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- EMDB-30525: The overall structure of nucleotide free Acinetobacter MlaFEDB complex -

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Basic information

Entry
Database: EMDB / ID: EMD-30525
TitleThe overall structure of nucleotide free Acinetobacter MlaFEDB complex
Map datacryo EM map of the nucleotide free Acinetobacter MlaFEDB complex
Sample
  • Complex: nucleotide free Acinetobacter MlaFEDB complex
    • Protein or peptide: Intermembrane phospholipid transport system permease protein MlaE
    • Protein or peptide: ABC transporter ATP-binding protein
    • Protein or peptide: Anti-sigma factor antagonist
    • Protein or peptide: MCE family protein
  • Ligand: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
KeywordsMEMBRANE PROTEIN
Function / homology
Function and homology information


phospholipid transporter activity / ATP-binding cassette (ABC) transporter complex / phospholipid binding / ATP hydrolysis activity / ATP binding / membrane
Similarity search - Function
: / ABC transport permease subunit MlaE, Proteobacteria / : / ABC transporter permease MalE / Permease MlaE / STAS domain / Mce/MlaD / MlaD protein / STAS domain / STAS domain superfamily ...: / ABC transport permease subunit MlaE, Proteobacteria / : / ABC transporter permease MalE / Permease MlaE / STAS domain / Mce/MlaD / MlaD protein / STAS domain / STAS domain superfamily / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ABC transporter ATP-binding protein / ABC transporter periplasmic substrate-binding protein / Intermembrane phospholipid transport system permease protein MlaE / Anti-sigma factor antagonist
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsZhang YY / Fan QX
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31930059 China
CitationJournal: Cell Discov / Year: 2020
Title: Cryo-EM structures of Acinetobacter baumannii glycerophospholipid transporter.
Authors: Yuanyuan Zhang / Qiongxuan Fan / Ximin Chi / Qiang Zhou / Yanyan Li /
History
DepositionSep 9, 2020-
Header (metadata) releaseDec 16, 2020-
Map releaseDec 16, 2020-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7d06
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30525.png

Downloads & links

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Map

FileDownload / File: emd_30525.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcryo EM map of the nucleotide free Acinetobacter MlaFEDB complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 200 pix.
= 217.4 Å		1.09 Å/pix.
x 200 pix.
= 217.4 Å		1.09 Å/pix.
x 200 pix.
= 217.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.087 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.095294684 - 0.19119063
Average (Standard dev.)0.0003103617 (±0.007518547)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 217.40001 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0871.0871.087
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z217.400217.400217.400
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ360360360
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.0950.1910.000

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Supplemental data

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Sample components

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Entire : nucleotide free Acinetobacter MlaFEDB complex

EntireName: nucleotide free Acinetobacter MlaFEDB complex
Components
  • Complex: nucleotide free Acinetobacter MlaFEDB complex
    • Protein or peptide: Intermembrane phospholipid transport system permease protein MlaE
    • Protein or peptide: ABC transporter ATP-binding protein
    • Protein or peptide: Anti-sigma factor antagonist
    • Protein or peptide: MCE family protein
  • Ligand: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE

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Supramolecule #1: nucleotide free Acinetobacter MlaFEDB complex

SupramoleculeName: nucleotide free Acinetobacter MlaFEDB complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Acinetobacter baumannii (bacteria)

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Macromolecule #1: Intermembrane phospholipid transport system permease protein MlaE

MacromoleculeName: Intermembrane phospholipid transport system permease protein MlaE
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii (bacteria)
Molecular weightTheoretical: 27.322443 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString: MNTIAWLGRL VIERIRGIGV AALMLLQIIF SLPSAGGFGR FVYQMHRVGV MSLLIITVSG LFIGLVLGLQ GYSILVNVGS ESMLGTMVS LTLLRELAPV VAALLFAGRA GSALTAEIGS MKQSEQLASM EMIGVDPLKQ IVSPRLWAGI VSLPMLTVIF A AIGIVGGK ...String:
MNTIAWLGRL VIERIRGIGV AALMLLQIIF SLPSAGGFGR FVYQMHRVGV MSLLIITVSG LFIGLVLGLQ GYSILVNVGS ESMLGTMVS LTLLRELAPV VAALLFAGRA GSALTAEIGS MKQSEQLASM EMIGVDPLKQ IVSPRLWAGI VSLPMLTVIF A AIGIVGGK LVGVDFLGVD EGSFWSGMQN NVQFGHDVVN GIIKSIVFAL LCTWIAVFQG YACDPTPEGI ATAMTRTVVY SS LCVLGFD FVLTAVMFGG I

