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- PDB-6bth: Crystal structure of human cellular retinol binding protein 2 (CR... -

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Basic information

Entry
Database: PDB / ID: 6bth
TitleCrystal structure of human cellular retinol binding protein 2 (CRBP2) in complex with 2-arachidonoylglycerol (2-AG)
ComponentsRetinol-binding protein 2
KeywordsLIPID BINDING PROTEIN / endocannabinoid / 2-arachidonoylglycerol / 2-AG / retinol / vitamin A
Function / homology
Function and homology information


vitamin A metabolic process / 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 / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-ECB / DI(HYDROXYETHYL)ETHER / Retinol-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsSilvaroli, J.A. / Blaner, W.S. / Lodowski, D.T. / Golczak, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI)R01-EY023948 United States
CitationJournal: Sci Adv / Year: 2020
Title: Retinol-binding protein 2 (RBP2) binds monoacylglycerols and modulates gut endocrine signaling and body weight.
Authors: Lee, S.A. / Yang, K.J.Z. / Brun, P.J. / Silvaroli, J.A. / Yuen, J.J. / Shmarakov, I. / Jiang, H. / Feranil, J.B. / Li, X. / Lackey, A.I. / Krezel, W. / Leibel, R.L. / Libien, J. / Storch, J. ...Authors: Lee, S.A. / Yang, K.J.Z. / Brun, P.J. / Silvaroli, J.A. / Yuen, J.J. / Shmarakov, I. / Jiang, H. / Feranil, J.B. / Li, X. / Lackey, A.I. / Krezel, W. / Leibel, R.L. / Libien, J. / Storch, J. / Golczak, M. / Blaner, W.S.
History
DepositionDec 6, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2May 20, 2020Group: 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 1.3Oct 4, 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)33,4667
Polymers32,3902
Non-polymers1,0755
Water9,476526
1
A: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8925
Polymers16,1951
Non-polymers6974
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Retinol-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5742
Polymers16,1951
Non-polymers3791
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.138, 67.328, 87.319
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 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 / Cell line (production host): Bl21(DE) / Production host: Escherichia coli (E. coli) / References: UniProt: P50120
#2: Chemical ChemComp-ECB / 1,3-dihydroxypropan-2-yl (5Z,8Z,11Z,14Z)-icosa-5,8,11,14-tetraenoate / 2-arachidonoylglycerol / 2-Arachidonoylglycerol


Mass: 378.545 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H38O4 / Feature type: SUBJECT OF INVESTIGATION / Comment: agonist*YM
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 526 / 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: 2.64 Å3/Da / Density % sol: 53.38 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris HCl, PEG 3350 22-28% / PH range: 7.5 - 8.5

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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-F / Detector: PIXEL / Date: Nov 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.35→48.39 Å / Num. obs: 71655 / % possible obs: 94.6 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.032 / Net I/σ(I): 11.7
Reflection shellResolution: 1.35→1.42 Å / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 10211 / CC1/2: 0.66 / Rpim(I) all: 0.45 / % possible all: 93.3

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QYP

4qyp


Resolution: 1.35→48.39 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.24
RfactorNum. reflection% reflection
Rfree0.164 3648 5.09 %
Rwork0.1261 --
obs0.1279 71604 94.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.35→48.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2236 0 75 526 2837
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082409
X-RAY DIFFRACTIONf_angle_d0.9443229
X-RAY DIFFRACTIONf_dihedral_angle_d24.296924
X-RAY DIFFRACTIONf_chiral_restr0.086340
X-RAY DIFFRACTIONf_plane_restr0.006420
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.36690.34181530.29752477X-RAY DIFFRACTION91
1.3669-1.38560.30471350.27272582X-RAY DIFFRACTION93
1.3856-1.40540.28591620.24872539X-RAY DIFFRACTION94
1.4054-1.42640.27321350.22882559X-RAY DIFFRACTION94
1.4264-1.44870.24151260.20382613X-RAY DIFFRACTION94
1.4487-1.47250.25191430.18962588X-RAY DIFFRACTION95
1.4725-1.49790.23521400.17492592X-RAY DIFFRACTION93
1.4979-1.52510.22751430.16242531X-RAY DIFFRACTION93
1.5251-1.55440.21281220.15062588X-RAY DIFFRACTION94
1.5544-1.58620.18931150.13482419X-RAY DIFFRACTION87
1.5862-1.62070.13591460.11352605X-RAY DIFFRACTION95
1.6207-1.65840.1671520.1092622X-RAY DIFFRACTION96
1.6584-1.69980.16251490.1092634X-RAY DIFFRACTION96
1.6998-1.74580.14771420.10052668X-RAY DIFFRACTION96
1.7458-1.79720.14551370.09562653X-RAY DIFFRACTION96
1.7972-1.85520.15721610.1032660X-RAY DIFFRACTION96
1.8552-1.92150.16081460.12642X-RAY DIFFRACTION96
1.9215-1.99840.14521360.10162664X-RAY DIFFRACTION96
1.9984-2.08940.13881450.10142649X-RAY DIFFRACTION95
2.0894-2.19950.13851300.10232417X-RAY DIFFRACTION87
2.1995-2.33730.14341410.10392701X-RAY DIFFRACTION96
2.3373-2.51780.15151460.11392713X-RAY DIFFRACTION98
2.5178-2.77110.16491390.12272734X-RAY DIFFRACTION97
2.7711-3.17210.15891360.12652727X-RAY DIFFRACTION96
3.1721-3.99620.15431310.11832639X-RAY DIFFRACTION92

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