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- PDB-6e5l: Crystal structure of human cellular retinol binding protein 1 in ... -

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Basic information

Entry
Database: PDB / ID: 6e5l
TitleCrystal structure of human cellular retinol binding protein 1 in complex with abnormal-cannabidiol (abn-CBD)
ComponentsRetinol-binding protein 1
KeywordsLIPID BINDING PROTEIN / vitamin A / retinol / abn-CBD / abnormal cannabidiol
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 beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-HVD / Retinol-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.17 Å
AuthorsSilvaroli, J.A. / Banerjee, S. / Kiser, P.D. / Golczak, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI)EY023948 United States
CitationJournal: Acs Chem.Biol. / Year: 2019
Title: Abnormal Cannabidiol Modulates Vitamin A Metabolism by Acting as a Competitive Inhibitor of CRBP1.
Authors: Silvaroli, J.A. / Widjaja-Adhi, M.A.K. / Trischman, T. / Chelstowska, S. / Horwitz, S. / Banerjee, S. / Kiser, P.D. / Blaner, W.S. / Golczak, M.
History
DepositionJul 20, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2019Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.2Aug 28, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 2023Group: 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

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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)16,8832
Polymers16,5691
Non-polymers3141
Water5,441302
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.219, 40.890, 92.139
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 16568.869 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) / References: UniProt: P09455
#2: Chemical ChemComp-HVD / (1'R,2'R)-5'-methyl-6-pentyl-2'-(prop-1-en-2-yl)-1',2',3',4'-tetrahydro[1,1'-biphenyl]-2,4-diol


Mass: 314.462 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / Source method: isolated from a natural source / Formula: H2O

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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: 2.12 Å3/Da / Density % sol: 41.87 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1 M BisTris, pH 5.5, and 25% PEG 3350

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: CCD / Date: Nov 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.17→46.07 Å / Num. obs: 47869 / % possible obs: 99.3 % / Redundancy: 5.8 % / CC1/2: 0.99 / Rpim(I) all: 0.05 / Rsym value: 0.12 / Net I/σ(I): 11.6
Reflection shellResolution: 1.17→1.19 Å / Mean I/σ(I) obs: 5.5 / Num. unique obs: 2384 / CC1/2: 0.69 / Rsym value: 0.6 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5H8T

5h8t


Resolution: 1.17→46.07 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 11.95
RfactorNum. reflection% reflection
Rfree0.146 2385 4.98 %
Rwork0.1184 --
obs0.1198 47869 99.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.17→46.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1158 0 23 302 1483
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071290
X-RAY DIFFRACTIONf_angle_d0.9161749
X-RAY DIFFRACTIONf_dihedral_angle_d17.947500
X-RAY DIFFRACTIONf_chiral_restr0.08180
X-RAY DIFFRACTIONf_plane_restr0.005226
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.17-1.19390.15391360.12722629X-RAY DIFFRACTION99
1.1939-1.21980.13611420.10742624X-RAY DIFFRACTION100
1.2198-1.24820.12221420.10782682X-RAY DIFFRACTION100
1.2482-1.27940.14321180.10062663X-RAY DIFFRACTION99
1.2794-1.3140.13841340.10282634X-RAY DIFFRACTION99
1.314-1.35270.13641370.09992641X-RAY DIFFRACTION100
1.3527-1.39640.13851440.10322662X-RAY DIFFRACTION99
1.3964-1.44630.1661310.10312660X-RAY DIFFRACTION99
1.4463-1.50420.14221350.09832668X-RAY DIFFRACTION99
1.5042-1.57270.13291370.09442663X-RAY DIFFRACTION99
1.5727-1.65560.13531430.09622654X-RAY DIFFRACTION100
1.6556-1.75930.13111520.09992664X-RAY DIFFRACTION99
1.7593-1.89510.11751440.10892676X-RAY DIFFRACTION99
1.8951-2.08590.13361430.10962710X-RAY DIFFRACTION99
2.0859-2.38770.14111470.12062704X-RAY DIFFRACTION99
2.3877-3.00810.14591420.13682688X-RAY DIFFRACTION97
3.0081-46.10540.17411580.14472862X-RAY DIFFRACTION98

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