9OKP | pdb_00009okp

CryoEM structure of the E. coli zinc ABC transporter ZnuB-ZnuC E146Q in complex with ATP

PDB DOI: https://doi.org/10.2210/pdb9OKP/pdb
EM Map EMD-70571: EMDB EMDataResource

Classification: METAL TRANSPORT
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-05-11 Released: 2026-05-27
Deposition Author(s): Pang, C., Nguyen, H., Zhang, Q., Bahar, I., Liu, Q.
Funding Organization(s): Department of Energy (DOE, United States), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structural mechanism of transport and regulation in zinc ABC transporters

Pang, C., Nguyen, H., Zhang, Q., Bahar, I., Liu, Q.

To be published.

Macromolecule Content

Total Structure Weight: 112.46 kDa
Atom Count: 7,696
Modeled Residue Count: 1,002
Deposited Residue Count: 1,022
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
High-affinity zinc uptake system membrane protein ZnuB	A [auth B], B [auth C]	260	Escherichia coli	Mutation(s): 0 Gene Names: znuB, ACU57_21190, BANRA_00316, BANRA_02430, BGM66_000403, BTB68_002643, BvCmsKKP061_01839, CIG67_05295, CTR35_000327, DL968_14210... 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
UniProt
Find proteins for P39832 (Escherichia coli (strain K12)) Explore P39832 Go to UniProtKB: P39832
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P39832
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
High-affinity zinc transporter ATPase	C [auth D], D [auth E]	251	Escherichia coli	Mutation(s): 0 Gene Names: znuC, A2J79_001074, A5U30_001163, ACU57_21195, BANRA_00317, BANRA_02431, BANRA_02514, BCB93_003247, BG944_000027, BGM66_000402... 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 EC: 3.6.3 (PDB Primary Data), 7.2.2.20 (UniProt)
UniProt
Find proteins for P0A9X1 (Escherichia coli (strain K12)) Explore P0A9X1 Go to UniProtKB: P0A9X1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A9X1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP (Subject of Investigation/LOI) Query on ATP Download:Ideal Coordinates CCD File SDF format, chain I [auth E] SDF format, chain E [auth D] MOL2 format, chain I [auth E] MOL2 format, chain E [auth D] mmCIF format, chain I [auth E] mmCIF format, chain E [auth D]	E [auth D], I [auth E]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain E [auth D] Focus chain I [auth E] Interactions & Density Focus chain E [auth D] Focus chain I [auth E]
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain L [auth E] SDF format, chain K [auth E] SDF format, chain H [auth D] SDF format, chain G [auth D] MOL2 format, chain L [auth E] MOL2 format, chain K [auth E] MOL2 format, chain H [auth D] MOL2 format, chain G [auth D] mmCIF format, chain L [auth E] mmCIF format, chain K [auth E] mmCIF format, chain H [auth D] mmCIF format, chain G [auth D]	G [auth D], H [auth D], K [auth E], L [auth E]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain G [auth D] Focus chain H [auth D] Focus chain K [auth E] Focus chain L [auth E] Interactions & Density Focus chain G [auth D] Focus chain H [auth D] Focus chain K [auth E] Focus chain L [auth E]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain J [auth E] SDF format, chain F [auth D] MOL2 format, chain J [auth E] MOL2 format, chain F [auth D] mmCIF format, chain J [auth E] mmCIF format, chain F [auth D]	F [auth D], J [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth D] Focus chain J [auth E] Interactions & Density Focus chain F [auth D] Focus chain J [auth E]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.18.2_3874:

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-05-27

Deposition Author(s):

Funding Organization	Location	Grant Number
Department of Energy (DOE, United States)	United States	--
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--