UniProtKB: Intermembrane phospholipid transport system permease protein MlaE

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Macromolecule #2: ABC transporter ATP-binding protein

MacromoleculeName: ABC transporter ATP-binding protein / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii (bacteria)
Molecular weightTheoretical: 30.070455 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString: MMNNKTPLST QSLIEVKNLS FNRGERVIYD NISLNIRRGQ ITAIMGPSGT GKTTLLRLIG GQLVPDQGEV LLDGKDIAQM SRQELFAAR ARMGMLFQSG ALFTDMSVYE NVAFPIRAHT KLSENLIAEL VALKLESVGL RGTEQLMPTE LSGGMNRRVA L ARAIALDP ...String:
MMNNKTPLST QSLIEVKNLS FNRGERVIYD NISLNIRRGQ ITAIMGPSGT GKTTLLRLIG GQLVPDQGEV LLDGKDIAQM SRQELFAAR ARMGMLFQSG ALFTDMSVYE NVAFPIRAHT KLSENLIAEL VALKLESVGL RGTEQLMPTE LSGGMNRRVA L ARAIALDP DLIMYDEPFA GQDPIVKGVL TRLIRSLREA LDLTTIIVSH DVPETLSIAD YIYVVAEGKI QGEGTPEELQ AY ASPFVKQ FLTGSAEGPV EYQFSHQAYL DNEVRP

UniProtKB: ABC transporter ATP-binding protein

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Macromolecule #3: Anti-sigma factor antagonist

MacromoleculeName: Anti-sigma factor antagonist / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii (bacteria)
Molecular weightTheoretical: 11.91376 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString:
VVQYLNQELV VSGKIDFENA EQQYQAGLAI IKKQTSFPLI VDLKQLEHGN TLALAVLVQW LRQTPQKSGL HFKNVPEKML KIIQACHLQ EDLHLVLEHH HHHH

UniProtKB: Anti-sigma factor antagonist

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Macromolecule #4: MCE family protein

MacromoleculeName: MCE family protein / type: protein_or_peptide / ID: 4 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii (bacteria)
Molecular weightTheoretical: 24.135322 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString: MKSRTSELAV GIFVIIFGIA LFFLAMKVSG LVGTNLSDGY TMKAQFDNVN GLKPRAKVTM SGVTIGRVDS ITLDPVTRLA TVTFDLDGK LTSFNAEQLK EVQKNALDEL RYSSDYTQAT PAQQKTMEQQ LISNMNSITS IDEDAYIMVA TNGLLGEKYL K IVPGGGLN ...String:
MKSRTSELAV GIFVIIFGIA LFFLAMKVSG LVGTNLSDGY TMKAQFDNVN GLKPRAKVTM SGVTIGRVDS ITLDPVTRLA TVTFDLDGK LTSFNAEQLK EVQKNALDEL RYSSDYTQAT PAQQKTMEQQ LISNMNSITS IDEDAYIMVA TNGLLGEKYL K IVPGGGLN YLKRGDTISN TQGTMDLEDL ISKFITGGGA GKVAAGSSSA EEKAPASTDS SAQPSFVE

UniProtKB: ABC transporter periplasmic substrate-binding protein

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Macromolecule #5: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-...

MacromoleculeName: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
type: ligand / ID: 5 / Number of copies: 12 / Formula: PGV
Molecular weightTheoretical: 749.007 Da
Chemical component information

ChemComp-PGV:
(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE / phospholipid*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.6) / Number images used: 314199
Initial angle assignmentType: OTHER
Final angle assignmentType: MAXIMUM LIKELIHOOD

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