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

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Basic information

Entry
Database: PDB / ID: 8geu
TitleCrystal structure of human cellular retinol binding protein 1 in complex with methyl({3-[1-(4-methylphenyl)cyclopentyl]-1,2,4-oxadiazol-5-yl}methyl)[(1-methylpyrazol-4-yl)methyl]amine
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-ZCF / Retinol-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 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 7, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 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
A: Retinol-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2753
Polymers16,7001
Non-polymers5752
Water4,612256
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)37.151, 37.880, 101.968
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-ZCF / N-methyl-1-{3-[1-(4-methylphenyl)cyclopentyl]-1,2,4-oxadiazol-5-yl}-N-[(1-methyl-1H-pyrazol-4-yl)methyl]methanamine


Mass: 365.472 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N5O / 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.: 256 / 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: 2.15 Å3/Da / Density % sol: 42.74 %
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-E / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.47→37.88 Å / Num. obs: 25069 / % possible obs: 98.8 % / Redundancy: 5.8 % / Biso Wilson estimate: 12.08 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.046 / Rrim(I) all: 0.1 / Net I/σ(I): 20.6
Reflection shellResolution: 1.47→1.49 Å / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 4.2 / Num. unique obs: 1162 / CC1/2: 0.762 / Rpim(I) all: 0.397 / Rrim(I) all: 0.7 / % possible all: 94.5

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.47→34.91 Å / SU ML: 0.1186 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.8702
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2033 1196 4.83 %
Rwork0.1822 23584 -
obs0.1832 24780 97.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.57 Å2
Refinement stepCycle: LAST / Resolution: 1.47→34.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1152 0 41 256 1449
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01071224
X-RAY DIFFRACTIONf_angle_d1.2161649
X-RAY DIFFRACTIONf_chiral_restr0.0927168
X-RAY DIFFRACTIONf_plane_restr0.007207
X-RAY DIFFRACTIONf_dihedral_angle_d13.553169
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.47-1.530.25421270.23112493X-RAY DIFFRACTION94.89
1.53-1.60.2381340.18542633X-RAY DIFFRACTION99.6
1.6-1.680.19371440.17872609X-RAY DIFFRACTION99.78
1.68-1.780.23171360.18332657X-RAY DIFFRACTION99.93
1.79-1.920.2691240.20722557X-RAY DIFFRACTION96.02
1.92-2.120.23991060.18442615X-RAY DIFFRACTION97.01
2.12-2.420.20751310.19432527X-RAY DIFFRACTION93.66
2.42-3.050.17741180.18112714X-RAY DIFFRACTION99.61
3.05-34.910.17771760.16242779X-RAY DIFFRACTION97.88

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