9ZNP | pdb_00009znp

Sub-tomogram averaged structure of E. Coli DNA protection during starvation protein (DPS)

PDB DOI: https://doi.org/10.2210/pdb9ZNP/pdb
EM Map EMD-74453: EMDB EMDataResource

Classification: DNA BINDING PROTEIN
Organism(s): Escherichia coli
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-12-14 Released: 2026-08-05
Deposition Author(s): Yang, J.E., Sibert, B.S., Montemayor, E.J., Parrell, D., Larson, M.R., Kumar, A., Maindola, P., Cai, K., Wright, E.R.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Department of Energy (DOE, United States)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.00 Å
Aggregation State: PARTICLE
Reconstruction Method: SUBTOMOGRAM AVERAGING

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Sub-tomogram averaged structure of E. Coli DNA protection during starvation protein (DPS)

Yang, J.E., Sibert, B.S., Montemayor, E.J., Parrell, D., Larson, M.R., Kumar, A., Maindola, P., Cai, K., Wright, E.R.

To be published.

Macromolecule Content

Total Structure Weight: 225.31 kDa
Atom Count: 13,920
Modeled Residue Count: 1,848
Deposited Residue Count: 2,004
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA protection during starvation protein	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	167	Escherichia coli	Mutation(s): 0 Gene Names: dps, pexB, vtm, b0812, JW0797 EC: 1.16
UniProt
Find proteins for P0ABT2 (Escherichia coli (strain K12)) Explore P0ABT2 Go to UniProtKB: P0ABT2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0ABT2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FE Query on FE Download:Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth C] SDF format, chain R [auth D] SDF format, chain S [auth D] SDF format, chain T [auth E] SDF format, chain U [auth E] SDF format, chain V [auth F] SDF format, chain W [auth G] SDF format, chain X [auth J] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth D] MOL2 format, chain S [auth D] MOL2 format, chain T [auth E] MOL2 format, chain U [auth E] MOL2 format, chain V [auth F] MOL2 format, chain W [auth G] MOL2 format, chain X [auth J] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth D] mmCIF format, chain S [auth D] mmCIF format, chain T [auth E] mmCIF format, chain U [auth E] mmCIF format, chain V [auth F] mmCIF format, chain W [auth G] mmCIF format, chain X [auth J]	M [auth A] N [auth A] O [auth B] P [auth B] Q [auth C] M [auth A], N [auth A], O [auth B], P [auth B], Q [auth C], R [auth D], S [auth D], T [auth E], U [auth E], V [auth F], W [auth G], X [auth J]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth C] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth E] Focus chain U [auth E] Focus chain V [auth F] Focus chain W [auth G] Focus chain X [auth J] Interactions & Density Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth C] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth E] Focus chain U [auth E] Focus chain V [auth F] Focus chain W [auth G] Focus chain X [auth J]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.00 Å
Aggregation State: PARTICLE
Reconstruction Method: SUBTOMOGRAM AVERAGING

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION
MODEL REFINEMENT	PHENIX	1.21.2_5419

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-08-05

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM104540
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	U24GM139168
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	F32GM143854
Department of Energy (DOE, United States)	United States	DE-SC0018409