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- PDB-3v6o: Leptin Receptor-antibody complex -

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Basic information

Entry
Database: PDB / ID: 3v6o
TitleLeptin Receptor-antibody complex
Components
  • (Monoclonal antibody 9F8 fab fragment ...) x 2
  • Leptin receptor
KeywordsIMMUNE SYSTEM / Receptor-antibody complex / Cytokine receptor / Antibody Fab fragment / Immunoglobulin fold / Leptin Receptor-antibody complex
Function / homology
Function and homology information


multicellular organism development / leptin receptor activity / regulation of transport / bone growth / leptin-mediated signaling pathway / regulation of bone remodeling / response to leptin / sexual reproduction / regulation of feeding behavior / energy reserve metabolic process ...multicellular organism development / leptin receptor activity / regulation of transport / bone growth / leptin-mediated signaling pathway / regulation of bone remodeling / response to leptin / sexual reproduction / regulation of feeding behavior / energy reserve metabolic process / Signaling by Leptin / cell surface receptor signaling pathway via STAT / cytokine receptor activity / glycogen metabolic process / cytokine binding / peptide hormone binding / T cell differentiation / negative regulation of gluconeogenesis / phagocytosis / glial cell proliferation / transport across blood-brain barrier / energy homeostasis / negative regulation of autophagy / cholesterol metabolic process / gluconeogenesis / cytokine-mediated signaling pathway / transmembrane signaling receptor activity / glucose homeostasis / positive regulation of cold-induced thermogenesis / basolateral plasma membrane / angiogenesis / receptor complex / cell surface receptor signaling pathway / external side of plasma membrane / positive regulation of cell population proliferation / extracellular region / identical protein binding
Similarity search - Function
Leptin receptor, immunoglobulin-like domain / Obesity receptor immunoglobulin like domain / Short hematopoietin receptor, family 1, conserved site / Immunoglobulin C2-set-like, ligand-binding / Ig-like C2-type domain / Long hematopoietin receptor, Gp130 family 2, conserved site / Long hematopoietin receptor, gp130 family signature. / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. ...Leptin receptor, immunoglobulin-like domain / Obesity receptor immunoglobulin like domain / Short hematopoietin receptor, family 1, conserved site / Immunoglobulin C2-set-like, ligand-binding / Ig-like C2-type domain / Long hematopoietin receptor, Gp130 family 2, conserved site / Long hematopoietin receptor, gp130 family signature. / Fibronectin type III domain / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / CYSTEINE / Leptin receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsCarpenter, B. / Hemsworth, G.R. / Ross, R.J. / Artymiuk, P.J.
CitationJournal: Structure / Year: 2012
Title: Structure of the human obesity receptor leptin-binding domain reveals the mechanism of leptin antagonism by a monoclonal antibody.
Authors: Carpenter, B. / Hemsworth, G.R. / Wu, Z. / Maamra, M. / Strasburger, C.J. / Ross, R.J. / Artymiuk, P.J.
History
DepositionDec 20, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2012Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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: Monoclonal antibody 9F8 fab fragment Heavy chain
D: Monoclonal antibody 9F8 fab fragment Heavy chain
E: Monoclonal antibody 9F8 fab fragment Light chain
F: Monoclonal antibody 9F8 fab fragment Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,45647
Polymers141,6916
Non-polymers2,76541
Water15,331851
1
A: Leptin receptor
C: Monoclonal antibody 9F8 fab fragment Heavy chain
E: Monoclonal antibody 9F8 fab fragment Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,97421
Polymers70,8463
Non-polymers1,12818
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5220 Å2
ΔGint-33 kcal/mol
Surface area29270 Å2
MethodPISA
2
B: Leptin receptor
D: Monoclonal antibody 9F8 fab fragment Heavy chain
F: Monoclonal antibody 9F8 fab fragment Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,48226
Polymers70,8463
Non-polymers1,63723
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5350 Å2
ΔGint-31 kcal/mol
Surface area29250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.814, 118.829, 171.281
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Antibody , 2 types, 4 molecules CDEF

#2: Antibody Monoclonal antibody 9F8 fab fragment Heavy chain


Mass: 23592.359 Da / Num. of mol.: 2 / Fragment: Fab fragment of monoclonal antibody H chain / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Antibody Monoclonal antibody 9F8 fab fragment Light chain


Mass: 23873.506 Da / Num. of mol.: 2 / Fragment: Fab fragment of monoclonal antibody L chain / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)

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Protein / Sugars , 2 types, 3 molecules AB

#1: Protein Leptin receptor / LEP-R / HuB219 / OB receptor / OB-R


Mass: 23379.795 Da / Num. of mol.: 2 / Fragment: Leptin binding domain of human obesity receptor
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DB, LEPR, OBR / Plasmid: pET21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIPL / References: UniProt: P48357
#8: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
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

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Non-polymers , 5 types, 891 molecules

