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- PDB-5uw2: Structure of E. coli MCE protein MlaD, periplasmic domain -

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Basic information

Entry
Database: PDB / ID: 5uw2
TitleStructure of E. coli MCE protein MlaD, periplasmic domain
ComponentsProbable phospholipid ABC transporter-binding protein MlaD
KeywordsTRANSPORT PROTEIN / MCE protein / bacterial lipid transport
Function / homologyProbable phospholipid ABC transporter-binding protein MlaD / : / Mce/MlaD / MlaD protein / phospholipid transporter activity / phospholipid binding / plasma membrane / Intermembrane phospholipid transport system binding protein MlaD
Function and homology information
Biological speciesEscherichia coli O157:H7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 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 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 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

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Assembly

Deposited unit
A: Probable phospholipid ABC transporter-binding protein MlaD
B: Probable phospholipid ABC transporter-binding protein MlaD
C: Probable phospholipid ABC transporter-binding protein MlaD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3119
Polymers53,9193
Non-polymers3926
Water00
1
A: Probable phospholipid ABC transporter-binding protein MlaD
B: Probable phospholipid ABC transporter-binding protein MlaD
C: Probable phospholipid ABC transporter-binding protein MlaD
hetero molecules

A: Probable phospholipid ABC transporter-binding protein MlaD
B: Probable phospholipid ABC transporter-binding protein MlaD
C: Probable phospholipid ABC transporter-binding protein MlaD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,62218
Polymers107,8376
Non-polymers78512
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area11210 Å2
ΔGint-401 kcal/mol
Surface area33790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.360, 63.820, 91.150
Angle α, β, γ (deg.)90.00, 130.01, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Probable phospholipid ABC transporter-binding protein MlaD


Mass: 17972.891 Da / Num. of mol.: 3 / Fragment: UNP residues 32-183
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: mlaD, Z4556, ECs4072 / Production host: Escherichia coli (E. coli) / References: UniProt: P64605
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn

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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: 2.53 Å3/Da / Density % sol: 51.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M zinc acetate, 0.1 M MES pH 6.0, and 15% ethanol

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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 315r / Detector: CCD / Date: Feb 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.116 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. obs: 12551 / % possible obs: 97.8 % / Redundancy: 3.7 % / CC1/2: 0.47 / Net I/σ(I): 14.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UW8

5uw8


Resolution: 2.85→33.599 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 34.63
RfactorNum. reflection% reflection
Rfree0.2648 589 5.08 %
Rwork0.2394 --
obs0.2406 11594 91.09 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å
Refinement stepCycle: LAST / Resolution: 2.85→33.599 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2557 0 6 0 2563
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032596
X-RAY DIFFRACTIONf_angle_d0.7373526
X-RAY DIFFRACTIONf_dihedral_angle_d9.53950
X-RAY DIFFRACTIONf_chiral_restr0.028426
X-RAY DIFFRACTIONf_plane_restr0.003447
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-3.13660.37831260.3622356X-RAY DIFFRACTION79
3.1366-3.59010.30911460.28572767X-RAY DIFFRACTION92
3.5901-4.52140.29351580.24222952X-RAY DIFFRACTION98
4.5214-33.60150.23231590.21662930X-RAY DIFFRACTION95
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.21030.1951-0.56653.8698-2.52.47050.07330.0872-0.350.45040.04210.0766-0.41680.51140.00071.04820.0227-0.25740.8943-0.10311.043117.981125.742719.6262
20.5456-1.4116-0.23293.50790.58473.29310.0637-0.02660.359-0.00730.316-0.7627-0.54390.76080.00060.8444-0.06320.01751.0014-0.15921.241225.749825.3126-5.6183
34.2259-1.77840.94342.67670.81632.7218-0.27930.21870.2141-0.42480.0666-0.081-0.33310.27060.00021.1164-0.13220.11270.7670.03660.78188.103125.4868-25.0812
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C

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