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- PDB-7k7m: Crystal Structure of a membrane protein -

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Basic information

Entry
Database: PDB / ID: 7k7m
TitleCrystal Structure of a membrane protein
ComponentsDrug exporters of the RND superfamily-like protein
KeywordsMEMBRANE PROTEIN / transporter
Function / homology
Function and homology information


phosphatidylethanolamine transfer activity / phosphatidylglycerol binding / trehalose transmembrane transporter activity / trehalose transport / mycolate cell wall layer assembly / cell wall biogenesis / diacylglycerol binding / cell pole / cell tip / mycolic acid biosynthetic process ...phosphatidylethanolamine transfer activity / phosphatidylglycerol binding / trehalose transmembrane transporter activity / trehalose transport / mycolate cell wall layer assembly / cell wall biogenesis / diacylglycerol binding / cell pole / cell tip / mycolic acid biosynthetic process / cell septum / phospholipid transport / cardiolipin binding / phosphatidylethanolamine binding / phosphatidylinositol binding / regulation of membrane potential / cell wall organization / response to xenobiotic stimulus / response to antibiotic / plasma membrane
Similarity search - Function
: / Membrane transport protein MMPL domain / MMPL family
Similarity search - Domain/homology
6-decanoyl-trehalose / Trehalose monomycolate exporter MmpL3
Similarity search - Component
Biological speciesMycolicibacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.33 Å
AuthorsSu, C.-C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: PLoS Biol / Year: 2021
Title: Structures of the mycobacterial membrane protein MmpL3 reveal its mechanism of lipid transport.
Authors: Chih-Chia Su / Philip A Klenotic / Meng Cui / Meinan Lyu / Christopher E Morgan / Edward W Yu /
Abstract: The mycobacterial membrane protein large 3 (MmpL3) transporter is essential and required for shuttling the lipid trehalose monomycolate (TMM), a precursor of mycolic acid (MA)-containing trehalose ...The mycobacterial membrane protein large 3 (MmpL3) transporter is essential and required for shuttling the lipid trehalose monomycolate (TMM), a precursor of mycolic acid (MA)-containing trehalose dimycolate (TDM) and mycolyl arabinogalactan peptidoglycan (mAGP), in Mycobacterium species, including Mycobacterium tuberculosis and Mycobacterium smegmatis. However, the mechanism that MmpL3 uses to facilitate the transport of fatty acids and lipidic elements to the mycobacterial cell wall remains elusive. Here, we report 7 structures of the M. smegmatis MmpL3 transporter in its unbound state and in complex with trehalose 6-decanoate (T6D) or TMM using single-particle cryo-electron microscopy (cryo-EM) and X-ray crystallography. Combined with calculated results from molecular dynamics (MD) and target MD simulations, we reveal a lipid transport mechanism that involves a coupled movement of the periplasmic domain and transmembrane helices of the MmpL3 transporter that facilitates the shuttling of lipids to the mycobacterial cell wall.
History
DepositionSep 23, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Drug exporters of the RND superfamily-like protein
B: Drug exporters of the RND superfamily-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,0066
Polymers172,0202
Non-polymers1,9864
Water00
1
A: Drug exporters of the RND superfamily-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,0033
Polymers86,0101
Non-polymers9932
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Drug exporters of the RND superfamily-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,0033
Polymers86,0101
Non-polymers9932
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)180.378, 147.710, 138.192
Angle α, β, γ (deg.)90.000, 120.890, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Drug exporters of the RND superfamily-like protein


Mass: 86010.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / Gene: mmpL3, MSMEI_0243 / Production host: Escherichia coli (E. coli) / References: UniProt: I7G2R2
#2: Polysaccharide
alpha-D-glucopyranose-(1-1)-6-O-decanoyl-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 496.546 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: 6-decanoyl-trehalose
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2122h-1a_1-5][a2122h-1a_1-5_6*OCCCCCCCCCC/3=O]/1-2/a1-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(1+1)][a-D-Glcp]{}}LINUCSPDB-CARE
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: 4.59 Å3/Da / Density % sol: 73.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion / Details: 20mM Tris, 100mM NaAC and 25% PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.33→100 Å / Num. obs: 44875 / % possible obs: 99.1 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.046 / Rrim(I) all: 0.101 / Χ2: 0.966 / Net I/σ(I): 5.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.34-3.464.63.04144270.171.5783.4420.90299.3
3.46-3.64.72.04745010.3561.0512.3110.91499.5
3.6-3.764.61.11745070.6390.5781.2630.95699.4
3.76-3.964.50.65244430.8560.3410.7391.01299.3
3.96-4.214.20.35344580.9280.1930.4050.91798.3
4.21-4.534.80.245070.9740.1020.2250.9699.4
4.53-4.994.70.1244890.9920.0630.1360.98999.3
4.99-5.714.40.10844600.990.0570.1230.99398.4
5.71-7.24.70.0745290.9960.0350.0791.02299.5
7.2-1004.50.03145540.9980.0160.0350.99198.3

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Processing

Software
NameVersionClassification
PHENIX1.8refinement
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6OR2

6or2


Resolution: 3.33→98.66 Å / SU ML: 0.72 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 41.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.321 2115 4.76 %
Rwork0.2671 42308 -
obs0.2696 44423 97.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 241.42 Å2 / Biso mean: 139.4473 Å2 / Biso min: 82.45 Å2
Refinement stepCycle: final / Resolution: 3.33→98.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11505 0 136 0 11641
Biso mean--154.33 --
Num. residues----1513
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.33-3.410.47771200.4466228280
3.41-3.490.38981400.38282298
3.49-3.590.40861500.3666282799
3.59-3.690.38341480.3486286699
3.69-3.810.37411290.3176286099
3.81-3.950.38531410.31284799
3.95-4.110.33811550.2945281898
4.11-4.290.35371400.2762287599
4.29-4.520.31231460.24622844100
4.52-4.80.2951630.2336285299
4.8-5.170.30061360.2353286399
5.17-5.70.3641350.2545284398
5.7-6.520.31461310.27012921100
6.52-8.210.26241360.2495286198
8.21-98.660.30391450.2482292799

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