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- PDB-2wqa: Complex of TTR and RBP4 and Oleic Acid -

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Basic information

Entry
Database: PDB / ID: 2wqa
TitleComplex of TTR and RBP4 and Oleic Acid
Components
  • RETINOL-BINDING PROTEIN 4
  • TRANSTHYRETIN
KeywordsHYDROLASE/SIGNALING PROTEIN / HYDROLASE-SIGNALING PROTEIN COMPLEX / THYROID HORMONE / RETINOL-BINDING / DISEASE MUTATION / SENSORY TRANSDUCTION / VITAMIN A / NEUROPATHY / AMYLOIDOSIS / VISION / HORMONE / AMYLOID
Function / homology
Function and homology information


Retinoid metabolism disease events / urinary bladder development / vitamin A import into cell / embryonic retina morphogenesis in camera-type eye / retinol transport / female genitalia morphogenesis / retinol transmembrane transporter activity / embryonic organ morphogenesis / maintenance of gastrointestinal epithelium / embryonic skeletal system development ...Retinoid metabolism disease events / urinary bladder development / vitamin A import into cell / embryonic retina morphogenesis in camera-type eye / retinol transport / female genitalia morphogenesis / retinol transmembrane transporter activity / embryonic organ morphogenesis / maintenance of gastrointestinal epithelium / embryonic skeletal system development / negative regulation of cardiac muscle cell proliferation / detection of light stimulus involved in visual perception / retinal metabolic process / molecular carrier activity / eye development / heart trabecula formation / retinal binding / retinol metabolic process / cardiac muscle tissue development / retinol binding / positive regulation of immunoglobulin production / Defective visual phototransduction due to STRA6 loss of function / negative regulation of glomerular filtration / response to muscle activity / The canonical retinoid cycle in rods (twilight vision) / uterus development / hormone binding / vagina development / purine nucleobase metabolic process / molecular sequestering activity / Non-integrin membrane-ECM interactions / phototransduction, visible light / response to retinoic acid / retinoid metabolic process / Retinoid metabolism and transport / lung development / gluconeogenesis / response to insulin / hormone activity / positive regulation of insulin secretion / male gonad development / azurophil granule lumen / glucose homeostasis / heart development / response to ethanol / spermatogenesis / Amyloid fiber formation / response to xenobiotic stimulus / Neutrophil degranulation / protein-containing complex binding / protein-containing complex / extracellular space / extracellular exosome / extracellular region / identical protein binding
Similarity search - Function
Retinol binding protein/Purpurin / Lipocalin, ApoD type / Transthyretin/hydroxyisourate hydrolase domain / Lipocalin family conserved site / Transthyretin, conserved site / Transthyretin signature 2. / Transthyretin, thyroxine binding site / Transthyretin signature 1. / Transthyretin / Transthyretin/hydroxyisourate hydrolase ...Retinol binding protein/Purpurin / Lipocalin, ApoD type / Transthyretin/hydroxyisourate hydrolase domain / Lipocalin family conserved site / Transthyretin, conserved site / Transthyretin signature 2. / Transthyretin, thyroxine binding site / Transthyretin signature 1. / Transthyretin / Transthyretin/hydroxyisourate hydrolase / Transthyretin/hydroxyisourate hydrolase domain / Transthyretin/hydroxyisourate hydrolase domain superfamily / HIUase/Transthyretin family / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin beta-barrel core domain / Calycin / Lipocalin / Lipocalin signature. / Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
OLEIC ACID / Retinol-binding protein 4 / Transthyretin
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsNanao, M. / Mercer, D. / Nguyen, L. / Buckley, D. / Stout, T.J.
CitationJournal: To be Published
Title: Crystal Structure of Rbp4 Bound to Linoleic Acid and Ttr
Authors: Nanao, M. / Stout, T.J.
History
DepositionAug 14, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2019Group: Data collection / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc / pdbx_database_status
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE ... THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRANSTHYRETIN
B: TRANSTHYRETIN
C: TRANSTHYRETIN
D: TRANSTHYRETIN
E: RETINOL-BINDING PROTEIN 4
F: RETINOL-BINDING PROTEIN 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,87519
Polymers96,2536
Non-polymers1,62213
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9600 Å2
ΔGint-79.5 kcal/mol
Surface area44250 Å2
MethodPQS
Unit cell
Length a, b, c (Å)138.662, 138.662, 122.789
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein
TRANSTHYRETIN / PREALBUMIN / TBPA / TTR / ATTR


Mass: 13921.491 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P02766
#2: Protein RETINOL-BINDING PROTEIN 4 / PLASMA RETINOL-BINDING PROTEIN / PLASMA RETINOL-BINDING PROTEIN(1-182) / PLASMA RETINOL-BINDING ...PLASMA RETINOL-BINDING PROTEIN / PLASMA RETINOL-BINDING PROTEIN(1-182) / PLASMA RETINOL-BINDING PROTEIN(1-181) / PLASMA RETINOL-BINDING PROTEIN(1-179) / PLASMA RETINOL-BINDING PROTEIN(1-176) / PRBP / RBP / RBP4


Mass: 20283.658 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: P02753
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H34O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 6.39 Å3/Da / Density % sol: 80.6 % / Description: NONE

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 14, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. obs: 54072 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 21.97
Reflection shellResolution: 2.85→2.99 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2.95 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JYD

1jyd


Resolution: 2.85→92.06 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.92 / SU B: 10.871 / SU ML: 0.209 / Cross valid method: THROUGHOUT / ESU R: 0.339 / ESU R Free: 0.264 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25319 2758 5.1 %RANDOM
Rwork0.22655 ---
obs0.2279 51275 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 83.135 Å2
Baniso -1Baniso -2Baniso -3
1-2.5 Å20 Å20 Å2
2--2.5 Å20 Å2
3----5 Å2
Refinement stepCycle: LAST / Resolution: 2.85→92.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6455 0 95 47 6597
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0226696
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5621.9519085
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.395814
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.66423.826311
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.797151060
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0951540
X-RAY DIFFRACTIONr_chiral_restr0.10.2981
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025084
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2280.22532
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3150.24401
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2230
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3470.224
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2080.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9771.54161
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.61526577
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.02132854
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2564.52508
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.85→2.924 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.402 220 -
Rwork0.344 3739 -
obs--99.4 %

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