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- PDB-7f47: Cryo-EM structure of Rhizobium etli MprF -

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Basic information

Entry
Database: PDB / ID: 7f47
TitleCryo-EM structure of Rhizobium etli MprF
ComponentsHypothetical conserved protein
KeywordsMEMBRANE PROTEIN / flippase / aminoacyl-tRNA / phosphatidylglycerol
Function / homology
Function and homology information


aminoacyltransferase activity / phospholipid homeostasis / plasma membrane
Similarity search - Function
: / Phosphatidylglycerol lysyltransferase, C-terminal / Phosphatidylglycerol lysyltransferase, C-terminal / Acyl-CoA N-acyltransferase
Similarity search - Domain/homology
Chem-1K1 / Chem-PGW / Hypothetical conserved protein
Similarity search - Component
Biological speciesRhizobium etli (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.99 Å
AuthorsNishimura, M. / Hirano, H. / Kobayashi, K. / Gill, C.P. / Phan, C.N.K. / Kise, Y. / Kusakizako, T. / Yamashita, K. / Ito, Y. / Roy, H. ...Nishimura, M. / Hirano, H. / Kobayashi, K. / Gill, C.P. / Phan, C.N.K. / Kise, Y. / Kusakizako, T. / Yamashita, K. / Ito, Y. / Roy, H. / Nishizawa, T. / Nureki, O.
CitationJournal: To Be Published
Title: Cryo-EM structure of Rhizobium etli MprF
Authors: Nishimura, M.
History
DepositionJun 17, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2022Group: Derived calculations / Category: atom_type / Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z
Revision 1.2Jun 12, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / pdbx_initial_refinement_model / refine
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _refine.ls_d_res_high / _refine.ls_d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical conserved protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,5453
Polymers93,9191
Non-polymers1,6262
Water724
1
A: Hypothetical conserved protein
hetero molecules

A: Hypothetical conserved protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,0896
Polymers187,8372
Non-polymers3,2524
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
2


  • Idetical with deposited unit
  • point asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit in distinct coordinate
  • point asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: C2 (2 fold cyclic))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(-1), (-1), (1)193.224, 193.224

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Components

#1: Protein Hypothetical conserved protein


Mass: 93918.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium etli (strain CFN 42 / ATCC 51251) (bacteria)
Gene: RHE_CH03486 / Plasmid: pTSP1 / Details (production host): pET-modified vector / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2K4J4
#2: Chemical ChemComp-PGW / (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate / 1-Palmitoyl-2-Oleoyl-sn-Glycero-3-[Phospho-(1-glycerol)] / PHOSPHATIDYLGLYCEROL


Mass: 749.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H77O10P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#3: Chemical ChemComp-1K1 / [(2R)-1-[[(2R)-3-[(2S)-2,6-bis(azanyl)hexanoyl]oxy-2-oxidanyl-propoxy]-oxidanyl-phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (E)-octadec-9-enoate


Mass: 877.179 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C46H89N2O11P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: MprF / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.187 MDa / Experimental value: NO
Source (natural)Organism: Rhizobium etli CFN 42 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: DE3 / Plasmid: pTSP1
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTris-HClC4H11NO3-HCl1
2150 mMsodium chlorideNaCl1
30.06 %GDNC56H92O251
4100 uMTCEPC9H15O6P1
SpecimenConc.: 6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: a waiting time of 10 s and a blotting time of 4 s

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Details: CDS mode
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingAverage exposure time: 5 sec. / Electron dose: 56 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3159
EM imaging opticsEnergyfilter name: GIF Bioquantum

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Processing

SoftwareName: REFMAC / Version: 5.8.0272 / Classification: refinement / Contact author: Garib N. Murshudov / Contact author email: garib[at]mrc-lmb.cam.ac.uk / Date: Feb 9, 2020
Description: (un)restrained refinement or idealisation of macromolecular structures
EM software
IDNameVersionCategory
1RELION3.1particle selection
2SerialEMimage acquisition
4CTFFINDCTF correction
7Cootmodel fitting
9RELION3.1initial Euler assignment
10RELION3.1final Euler assignment
12RELION3.13D reconstruction
13REFMACmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.99 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 307241 / Symmetry type: POINT
Atomic model buildingSpace: RECIPROCAL
Atomic model buildingPDB-ID: 5VRV

