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- PDB-5d8j: Development of a therapeutic monoclonal antibody targeting secret... -

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Basic information

Entry
Database: PDB / ID: 5d8j
TitleDevelopment of a therapeutic monoclonal antibody targeting secreted aP2 to treat type 2 diabetes.
Components
  • Fatty acid-binding protein, adipocyte
  • HA3 Fab Heavy Chain
  • HA3 Fab Light Chain
KeywordsIMMUNE SYSTEM / AP2 / Fabp4 / Diabetes / metabolic syndrome
Function / homology
Function and homology information


Triglyceride catabolism / hormone receptor binding / long-chain fatty acid transmembrane transporter activity / long-chain fatty acid binding / cellular response to lithium ion / white fat cell differentiation / long-chain fatty acid transport / brown fat cell differentiation / cholesterol homeostasis / response to bacterium ...Triglyceride catabolism / hormone receptor binding / long-chain fatty acid transmembrane transporter activity / long-chain fatty acid binding / cellular response to lithium ion / white fat cell differentiation / long-chain fatty acid transport / brown fat cell differentiation / cholesterol homeostasis / response to bacterium / positive regulation of inflammatory response / cellular response to tumor necrosis factor / positive regulation of cold-induced thermogenesis / negative regulation of DNA-templated transcription / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Cytosolic fatty-acid binding proteins signature. / Intracellular lipid binding protein / Cytosolic fatty-acid binding / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin beta-barrel core domain / Calycin / Lipocalin / Immunoglobulins / Beta Barrel ...Cytosolic fatty-acid binding proteins signature. / Intracellular lipid binding protein / Cytosolic fatty-acid binding / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin beta-barrel core domain / Calycin / Lipocalin / Immunoglobulins / Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Fatty acid-binding protein, adipocyte
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsDoyle, C. / Birrane, G.
CitationJournal: Sci Transl Med / Year: 2015
Title: Development of a therapeutic monoclonal antibody that targets secreted fatty acid-binding protein aP2 to treat type 2 diabetes.
Authors: Burak, M.F. / Inouye, K.E. / White, A. / Lee, A. / Tuncman, G. / Calay, E.S. / Sekiya, M. / Tirosh, A. / Eguchi, K. / Birrane, G. / Lightwood, D. / Howells, L. / Odede, G. / Hailu, H. / ...Authors: Burak, M.F. / Inouye, K.E. / White, A. / Lee, A. / Tuncman, G. / Calay, E.S. / Sekiya, M. / Tirosh, A. / Eguchi, K. / Birrane, G. / Lightwood, D. / Howells, L. / Odede, G. / Hailu, H. / West, S. / Garlish, R. / Neale, H. / Doyle, C. / Moore, A. / Hotamisligil, G.S.
History
DepositionAug 17, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.2Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fatty acid-binding protein, adipocyte
H: HA3 Fab Heavy Chain
L: HA3 Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1604
Polymers62,0643
Non-polymers961
Water23413
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5430 Å2
ΔGint-47 kcal/mol
Surface area24980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.499, 66.040, 75.678
Angle α, β, γ (deg.)90.00, 111.67, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Fatty acid-binding protein, adipocyte / 3T3-L1 lipid-binding protein / Adipocyte lipid-binding protein / ALBP / Adipocyte-type fatty acid- ...3T3-L1 lipid-binding protein / Adipocyte lipid-binding protein / ALBP / Adipocyte-type fatty acid-binding protein / AFABP / Fatty acid-binding protein 4 / Myelin P2 protein homolog / P15 / P2 adipocyte protein / Protein 422


Mass: 14815.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Fabp4, Ap2 / Production host: Escherichia coli (E. coli) / References: UniProt: P04117
#2: Antibody HA3 Fab Heavy Chain


Mass: 23733.488 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody HA3 Fab Light Chain


Mass: 23515.869 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster)
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.02 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 100mM 2-(N-morpholino)ethanesulfonic acid, 150mM ammonium sulfate, 24% PEG 4000

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 29, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.23→33.03 Å / Num. obs: 13077 / % possible obs: 98.6 % / Observed criterion σ(I): 6.8 / Redundancy: 2.6 % / Rmerge(I) obs: 0.011 / Net I/σ(I): 6.8
Reflection shellResolution: 2.23→2.37 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.352 / Mean I/σ(I) obs: 1.7 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
PHASERphasing
SCALAdata scaling
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→33.02 Å / Cor.coef. Fo:Fc: 0.893 / Cor.coef. Fo:Fc free: 0.795 / SU ML: 0.404 / Cross valid method: THROUGHOUT / ESU R Free: 0.493 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26922 664 5.1 %RANDOM
Rwork0.20485 ---
obs0.20821 12264 97.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.673 Å2
Baniso -1Baniso -2Baniso -3
1--1.56 Å20 Å21.2 Å2
2--0.29 Å20 Å2
3---0.24 Å2
Refinement stepCycle: 1 / Resolution: 3→33.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4308 0 5 13 4326
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.024412
X-RAY DIFFRACTIONr_bond_other_d0.0020.024060
X-RAY DIFFRACTIONr_angle_refined_deg1.7291.9475998
X-RAY DIFFRACTIONr_angle_other_deg1.00339411
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5915559
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.21124.491167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.00915730
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.1751516
X-RAY DIFFRACTIONr_chiral_restr0.0940.2686
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214926
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02958
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.390.8942248
X-RAY DIFFRACTIONr_mcbond_other0.390.8942247
X-RAY DIFFRACTIONr_mcangle_it0.7331.3392803
X-RAY DIFFRACTIONr_mcangle_other0.7331.3392804
X-RAY DIFFRACTIONr_scbond_it0.20.8992164
X-RAY DIFFRACTIONr_scbond_other0.1960.8962158
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.4151.3253189
X-RAY DIFFRACTIONr_long_range_B_refined2.0768.12717741
X-RAY DIFFRACTIONr_long_range_B_other2.0768.12817740
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 39 -
Rwork0.291 876 -
obs--95.41 %
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)
12.40710.08161.32723.29610.40742.7196-0.09870.10020.1883-0.15990.03140.1626-0.04190.08910.06730.2803-0.0262-0.08090.0918-0.00130.0446-39.923-6.4531.06
22.87690.91620.42431.0046-0.39390.9765-0.0102-0.00740.20570.0415-0.0318-0.2299-0.01950.01210.0420.34330.0214-0.13860.04010.0130.2583-11.957.64814.234
32.7132-1.02330.06365.32990.24381.8541-0.04740.01720.1538-0.28580.0397-0.0277-0.02630.09280.00770.3592-0.0729-0.08070.07340.00410.02920.7032.68528.573
43.8919-0.13830.53711.8222-0.57311.48260.1252-0.1875-0.22980.2322-0.1196-0.2010.07770.0536-0.00560.3501-0.0244-0.14740.11560.02480.0986-14.407-11.81723.727
51.30082.25420.81656.93111.47031.13740.0494-0.18470.22860.5714-0.18870.58770.0085-0.24040.13930.35550.03910.03260.1893-0.00110.090613.657-0.81942.785
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L108 - 214
2X-RAY DIFFRACTION2B1 - 119
3X-RAY DIFFRACTION3B120 - 220
4X-RAY DIFFRACTION4C1 - 107
5X-RAY DIFFRACTION5C108 - 214

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