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- PDB-7wc3: X-ray structure of the human adipocyte fatty acid-binding protein... -

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Basic information

Entry
Database: PDB / ID: 7wc3
TitleX-ray structure of the human adipocyte fatty acid-binding protein complexed with the fluorescent probe HA728
ComponentsFatty acid-binding protein, adipocyte
KeywordsLIPID BINDING PROTEIN / FABP / A-FABP / Complex / Binding protein / fluorescent probe
Function / homology
Function and homology information


hormone receptor binding / long-chain fatty acid transmembrane transporter activity / long-chain fatty acid binding / cellular response to lithium ion / Triglyceride catabolism / white fat cell differentiation / long-chain fatty acid transport / fatty acid transport / brown fat cell differentiation / lipid droplet ...hormone receptor binding / long-chain fatty acid transmembrane transporter activity / long-chain fatty acid binding / cellular response to lithium ion / Triglyceride catabolism / white fat cell differentiation / long-chain fatty acid transport / fatty acid transport / brown fat cell differentiation / lipid droplet / cholesterol homeostasis / fatty acid binding / response to bacterium / Transcriptional regulation of white adipocyte differentiation / positive regulation of inflammatory response / cellular response to tumor necrosis factor / positive regulation of cold-induced thermogenesis / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / negative regulation of DNA-templated transcription / extracellular exosome / nucleus / cytosol / 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
Similarity search - Domain/homology
Chem-8QU / Fatty acid-binding protein, adipocyte
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsTakahashi, J. / Matsuoka, S. / Tsuchikawa, H. / Sonoyama, M. / Inoue, Y. / Hayashi, F. / Murata, M. / Sugiyama, S.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19K06588 Japan
Japan Science and TechnologyJPMJTM19DC Japan
Japan Science and TechnologyJPMJER1005 Japan
CitationJournal: To Be Published
Title: X-ray structure of the human adipocyte fatty acid-binding protein complexed with the fluorescent probe HA728
Authors: Takahashi, J. / Matsuoka, S. / Tsuchikawa, H. / Sonoyama, M. / Inoue, Y. / Hayashi, F. / Murata, M. / Sugiyama, S.
History
DepositionDec 18, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 21, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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: Fatty acid-binding protein, adipocyte
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0322
Polymers14,7401
Non-polymers2921
Water3,495194
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.980, 71.665, 31.637
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Fatty acid-binding protein, adipocyte / Adipocyte lipid-binding protein / ALBP / Adipocyte-type fatty acid-binding protein / A-FABP / AFABP ...Adipocyte lipid-binding protein / ALBP / Adipocyte-type fatty acid-binding protein / A-FABP / AFABP / Fatty acid-binding protein 4


Mass: 14739.899 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FABP4 / Production host: Escherichia coli (E. coli) / References: UniProt: P15090
#2: Chemical ChemComp-8QU / (3S)-1-(4-nitro-2,1,3-benzoxadiazol-7-yl)piperidine-3-carboxylic acid


Mass: 292.247 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H12N4O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.09 Å3/Da / Density % sol: 41.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1M Tris-HCL (pH8.0), 35% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.5→42.6 Å / Num. obs: 16963 / % possible obs: 85 % / Redundancy: 5.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.033 / Rpim(I) all: 0.021 / Net I/σ(I): 25.5
Reflection shellResolution: 1.5→1.53 Å / Rmerge(I) obs: 0.228 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 303 / CC1/2: 0.926 / Rpim(I) all: 0.199

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FR2

3fr2


Resolution: 1.5→35.86 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.974 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17548 862 5.1 %RANDOM
Rwork0.12273 ---
obs0.12537 16068 84.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.145 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20 Å20 Å2
2--0.12 Å2-0 Å2
3----0.33 Å2
Refinement stepCycle: 1 / Resolution: 1.5→35.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1008 0 21 194 1223
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0131152
X-RAY DIFFRACTIONr_bond_other_d0.0020.0171116
X-RAY DIFFRACTIONr_angle_refined_deg2.0281.6721568
X-RAY DIFFRACTIONr_angle_other_deg1.5241.6072596
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1435151
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.27822.35351
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.10615224
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.647157
X-RAY DIFFRACTIONr_chiral_restr0.0960.2154
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021323
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02237
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_it2.7092.04574
X-RAY DIFFRACTIONr_mcbond_other2.7062.039573
X-RAY DIFFRACTIONr_mcangle_it3.1873.069735
X-RAY DIFFRACTIONr_mcangle_other3.1853.07736
X-RAY DIFFRACTIONr_scbond_it3.7152.446578
X-RAY DIFFRACTIONr_scbond_other3.6432.434566
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2173.462816
X-RAY DIFFRACTIONr_long_range_B_refined4.61626.6861284
X-RAY DIFFRACTIONr_long_range_B_other4.35925.5751226
X-RAY DIFFRACTIONr_rigid_bond_restr4.53432268
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 30 -
Rwork0.186 455 -
obs--33.61 %

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