 60
15X-RAY DIFFRACTION15{ C|61 - C|86 }C61 - 86
16X-RAY DIFFRACTION16{ C|87 - C|94 }C87 - 94
17X-RAY DIFFRACTION17{ C|95 - C|103 }C95 - 103
18X-RAY DIFFRACTION18{ C|104 - C|132 }C104 - 132
19X-RAY DIFFRACTION19{ D|5 - D|28 }D5 - 28
20X-RAY DIFFRACTION20{ D|29 - D|42 }D29 - 42
21X-RAY DIFFRACTION21{ D|43 - D|54 }D43 - 54
22X-RAY DIFFRACTION22{ D|55 - D|70 }D55 - 70
23X-RAY DIFFRACTION23{ D|71 - D|86 }D71 - 86
24X-RAY DIFFRACTION24{ D|87 - D|103 }D87 - 103
25X-RAY DIFFRACTION25{ D|104 - D|132 }D104 - 132
26X-RAY DIFFRACTION26{ E|657 - E|657 }E657
27X-RAY DIFFRACTION27{ E|686 - E|686 }E686
28X-RAY DIFFRACTION28{ F|657 - F|657 }F657
29X-RAY DIFFRACTION29{ F|686 - F|686 }F686
30X-RAY DIFFRACTION30{ L|1 - L|10 }L1 - 10

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