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- PDB-5ktf: Structure of the C-terminal transmembrane domain of scavenger rec... -

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Basic information

Entry
Database: PDB / ID: 5ktf
TitleStructure of the C-terminal transmembrane domain of scavenger receptor BI (SR-BI)
ComponentsScavenger receptor class B member 1
KeywordsSIGNALING PROTEIN / SR-BI / transmembrane domain / cholesterol
Function / homology
Function and homology information


vitamin transmembrane transport / high-density lipoprotein particle receptor activity / Scavenging by Class B Receptors / HDL clearance / intestinal lipid absorption / recognition of apoptotic cell / positive regulation of cholesterol storage / regulation of phosphatidylcholine catabolic process / lipopolysaccharide immune receptor activity / apolipoprotein A-I binding ...vitamin transmembrane transport / high-density lipoprotein particle receptor activity / Scavenging by Class B Receptors / HDL clearance / intestinal lipid absorption / recognition of apoptotic cell / positive regulation of cholesterol storage / regulation of phosphatidylcholine catabolic process / lipopolysaccharide immune receptor activity / apolipoprotein A-I binding / detection of lipopolysaccharide / cholesterol import / low-density lipoprotein particle clearance / blood vessel endothelial cell migration / high-density lipoprotein particle binding / adhesion of symbiont to host / positive regulation of triglyceride biosynthetic process / low-density lipoprotein particle binding / lipopolysaccharide transport / high-density lipoprotein particle clearance / high-density lipoprotein particle remodeling / phospholipid transport / reverse cholesterol transport / cholesterol transport / cholesterol catabolic process / triglyceride homeostasis / endothelial cell proliferation / cholesterol efflux / apolipoprotein binding / cholesterol homeostasis / lipopolysaccharide binding / caveola / amyloid-beta binding / lysosome / cell surface / membrane / plasma membrane / cytoplasm
Similarity search - Function
CD36/scavenger receptor class B member 1 / CD36 family / CD36 family
Similarity search - Domain/homology
Scavenger receptor class B member 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR
AuthorsChadwick, A.C. / Peterson, F.C. / Volkman, B.F. / Sahoo, D.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01HL58012 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI058072 United States
American Heart AssociationAHA14PRE185800221 United States
CitationJournal: Structure / Year: 2017
Title: NMR Structure of the C-Terminal Transmembrane Domain of the HDL Receptor, SR-BI, and a Functionally Relevant Leucine Zipper Motif.
Authors: Chadwick, A.C. / Jensen, D.R. / Hanson, P.J. / Lange, P.T. / Proudfoot, S.C. / Peterson, F.C. / Volkman, B.F. / Sahoo, D.
History
DepositionJul 11, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2017Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Data collection
Category: pdbx_audit_support / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.5May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Scavenger receptor class B member 1


Theoretical massNumber of molelcules
Total (without water)8,1861
Polymers8,1861
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / -
Representative

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Components

#1: Protein Scavenger receptor class B member 1 / SRB1 / SR-BI


Mass: 8185.792 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Scarb1, Srb1 / Plasmid: pQE30-SMT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-[pREP4] / References: UniProt: Q61009

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111anisotropic23D 1H-15N NOESY
121anisotropic23D 1H-13C NOESY aliphatic
131anisotropic23D 1H-13C NOESY aromatic

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Sample preparation

DetailsType: micelle
Contents: 1 mM [U-99% 13C; U-99% 15N] scavenger receptor BI (SR-BI), 5.0 w/v [U-2H] LPPG, 0.02 w/v sodium azide, 90% H2O/10% D2O
Label: SR-BI / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMscavenger receptor BI (SR-BI)[U-99% 13C; U-99% 15N]1
5.0 w/vLPPG[U-2H]1
0.02 w/vsodium azidenatural abundance1
Sample conditionsIonic strength: 0 Not defined / Label: conditon_1 / pH: 6.8 / Pressure: 1 atm / Temperature: 313 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III5001
Bruker AVANCEBrukerAVANCE6002

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
XEASYBartels et al.chemical shift assignment
XEASYBartels et al.peak picking
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Cloregeometry optimization
NMR ensembleConformers submitted total number: 20

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