5vrv


Accession code: 5VRV / Source name: PDB / Type: experimental model
RefinementResolution: 2.99→2.99 Å / Cor.coef. Fo:Fc: 0.691 / WRfactor Rwork: 0.42 / SU B: 10.347 / SU ML: 0.185 / Average fsc overall: 0.612 / Average fsc work: 0.612 / ESU R: 0.201
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rwork0.4196 230364 -
all0.42 --
obs--100 %
Solvent computationSolvent model: BABINET MODEL
Displacement parametersBiso mean: 161.053 Å2
Baniso -1Baniso -2Baniso -3
1-1.574 Å21.218 Å20 Å2
2--2.021 Å2-0 Å2
3----3.594 Å2
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0070.0136573
ELECTRON MICROSCOPYr_bond_other_d0.0010.0176543
ELECTRON MICROSCOPYr_ext_dist_refined_d0.2660.1585
ELECTRON MICROSCOPYr_angle_refined_deg1.4431.6258917
ELECTRON MICROSCOPYr_angle_other_deg1.3421.56214966
ELECTRON MICROSCOPYr_dihedral_angle_1_deg5.5735827
ELECTRON MICROSCOPYr_dihedral_angle_2_deg29.55420.205293
ELECTRON MICROSCOPYr_dihedral_angle_3_deg19.09151018
ELECTRON MICROSCOPYr_dihedral_angle_4_deg20.5451546
ELECTRON MICROSCOPYr_chiral_restr0.0460.2856
ELECTRON MICROSCOPYr_gen_planes_refined0.0070.027298
ELECTRON MICROSCOPYr_gen_planes_other0.0020.021546
ELECTRON MICROSCOPYr_nbd_refined0.2150.22698
ELECTRON MICROSCOPYr_symmetry_nbd_other0.1680.211634
ELECTRON MICROSCOPYr_nbtor_refined0.1690.26562
ELECTRON MICROSCOPYr_symmetry_nbtor_other0.0780.26922
ELECTRON MICROSCOPYr_xyhbond_nbd_refined0.1250.2172
ELECTRON MICROSCOPYr_symmetry_xyhbond_nbd_other0.1220.22
ELECTRON MICROSCOPYr_symmetry_nbd_refined0.0530.22
ELECTRON MICROSCOPYr_nbd_other0.1550.216
ELECTRON MICROSCOPYr_symmetry_xyhbond_nbd_refined0.2080.22
ELECTRON MICROSCOPYr_mcbond_it13.35816.1453317
ELECTRON MICROSCOPYr_mcbond_other13.3616.1243316
ELECTRON MICROSCOPYr_mcangle_it20.0224.2444141
ELECTRON MICROSCOPYr_mcangle_other20.01724.2694142
ELECTRON MICROSCOPYr_scbond_it14.21218.0443256
ELECTRON MICROSCOPYr_scbond_other14.2118.0433257
ELECTRON MICROSCOPYr_scangle_it22.44626.2874776
ELECTRON MICROSCOPYr_scangle_other22.44426.2874777
ELECTRON MICROSCOPYr_lrange_it41.36307.90827420
ELECTRON MICROSCOPYr_lrange_other41.359307.90627421
LS refinement shell

Refine-ID: ELECTRON MICROSCOPY / Num. reflection Rfree: _ / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Num. reflection RworkNum. reflection allFsc work
2.7-2.7717023170230.146
2.77-2.84616646166460.182
2.846-2.92816196161960.234
2.928-3.01915674156740.279
3.019-3.11715180151800.404
3.117-3.22714680146800.535
3.227-3.34914253142530.63
3.349-3.48513582135820.78
3.485-3.6413095130950.831
3.64-3.81812549125490.898
3.818-4.02411934119340.919
4.024-4.26811247112470.935
4.268-4.56210585105850.951
4.562-4.927988298820.947
4.927-5.397899889980.919
5.397-6.033817781770.87
6.033-6.964722772270.808
6.964-8.523613161310.835
8.523-12.03468846880.852
12.03-136.452262126210.138

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