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- PDB-5nu7: Structure of human holo plasma RBP4 -

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Basic information

Entry
Database: PDB / ID: 5nu7
TitleStructure of human holo plasma RBP4
ComponentsRetinol-binding protein 4
KeywordsTRANSPORT PROTEIN / RBP4 / plasma retinol-binding protein / lipocalin / retinol
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 / cardiac muscle tissue development / retinol metabolic process / retinol binding / positive regulation of immunoglobulin production / Defective visual phototransduction due to STRA6 loss of function / response to muscle activity / The canonical retinoid cycle in rods (twilight vision) / uterus development / vagina development / phototransduction, visible light / response to retinoic acid / Retinoid metabolism and transport / lung development / gluconeogenesis / response to insulin / positive regulation of insulin secretion / male gonad development / glucose homeostasis / heart development / response to ethanol / spermatogenesis / response to xenobiotic stimulus / protein-containing complex binding / protein-containing complex / extracellular space / extracellular exosome / extracellular region
Similarity search - Function
Retinol binding protein/Purpurin / Lipocalin, ApoD type / Lipocalin family conserved site / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin beta-barrel core domain / Calycin / Lipocalin / Lipocalin signature. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
RETINOL / Retinol-binding protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsPerduca, M. / Monaco, H.L. / Galliano, M.
CitationJournal: Biochim. Biophys. Acta / Year: 2018
Title: Human plasma retinol-binding protein (RBP4) is also a fatty acid-binding protein.
Authors: Perduca, M. / Nicolis, S. / Mannucci, B. / Galliano, M. / Monaco, H.L.
History
DepositionApr 28, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Retinol-binding protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3063
Polymers20,9841
Non-polymers3222
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area920 Å2
ΔGint-7 kcal/mol
Surface area9350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.097, 103.097, 73.552
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Retinol-binding protein 4 / Plasma retinol-binding protein / RBP


Mass: 20984.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P02753
#2: Chemical ChemComp-RTL / RETINOL


Mass: 286.452 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H30O
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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 / Number of used crystals: 1

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Sample preparation

Crystal growTemperature: 277 K / Method: microdialysis / Details: 4.5 M NaCl, 20 mM Na cacodylate, pH 6.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→38.16 Å / Num. obs: 46674 / % possible obs: 99.5 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 12.6
Reflection shellResolution: 1.5→1.58 Å / Rmerge(I) obs: 0.462 / Mean I/σ(I) obs: 2.8 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
iMOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BRP

1brp


Resolution: 1.5→30 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.961 / SU B: 3.135 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.059
RfactorNum. reflection% reflectionSelection details
Rfree0.2096 2287 4.9 %RANDOM
Rwork0.17973 ---
obs0.18114 44136 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 41.232 Å2
Baniso -1Baniso -2Baniso -3
1-0.57 Å20.29 Å2-0 Å2
2--0.57 Å2-0 Å2
3----1.86 Å2
Refinement stepCycle: 1 / Resolution: 1.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1408 0 22 77 1507
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.021464
X-RAY DIFFRACTIONr_bond_other_d00.021340
X-RAY DIFFRACTIONr_angle_refined_deg0.6411.9471981
X-RAY DIFFRACTIONr_angle_other_deg0.46233068
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.8965173
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.60623.84678
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.79415241
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8591512
X-RAY DIFFRACTIONr_chiral_restr0.040.2203
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021692
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02373
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_it8.32.364696
X-RAY DIFFRACTIONr_mcbond_other8.3022.37697
X-RAY DIFFRACTIONr_mcangle_it9.0843.555869
X-RAY DIFFRACTIONr_mcangle_other9.0843.552869
X-RAY DIFFRACTIONr_scbond_it14.1223.08768
X-RAY DIFFRACTIONr_scbond_other14.1133.079769
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other15.0744.3821113
X-RAY DIFFRACTIONr_long_range_B_refined14.23921.811675
X-RAY DIFFRACTIONr_long_range_B_other14.31721.8131653
X-RAY DIFFRACTIONr_rigid_bond_restr16.33532803
X-RAY DIFFRACTIONr_sphericity_free17.405544
X-RAY DIFFRACTIONr_sphericity_bonded23.05752803
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 170 -
Rwork0.266 3245 -
obs--99.24 %
Refinement TLS params.Method: refined / Origin x: 19.7891 Å / Origin y: 13.6746 Å / Origin z: -0.1851 Å
111213212223313233
T0.1074 Å20.0288 Å2-0.08 Å2-0.0439 Å2-0.0387 Å2--0.0901 Å2
L1.4029 °2-0.1334 °20.1157 °2-2.0345 °2-0.1704 °2--1.6368 °2
S0.0041 Å °0.0165 Å °-0.0452 Å °0.0184 Å °0.1696 Å °0.0096 Å °0.2664 Å °-0.0558 Å °-0.1737 Å °

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