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- PDB-9okp: CryoEM structure of the E. coli zinc ABC transporter ZnuB-ZnuC E1... -

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Basic information

Entry
Database: PDB / ID: 9okp
TitleCryoEM structure of the E. coli zinc ABC transporter ZnuB-ZnuC E146Q in complex with ATP
Components
  • High-affinity zinc transporter ATPase
  • High-affinity zinc uptake system membrane protein ZnuB
KeywordsMETAL TRANSPORT / ATP-binding cassette / zinc transporter / zinc binding / AMP-PNP
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
ADENOSINE-5'-TRIPHOSPHATE / High-affinity zinc uptake system membrane protein ZnuB / High-affinity zinc transporter ATPase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsPang, C. / Nguyen, H. / Zhang, Q. / Bahar, I. / Liu, Q.
Funding support United States, 2items
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, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2026Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: High-affinity zinc uptake system membrane protein ZnuB
C: High-affinity zinc uptake system membrane protein ZnuB
D: High-affinity zinc transporter ATPase
E: High-affinity zinc transporter ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,46112
Polymers111,1364
Non-polymers1,3258
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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


Mass: 27658.463 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: znuB, ACU57_21190, BANRA_00316, BANRA_02430, BGM66_000403, BTB68_002643, BvCmsKKP061_01839, CIG67_05295, CTR35_000327, DL968_14210, E4K51_14025, FV293_18615, GNW61_11860, HEP30_000365, HV109_ ...Gene: znuB, ACU57_21190, BANRA_00316, BANRA_02430, BGM66_000403, BTB68_002643, BvCmsKKP061_01839, CIG67_05295, CTR35_000327, DL968_14210, E4K51_14025, FV293_18615, GNW61_11860, HEP30_000365, HV109_09645, HVY77_11070, HX136_14520, IH772_04995, J0541_002655, JNP96_15900, NCTC9045_02550, NCTC9706_04197, P6223_004059, WR15_05640
Production host: Escherichia coli (E. coli) / References: UniProt: A0A037YFR8
#2: Protein High-affinity zinc transporter ATPase / Lsa(C)_1_HM990671 / Mn2+/Zn2+ABC transporter ATP-binding protein / Putative ATP-binding component ...Lsa(C)_1_HM990671 / Mn2+/Zn2+ABC transporter ATP-binding protein / Putative ATP-binding component of a transport system / Zinc ABC transporter ATP-binding protein ZnuC / Zinc ABC transporter ATPase / Zinc import ATP-binding protein ZnuC


Mass: 27909.541 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: znuC, A2J79_001074, A5U30_001163, ACU57_21195, BANRA_00317, BANRA_02431, BANRA_02514, BCB93_003247, BG944_000027, BGM66_000402, BK300_16825, BMT50_21810, BRV02_002415, BTB68_002642, BTQ06_ ...Gene: znuC, A2J79_001074, A5U30_001163, ACU57_21195, BANRA_00317, BANRA_02431, BANRA_02514, BCB93_003247, BG944_000027, BGM66_000402, BK300_16825, BMT50_21810, BRV02_002415, BTB68_002642, BTQ06_04850, BXT93_21735, C1Q91_000377, C2M16_13800, C3F40_01300, C6669_19850, C719_002992, C7B02_20610, C9160_10450, C9194_08065, C9Z68_01535, CCS08_13535, CF22_000585, CG702_12665, CQ842_19325, CQ842_23670, CR538_10995, CTR35_000328, CV83915_04524, CWS33_16780, D3C88_04030, D3G36_01205, D4M65_03190, D4N09_01590, D9D43_05570, D9E49_20460, D9J61_10795, DIV22_08075, DNQ45_17740, DNX30_00600, DS732_15065, DTL43_11940, E2863_02289, E4K51_14030, E5H86_06985, ECs2568, EIZ93_04035, EN85_003613, EPS76_02960, EPS97_03255, EWK56_00630, ExPECSC038_01829, F7N46_03360, F9413_08505, F9B07_11365, FIJ20_05915, FOI11_003745, FOI11_16300, FPI65_11335, FV293_18620, FWK02_10230, FZU14_05085, G3V95_04575, GAI89_19405, GAJ12_12690, GKF66_00585, GP711_12565, GP965_18825, GP975_02130, GQM04_11170, GQM13_04265, GQM21_03700, GQN24_19110, GRC73_10315, GRW05_21245, GRW24_03220, GTP92_01415, GUC01_04420, HHH44_001583, HIE29_000800, HJQ60_004185, HKA49_000112, HLX92_06100, HLZ50_02640, HMV95_00340, HV209_08835, HVV39_26730, HVW04_01375, HX136_14515, I6H02_03380, IFC14_003186, J0541_002654, J5U05_000290, J8F57_003353, JNA68_05840, JNP96_15895, NCTC10418_03224, NCTC10429_03242, NCTC11181_00047, NCTC11341_06009, NCTC7922_02602, NCTC7927_02343, NCTC7928_06155, NCTC8500_02381, NCTC8603_01712, NCTC9045_02551, NCTC9073_05913, NCTC9702_02523, NOI85_06935, NY836_03130, OFN31_18900, OGM49_13630, P6223_004058, PWL68_004606, Q2V20_18870, Q2V64_09685, R8O40_000625, RZR61_00940, SAMEA3472044_01370, V9Z47_15460
Production host: Escherichia coli (E. coli)
References: UniProt: C3T5S7, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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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: E. coli zinc ABC transporter ZnuB-ZnuC in complex with ATP
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 700 nm
Image recordingElectron dose: 66 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.18.2_3874: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 18325 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0047832
ELECTRON MICROSCOPYf_angle_d0.59610665
ELECTRON MICROSCOPYf_dihedral_angle_d16.9331094
ELECTRON MICROSCOPYf_chiral_restr0.0411318
ELECTRON MICROSCOPYf_plane_restr0.0041313

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