#4: Chemical ChemComp-CYS / CYSTEINE


Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7NO2S
#5: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 31 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 851 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.22 Å3/Da / Density % sol: 61.81 %
Crystal growTemperature: 281 K / Method: vapor diffusion / pH: 4.6
Details: sodium acetate, PEG-4000, pH 4.6, vapor diffusion, temperature 281K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 5, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.95→49 Å / Num. all: 127050 / Num. obs: 127050 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 22.1 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 15.9
Reflection shellResolution: 1.95→2 Å / Rmerge(I) obs: 0.556 / Mean I/σ(I) obs: 3.8 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→49 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.947 / Occupancy max: 1 / Occupancy min: 1 / SU B: 6.891 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.12 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2135 6729 5 %RANDOM
Rwork0.1714 ---
all0.1735 127050 --
obs0.1735 -99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 117.01 Å2 / Biso mean: 38.3931 Å2 / Biso min: 12.06 Å2
Baniso -1Baniso -2Baniso -3
1-3.06 Å20 Å20 Å2
2---0.58 Å20 Å2
3----2.48 Å2
Refinement stepCycle: LAST / Resolution: 1.95→49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9486 0 177 851 10514
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0229879
X-RAY DIFFRACTIONr_bond_other_d0.0020.026643
X-RAY DIFFRACTIONr_angle_refined_deg1.841.95913399
X-RAY DIFFRACTIONr_angle_other_deg0.971316236
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.59351209
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.73324.256383
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.547151572
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7481538
X-RAY DIFFRACTIONr_chiral_restr0.1260.21509
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02110720
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021893
X-RAY DIFFRACTIONr_mcbond_it3.761.56134
X-RAY DIFFRACTIONr_mcbond_other1.5351.52449
X-RAY DIFFRACTIONr_mcangle_it5.19829982
X-RAY DIFFRACTIONr_scbond_it7.3433745
X-RAY DIFFRACTIONr_scangle_it9.2974.53417
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 494 -
Rwork0.254 9261 -
all-9755 -
obs--99.94 %
Refinement TLS params.

Method: refined / 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)
10.5756-0.3849-0.05490.27650.16991.3628-0.0086-0.01270.01530.04720.0446-0.00060.3160.1176-0.0360.16440.026-0.00760.09280.00210.049847.140140.3999-6.3344
26.2909-0.77613.69010.104-0.45232.1677-0.16610.20460.20640.02940.0249-0.0354-0.11070.13430.14130.05350.0272-0.07120.1912-0.03670.094871.68849.845216.4967
30.30860.5091-0.15720.8811-0.09841.33730.02770.01580.01480.00940.01420.0545-0.3762-0.06-0.04180.20510.03960.01630.0489-0.00110.058540.494869.7295.7121
47.85275.0629-5.6473.2828-3.58664.2211-0.25080.17-0.3972-0.22020.0877-0.293-0.0185-0.15630.1630.3189-0.05790.14470.10630.00850.093466.644570.8737-17.5072
50.19040.0514-0.00070.4135-0.14131.93380.0062-0.0466-0.0247-0.09320.01250.01590.00220.067-0.01880.05360.0031-0.00790.09760.010.061642.184351.5662-31.9768
60.10570.4594-0.00992.0165-0.09640.3970.0039-0.0165-0.01560.0468-0.0975-0.10450.03070.07430.09360.0831-0.0033-0.03030.0680.02790.097544.087779.6554-47.4473
70.12330.293-0.04430.7446-0.24351.47360.03970.0335-0.00950.16820.0382-0.0007-0.1566-0.0604-0.07790.14690.0120.01840.0744-0.00280.04941.738856.309531.0013
80.1016-0.4434-0.24592.63760.29061.62230.0320.00330.0001-0.0564-0.2219-0.256-0.24610.20750.18980.078-0.0549-0.01050.07790.07360.146253.754631.674245.9256
90.0397-0.12380.1591.2691-0.31010.9642-0.0404-0.0395-0.03130.08660.08350.0082-0.2556-0.2655-0.04310.08770.05770.00550.14460.02040.073130.699864.2918-18.272
100.2365-0.1097-0.22140.6937-0.70471.6005-0.18060.02210.0580.13030.1236-0.0116-0.0069-0.10270.0570.1881-0.0205-0.0660.06150.0510.074730.280386.3012-48.7786
110.0442-0.26980.06141.7518-0.59811.00090.0021-0.01150.004-0.09380.07380.03410.1854-0.176-0.07590.0742-0.0255-0.00130.09940.01140.067436.00840.192217.3735
120.09530.09870.30131.0711-0.61281.8592-0.0302-0.017-0.0138-0.0308-0.0008-0.0638-0.0408-0.0540.0310.13450.01860.01240.04080.04040.073443.524319.591147.5619
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A431 - 533
2X-RAY DIFFRACTION2A534 - 701
3X-RAY DIFFRACTION3B430 - 533
4X-RAY DIFFRACTION4B534 - 1001
5X-RAY DIFFRACTION5C3 - 119
6X-RAY DIFFRACTION6C120 - 222
7X-RAY DIFFRACTION7D3 - 119
8X-RAY DIFFRACTION8D120 - 221
9X-RAY DIFFRACTION9E4 - 106
10X-RAY DIFFRACTION10E107 - 216
11X-RAY DIFFRACTION11F4 - 106
12X-RAY DIFFRACTION12F107 - 216

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