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- EMDB-12321: structure of the full-length CmaX protein -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-12321
Titlestructure of the full-length CmaX protein
Map data
Sample
  • Complex: CmaX protein pentamer
    • Protein or peptide: CmaX protein
Keywordsdivalent transport / zinc transporter / CorA family / membrane protein / TRANSPORT PROTEIN
Function / homology
Function and homology information


metal ion transmembrane transporter activity / nickel cation transport / cobalt ion transport / zinc ion transport / plasma membrane
Similarity search - Function
Mg2+ transporter protein, CorA-like/Zinc transport protein ZntB / CorA, cytoplasmic domain / CorA, transmembrane region / CorA-like Mg2+ transporter protein
Similarity search - Domain/homology
Divalent cation transporter CmaX
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria) / Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.03 Å
AuthorsStetsenko A / Stehantsev P
Funding support1 items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)740.018.011
CitationJournal: Int J Biol Macromol / Year: 2021
Title: Structural and biochemical characterization of a novel ZntB (CmaX) transporter protein from Pseudomonas aeruginosa.
Authors: Artem Stetsenko / Pavlo Stehantsev / Natalia O Dranenko / Mikhail S Gelfand / Albert Guskov /
Abstract: The 2-TM-GxN family of membrane proteins is widespread in prokaryotes and plays an important role in transport of divalent cations. The canonical signature motif, which is also a selectivity filter, ...The 2-TM-GxN family of membrane proteins is widespread in prokaryotes and plays an important role in transport of divalent cations. The canonical signature motif, which is also a selectivity filter, has a composition of Gly-Met-Asn. Some members though deviate from this composition, however no data are available as to whether this has any functional implications. Here we report the functional and structural analysis of CmaX protein from a pathogenic Pseudomonas aeruginosa bacterium, which has a Gly-Ile-Asn signature motif. CmaX readily transports Zn, Mg, Cd, Ni and Co ions, but it does not utilize proton-symport as does ZntB from Escherichia coli. Together with the bioinformatics analysis, our data suggest that deviations from the canonical signature motif do not reveal any changes in substrate selectivity or transport and easily alter in course of evolution.
History
DepositionFeb 10, 2021-
Header (metadata) releaseJul 7, 2021-
Map releaseJul 7, 2021-
UpdateJul 9, 2025-
Current statusJul 9, 2025Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7nh9
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12321.png

Downloads & links

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Map

FileDownload / File: emd_12321.map.gz / Format: CCP4 / Size: 193.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.66 Å/pix.
x 370 pix.
= 242.72 Å		0.66 Å/pix.
x 370 pix.
= 242.72 Å		0.66 Å/pix.
x 370 pix.
= 242.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.656 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04 / Movie #1: 0.04
Minimum - Maximum-0.121830106 - 0.25278828
Average (Standard dev.)0.0008823037 (±0.008541658)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions370370370
Spacing370370370
CellA=B=C: 242.72 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.6560.6560.656
M x/y/z370370370
origin x/y/z0.0000.0000.000
length x/y/z242.720242.720242.720
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS370370370
D min/max/mean-0.1220.2530.001

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Supplemental data

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Sample components

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Entire : CmaX protein pentamer

EntireName: CmaX protein pentamer
Components
  • Complex: CmaX protein pentamer
    • Protein or peptide: CmaX protein

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Supramolecule #1: CmaX protein pentamer

SupramoleculeName: CmaX protein pentamer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)

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Macromolecule #1: CmaX protein

MacromoleculeName: CmaX protein / type: protein_or_peptide / ID: 1 / Details: N-terminal His tag and thrombin cleavage site / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Molecular weightTheoretical: 41.36502 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SSGLVPRGSH MASMTGGQQM GRGSMQAYES GDERGLIYGY VLNGRGGGRR VGRNQIAVLD LLPEESLWLH WDRGVPEAQ AWLRDSAGLS EFACDLLLEE ATRPRLLDLG AESLLVFLRG VNLNPGAEPE DMVSLRVFAD ARRVISLRLR P LKAVADLL ...String:
MGSSHHHHHH SSGLVPRGSH MASMTGGQQM GRGSMQAYES GDERGLIYGY VLNGRGGGRR VGRNQIAVLD LLPEESLWLH WDRGVPEAQ AWLRDSAGLS EFACDLLLEE ATRPRLLDLG AESLLVFLRG VNLNPGAEPE DMVSLRVFAD ARRVISLRLR P LKAVADLL EDLEAGKGPK TASEVVYYLA HYLTDRVDTL ISGIADQLDA VEELVEADER ASPDQHQLRT LRRRSAGLRR YL APQRDIY SQLARYKLSW FVEDDADYWN ELNNRLTRNL EELELIRERI SVLQEAESRR ITERMNRTMY LLGIITGFFL PMS FVTGLL GINVGGIPGA DAPHGFWLAC LLIGGVATFQ WWVFRRLRWL

UniProtKB: Divalent cation transporter CmaX

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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: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: PDB ENTRY / Details: 5N9Y
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.03 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 243386
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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