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- PDB-7jvy: Cellular retinol-binding protein 2 (CRBP2) in complex with 2-arac... -

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Basic information

Entry
Database: PDB / ID: 7jvy
TitleCellular retinol-binding protein 2 (CRBP2) in complex with 2-arachidonylglyceryl ether
ComponentsRetinol-binding protein 2
KeywordsLIPID BINDING PROTEIN / arachidonoylglycerol / monoacylglycerol / retinol-binding protein / lipid binding
Function / homology
Function and homology information


vitamin A metabolic process / molecular carrier activity / retinoid binding / retinal binding / retinol binding / epidermis development / fatty acid transport / Retinoid metabolism and transport / fatty acid binding / nucleus / cytosol
Similarity search - Function
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-VKV / Retinol-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsSilvaroli, J.A. / Banarjee, S. / Golczak, M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK122071 United States
National Institutes of Health/National Eye Institute (NIH/NEI)EY023948 United States
CitationJournal: J.Lipid Res. / Year: 2021
Title: Molecular basis for the interaction of cellular retinol binding protein 2 (CRBP2) with nonretinoid ligands.
Authors: Silvaroli, J.A. / Plau, J. / Adams, C.H. / Banerjee, S. / Widjaja-Adhi, M.A.K. / Blaner, W.S. / Golczak, M.
History
DepositionAug 24, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 7, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Oct 18, 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

Downloads & links

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Assembly

Deposited unit
A: Retinol-binding protein 2
B: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1204
Polymers32,3902
Non-polymers7292
Water11,494638
1
A: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5602
Polymers16,1951
Non-polymers3651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5602
Polymers16,1951
Non-polymers3651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.909, 67.660, 88.809
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 10 or resid 12...
d_2ens_1(chain "B" and (resid 1 through 10 or resid 12...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1THRMETA2 - 11
d_12ens_1SERPHEA14 - 18
d_13ens_1GLYVALA20 - 36
d_14ens_1LEULEUA39
d_15ens_1GLNSERA41 - 58
d_16ens_1PHEPHEA61
d_17ens_1ASNLYSA64 - 80
d_18ens_1LEUGLNA83 - 103
d_19ens_1GLYILEA106 - 117
d_110ens_1GLYLEUA120 - 125
d_111ens_1LEULEUA128
d_112ens_1CYSLYSA131 - 142
d_21ens_1THRMETB1 - 10
d_22ens_1SERPHEB12 - 16
d_23ens_1GLYVALB19 - 35
d_24ens_1LEULEUB37
d_25ens_1GLNSERB40 - 57
d_26ens_1PHEPHEB59
d_27ens_1ASNLYSB61 - 77
d_28ens_1LEUGLNB79 - 99
d_29ens_1GLYILEB101 - 112
d_210ens_1GLYLEUB114 - 119
d_211ens_1LEULEUB121
d_212ens_1CYSLYSB123 - 134

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Components

#1: Protein Retinol-binding protein 2 / Cellular retinol-binding protein II / CRBP-II


Mass: 16195.246 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBP2, CRBP2 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21De / References: UniProt: P50120
#2: Chemical ChemComp-VKV / 2-{[(5Z,8Z,11Z,14Z)-icosa-5,8,11,14-tetraen-1-yl]oxy}propane-1,3-diol / 2-Arachidonyl Glycerol Ether


Mass: 364.562 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H40O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 638 / 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: 2.69 Å3/Da / Density % sol: 54.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1 M Tris/HCl, PEG 3350 25% / PH range: 7.5 - 8.5

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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: Nov 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.3→53.82 Å / Num. obs: 85701 / % possible obs: 99.3 % / Redundancy: 5.9 % / Biso Wilson estimate: 12.09 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.051 / Rrim(I) all: 0.094 / Net I/σ(I): 10.6
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.594 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4167 / CC1/2: 0.637 / Rpim(I) all: 0.436 / Rrim(I) all: 0.741 / % possible all: 98.7

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Processing

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

6bti


Resolution: 1.3→53.82 Å / SU ML: 0.1231 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.4881
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1658 4305 5.03 %
Rwork0.1359 81274 -
obs0.1374 85579 99.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.2 Å2
Refinement stepCycle: LAST / Resolution: 1.3→53.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2220 0 52 638 2910
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00872423
X-RAY DIFFRACTIONf_angle_d1.23293260
X-RAY DIFFRACTIONf_chiral_restr0.1178343
X-RAY DIFFRACTIONf_plane_restr0.0055428
X-RAY DIFFRACTIONf_dihedral_angle_d23.8351347
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.766674826971 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.310.30121390.25552656X-RAY DIFFRACTION97.56
1.31-1.330.20191320.18582683X-RAY DIFFRACTION99.29
1.33-1.350.18621310.16642678X-RAY DIFFRACTION98.25
1.35-1.360.21781580.16092668X-RAY DIFFRACTION99.51
1.36-1.380.19141200.15642691X-RAY DIFFRACTION98.29
1.38-1.40.19881420.14342642X-RAY DIFFRACTION99.43
1.4-1.420.18071430.13322686X-RAY DIFFRACTION98.64
1.42-1.440.17781450.14082696X-RAY DIFFRACTION99.58
1.44-1.460.21151330.14522681X-RAY DIFFRACTION99.05
1.46-1.490.17361430.15322684X-RAY DIFFRACTION98.33
1.49-1.510.16071400.12292667X-RAY DIFFRACTION98.6
1.51-1.540.15611400.12092676X-RAY DIFFRACTION99.22
1.54-1.570.15671540.11162702X-RAY DIFFRACTION98.99
1.57-1.60.12861610.10612679X-RAY DIFFRACTION99.72
1.6-1.640.1341340.10282711X-RAY DIFFRACTION99.65
1.64-1.680.14861200.11322728X-RAY DIFFRACTION99.72
1.68-1.720.13721460.11292717X-RAY DIFFRACTION99.76
1.72-1.760.17791490.1142705X-RAY DIFFRACTION99.72
1.76-1.820.13991360.11992731X-RAY DIFFRACTION99.41
1.82-1.870.17171620.12662659X-RAY DIFFRACTION98.33
1.87-1.940.17951360.14762700X-RAY DIFFRACTION98.37
1.94-2.020.13911640.12532702X-RAY DIFFRACTION99.9
2.02-2.110.15551770.12852711X-RAY DIFFRACTION99.83
2.11-2.220.17811440.13062743X-RAY DIFFRACTION99.76
2.22-2.360.15381510.14052728X-RAY DIFFRACTION99.52
2.36-2.540.16911360.14712771X-RAY DIFFRACTION99.62
2.54-2.80.20521340.1452690X-RAY DIFFRACTION96.81
2.8-3.210.14721540.14452782X-RAY DIFFRACTION99.53
3.21-4.040.17461320.12812827X-RAY DIFFRACTION99.9
4.04-53.820.15751490.14342880X-RAY DIFFRACTION97.3

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