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- PDB-5uwa: Structure of E. coli phospholipid binding protein MlaC -

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Basic information

Entry
Database: PDB / ID: 5uwa
TitleStructure of E. coli phospholipid binding protein MlaC
ComponentsProbable phospholipid-binding protein MlaC
KeywordsTRANSPORT PROTEIN / phospholipid-binding protein / bacterial lipid transport
Function / homologyTgt2/MlaC superfamily / Toluene tolerance Ttg2/phospholipid-binding protein MlaC / MlaC protein / intermembrane phospholipid transfer / phospholipid transport / outer membrane-bounded periplasmic space / Chem-8ND / Intermembrane phospholipid transport system binding protein MlaC
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.501 Å
AuthorsBhabha, G. / Ekiert, D.C.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)K99GM112982 United States
Damon Runyon Cancer Research FoundationDRG-2140-12 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Cell / Year: 2017
Title: Architectures of Lipid Transport Systems for the Bacterial Outer Membrane.
Authors: Damian C Ekiert / Gira Bhabha / Georgia L Isom / Garrett Greenan / Sergey Ovchinnikov / Ian R Henderson / Jeffery S Cox / Ronald D Vale /
Abstract: How phospholipids are trafficked between the bacterial inner and outer membranes through the hydrophilic space of the periplasm is not known. We report that members of the mammalian cell entry (MCE) ...How phospholipids are trafficked between the bacterial inner and outer membranes through the hydrophilic space of the periplasm is not known. We report that members of the mammalian cell entry (MCE) protein family form hexameric assemblies with a central channel capable of mediating lipid transport. The E. coli MCE protein, MlaD, forms a ring associated with an ABC transporter complex in the inner membrane. A soluble lipid-binding protein, MlaC, ferries lipids between MlaD and an outer membrane protein complex. In contrast, EM structures of two other E. coli MCE proteins show that YebT forms an elongated tube consisting of seven stacked MCE rings, and PqiB adopts a syringe-like architecture. Both YebT and PqiB create channels of sufficient length to span the periplasmic space. This work reveals diverse architectures of highly conserved protein-based channels implicated in the transport of lipids between the membranes of bacteria and some eukaryotic organelles.
History
DepositionFeb 20, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2017Group: Database references
Revision 1.2Aug 9, 2017Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_related / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_related.content_type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable phospholipid-binding protein MlaC
B: Probable phospholipid-binding protein MlaC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2494
Polymers47,0252
Non-polymers1,2242
Water5,206289
1
A: Probable phospholipid-binding protein MlaC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1252
Polymers23,5131
Non-polymers6121
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Probable phospholipid-binding protein MlaC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1252
Polymers23,5131
Non-polymers6121
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.630, 115.890, 133.220
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 Probable phospholipid-binding protein MlaC


Mass: 23512.613 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: mlaC, yrbC, b3192, JW3159 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ADV7
#2: Chemical ChemComp-8ND / (2S)-3-(2-aminoethoxy)propane-1,2-diyl dihexadecanoate


Mass: 611.979 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C37H73NO5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 289 / 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: 2.76 Å3/Da / Density % sol: 55.44 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.1 M citric acid pH 3.5 and 1.6 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.116 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.116 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 83295 / % possible obs: 98.5 % / Redundancy: 7.2 % / CC1/2: 0.57 / Net I/σ(I): 22.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: based on homology model with 2QGU as a template

2qgu


Resolution: 1.501→43.718 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 17.02
RfactorNum. reflection% reflection
Rfree0.1675 1894 2.4 %
Rwork0.138 --
obs0.1387 79050 93.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å
Refinement stepCycle: LAST / Resolution: 1.501→43.718 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2978 0 80 289 3347
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093310
X-RAY DIFFRACTIONf_angle_d1.2024497
X-RAY DIFFRACTIONf_dihedral_angle_d14.1561316
X-RAY DIFFRACTIONf_chiral_restr0.046478
X-RAY DIFFRACTIONf_plane_restr0.006590
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5012-1.53870.32451190.25934660X-RAY DIFFRACTION80
1.5387-1.58030.26421140.20644825X-RAY DIFFRACTION84
1.5803-1.62680.23921230.1815050X-RAY DIFFRACTION87
1.6268-1.67930.23141300.16145222X-RAY DIFFRACTION89
1.6793-1.73940.18991300.1365320X-RAY DIFFRACTION92
1.7394-1.8090.19661310.12395427X-RAY DIFFRACTION93
1.809-1.89130.1741340.1145571X-RAY DIFFRACTION95
1.8913-1.9910.17061400.10765663X-RAY DIFFRACTION97
1.991-2.11580.16121410.10685746X-RAY DIFFRACTION98
2.1158-2.27910.15691420.10875773X-RAY DIFFRACTION98
2.2791-2.50850.15331440.12125818X-RAY DIFFRACTION99
2.5085-2.87140.16181460.13855920X-RAY DIFFRACTION99
2.8714-3.61740.13811470.14295948X-RAY DIFFRACTION99
3.6174-43.73660.17031530.15046213X-RAY DIFFRACTION99

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