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- PDB-8gd2: Crystal structure of human cellular retinol binding protein 1 in ... -

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Basic information

Entry
Database: PDB / ID: 8gd2
TitleCrystal structure of human cellular retinol binding protein 1 in complex with N-methyl-1-{3-[1-(4-methylphenyl)cyclopentyl]-1,2,4-oxadiazol-5-yl}-N-(2-thienylmethyl)methanamine
ComponentsRetinol-binding protein 1
KeywordsRetinol-binding protein / RBP1 / CRBP1 / retinol-binding / retinol / vitamin A
Function / homology
Function and homology information


Defective visual phototransduction due to LRAT loss of function / all-trans-retinol binding / retinoic acid biosynthetic process / vitamin A metabolic process / retinoid binding / retinal binding / The canonical retinoid cycle in rods (twilight vision) / lipid homeostasis / fatty acid transport / Retinoid metabolism and transport ...Defective visual phototransduction due to LRAT loss of function / all-trans-retinol binding / retinoic acid biosynthetic process / vitamin A metabolic process / retinoid binding / retinal binding / The canonical retinoid cycle in rods (twilight vision) / lipid homeostasis / fatty acid transport / Retinoid metabolism and transport / lipid droplet / fatty acid binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Retinol-binding protein 1 / 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-Z5H / Retinol-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.13 Å
AuthorsPlau, J. / Golczak, M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI)EY023948 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK122071 United States
CitationJournal: Acs Chem.Biol. / Year: 2023
Title: Discovery of Nonretinoid Inhibitors of CRBP1: Structural and Dynamic Insights for Ligand-Binding Mechanisms.
Authors: Plau, J. / Morgan, C.E. / Fedorov, Y. / Banerjee, S. / Adams, D.J. / Blaner, W.S. / Yu, E.W. / Golczak, M.
History
DepositionMar 3, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Retinol-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2773
Polymers16,7001
Non-polymers5772
Water5,639313
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)37.329, 37.685, 101.544
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Retinol-binding protein 1 / Cellular retinol-binding protein / CRBP / Cellular retinol-binding protein I / CRBP-I


Mass: 16700.064 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBP1, CRBP1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE / References: UniProt: P09455
#2: Chemical ChemComp-Z5H / N-methyl-1-{3-[1-(4-methylphenyl)cyclopentyl]-1,2,4-oxadiazol-5-yl}-N-[(thiophen-2-yl)methyl]methanamine


Mass: 367.508 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H25N3OS / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 313 / 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: 2.14 Å3/Da / Density % sol: 42.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M Bis-Tris, pH 5.5 and 25% poly ethylene glycol 3350 (w/v).

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.13→101.54 Å / Num. obs: 51376 / % possible obs: 94.2 % / Redundancy: 5.8 % / Biso Wilson estimate: 10.66 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.017 / Rrim(I) all: 0.043 / Net I/σ(I): 20.6
Reflection shellResolution: 1.13→1.15 Å / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 5 / Num. unique obs: 1747 / CC1/2: 0.96 / R split: 0.202 / Rrim(I) all: 0.307 / % possible all: 67.7

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6E5L

6e5l


Resolution: 1.13→35.33 Å / SU ML: 0.1008 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.6798
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1835 4939 5.17 %
Rwork0.1621 90680 -
obs0.1632 51276 92.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.94 Å2
Refinement stepCycle: LAST / Resolution: 1.13→35.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1152 0 40 313 1505
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01511300
X-RAY DIFFRACTIONf_angle_d1.65451758
X-RAY DIFFRACTIONf_chiral_restr0.3137175
X-RAY DIFFRACTIONf_plane_restr0.0093226
X-RAY DIFFRACTIONf_dihedral_angle_d18.5203184
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.13-1.140.3358780.23521952X-RAY DIFFRACTION59.74
1.14-1.160.24721320.22152251X-RAY DIFFRACTION68.93
1.16-1.170.26761050.2142460X-RAY DIFFRACTION73.5
1.17-1.180.22181420.21982678X-RAY DIFFRACTION81.81
1.18-1.20.22221440.21652818X-RAY DIFFRACTION85.14
1.2-1.220.24471870.20192882X-RAY DIFFRACTION88.88
1.22-1.230.20231650.20152952X-RAY DIFFRACTION89.72
1.23-1.250.22221360.20053015X-RAY DIFFRACTION90.62
1.25-1.270.23431470.19913078X-RAY DIFFRACTION93.61
1.27-1.290.23891720.19913109X-RAY DIFFRACTION93.21
1.29-1.310.2031870.19633019X-RAY DIFFRACTION94.38
1.31-1.340.2261720.19073131X-RAY DIFFRACTION94.53
1.34-1.360.2181770.19073103X-RAY DIFFRACTION95.52
1.36-1.390.20221940.18693152X-RAY DIFFRACTION95.63
1.39-1.420.24791530.18483156X-RAY DIFFRACTION96.58
1.42-1.460.20671650.17883187X-RAY DIFFRACTION96.29
1.46-1.490.20051970.17823124X-RAY DIFFRACTION96.15
1.49-1.530.18861680.17533192X-RAY DIFFRACTION97.39
1.53-1.580.17871690.16613203X-RAY DIFFRACTION96.87
1.58-1.630.18862160.16483168X-RAY DIFFRACTION97.41
1.63-1.690.20661650.16413223X-RAY DIFFRACTION97.81
1.69-1.750.20851640.15763204X-RAY DIFFRACTION97.4
1.75-1.830.17481710.16683211X-RAY DIFFRACTION97.55
1.83-1.930.16241480.15443190X-RAY DIFFRACTION97.01
1.93-2.050.19151870.15573176X-RAY DIFFRACTION96.28
2.05-2.210.1671720.15543236X-RAY DIFFRACTION97.93
2.21-2.430.17131630.14723198X-RAY DIFFRACTION97.99
2.43-2.780.16051820.15343220X-RAY DIFFRACTION97.93
2.78-3.510.17051610.14683220X-RAY DIFFRACTION97.41
3.51-35.330.16082200.13713172X-RAY DIFFRACTION97.92

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