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- EMDB-70570: CryoEM structure of the E. coli zinc ABC transporter ZnuB-ZnuC in... -

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Basic information

Entry
Database: EMDB / ID: EMD-70570
TitleCryoEM structure of the E. coli zinc ABC transporter ZnuB-ZnuC in complex with AMP-PNP
Map data
Sample
  • Complex: E. coli zinc ABC transporter ZnuB-ZnuC in complex with AMP-PNP
    • Protein or peptide: High-affinity zinc uptake system membrane protein ZnuB
    • Protein or peptide: High-affinity zinc transporter ATPase
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
  • Ligand: water
KeywordsATP-binding cassette / zinc transporter / zinc binding / METAL TRANSPORT
Function / homology
Function and homology information


Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances / zinc ion transport / response to zinc ion / transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / ATP hydrolysis activity / ATP binding
Similarity search - Function
ABC transporter, TroCD-like / ABC 3 transport family / : / ABC transporter, BtuC-like / 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
High-affinity zinc uptake system membrane protein ZnuB / High-affinity zinc transporter ATPase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsPang C / Nguyen H / Zhang Q / Bahar I / Liu Q
Funding support United States, 2 items
OrganizationGrant numberCountry
Department of Energy (DOE, United States) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: Structural mechanism of transport and regulation in zinc ABC transporters
Authors: Pang C / Nguyen H / Zhang Q / Bahar I / Liu Q
History
DepositionMay 11, 2025-
Header (metadata) releaseMay 27, 2026-
Map releaseMay 27, 2026-
UpdateMay 27, 2026-
Current statusMay 27, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70570.png

Downloads & links

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Map

FileDownload / File: emd_70570.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 160 pix.
= 170.496 Å		1.07 Å/pix.
x 160 pix.
= 170.496 Å		1.07 Å/pix.
x 160 pix.
= 170.496 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0656 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.367
Minimum - Maximum-0.63044304 - 2.0095248
Average (Standard dev.)0.007825445 (±0.0783201)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 170.496 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_70570_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map

Fileemd_70570_half_map_1.map
Annotationhalf map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map

Fileemd_70570_half_map_2.map
Annotationhalf map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : E. coli zinc ABC transporter ZnuB-ZnuC in complex with AMP-PNP

EntireName: E. coli zinc ABC transporter ZnuB-ZnuC in complex with AMP-PNP
Components
  • Complex: E. coli zinc ABC transporter ZnuB-ZnuC in complex with AMP-PNP
    • Protein or peptide: High-affinity zinc uptake system membrane protein ZnuB
    • Protein or peptide: High-affinity zinc transporter ATPase
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
  • Ligand: water

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Supramolecule #1: E. coli zinc ABC transporter ZnuB-ZnuC in complex with AMP-PNP

SupramoleculeName: E. coli zinc ABC transporter ZnuB-ZnuC in complex with AMP-PNP
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: High-affinity zinc uptake system membrane protein ZnuB

MacromoleculeName: High-affinity zinc uptake system membrane protein ZnuB
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 27.658463 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MIELLFPGWL AGIMLACAAG PLGSFVVWRR MSYFGDTLAH ASLLGVAFGL LLDVNPFYAV IAVTLLLAGG LVWLEKRPQL AIDTLLGIM AHSALSLGLV VVSLMSNIRV DLMAYLFGDL LAVTPEDLIS IAIGVVIVVA ILFWQWRNLL SMTISPDLAF V DGVKLQRV ...String:
MIELLFPGWL AGIMLACAAG PLGSFVVWRR MSYFGDTLAH ASLLGVAFGL LLDVNPFYAV IAVTLLLAGG LVWLEKRPQL AIDTLLGIM AHSALSLGLV VVSLMSNIRV DLMAYLFGDL LAVTPEDLIS IAIGVVIVVA ILFWQWRNLL SMTISPDLAF V DGVKLQRV KLLLMLVTAL TIGVAMKFVG ALIITSLLII PAATARRFAR TPEQMAGVAV LVGMVAVTGG LTFSAVYDTP AG PSVVLCA ALLFILSMMK KQA

UniProtKB: High-affinity zinc uptake system membrane protein ZnuB

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Macromolecule #2: High-affinity zinc transporter ATPase

MacromoleculeName: High-affinity zinc transporter ATPase / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 26.952467 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTSLVSLENV SVSFGQRRVL SDVSLELKPG KILTLLGPNG AGKSTLVRVV LGLVTPDEGV IKRNGKLRIG YVPQKLYLDT TLPLTVNRF LRLRPGTHKE DILPALKRVQ AGHLINAPMQ KLSGGETQRV LLARALLNRP QLLVLDEPTQ GVDVNGQVAL Y DLIDQLRR ...String:
MTSLVSLENV SVSFGQRRVL SDVSLELKPG KILTLLGPNG AGKSTLVRVV LGLVTPDEGV IKRNGKLRIG YVPQKLYLDT TLPLTVNRF LRLRPGTHKE DILPALKRVQ AGHLINAPMQ KLSGGETQRV LLARALLNRP QLLVLDEPTQ GVDVNGQVAL Y DLIDQLRR ELDCGVLMVS HDLHLVMAKT DEVLCLNHHI CCSGTPEVVS LHPEFISMFG PRGAEQLGIY RHHHNHRHDL QG RIV

UniProtKB: High-affinity zinc transporter ATPase

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Macromolecule #3: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 3 / Number of copies: 2 / Formula: ANP
Molecular weightTheoretical: 506.196 Da
Chemical component information

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #5: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 5 / Number of copies: 4 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 4 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 66.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.7000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 34187
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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