9H1N | pdb_00009h1n

Dihydrolipoamide Acetyltransferase (E2) PSBD in complex with the Pyruvate Dehydrogenase (E1) binding domain from E. coli

PDB DOI: https://doi.org/10.2210/pdb9H1N/pdb

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

Deposited: 2024-10-09 Released: 2025-10-29
Deposition Author(s): Bothe, S.N., Racunica, D., Glockshuber, R.
Funding Organization(s): Swiss National Science Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.54 Å
R-Value Free:
0.227 (Depositor), 0.226 (DCC)
R-Value Work:
0.204 (Depositor), 0.204 (DCC)
R-Value Observed:
0.205 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

A cooperative binding mechanism steers the recruitment of peripheral subunits in the E. coli pyruvate dehydrogenase complex

Bothe, S.N., Racunica, D., Zajec Hudnik, T., Zdanowicz, R., Bothe, A., Giese, C., Glockshuber, R.

To be published.

Macromolecule Content

Total Structure Weight: 18.48 kDa
Atom Count: 1,341
Modeled Residue Count: 148
Deposited Residue Count: 164
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyruvate dehydrogenase E1 component	A [auth C], B	49	Escherichia coli	Mutation(s): 0 Gene Names: aceE, b0114, JW0110 EC: 1.2.4.1
UniProt
Find proteins for P0AFG8 (Escherichia coli (strain K12)) Explore P0AFG8 Go to UniProtKB: P0AFG8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0AFG8
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex	C [auth A]	66	Escherichia coli	Mutation(s): 0 Gene Names: aceF, b0115, JW0111 EC: 2.3.1.12
UniProt
Find proteins for P06959 (Escherichia coli (strain K12)) Explore P06959 Go to UniProtKB: P06959
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P06959
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.54 Å
R-Value Free: 0.227 (Depositor), 0.226 (DCC)
R-Value Work: 0.204 (Depositor), 0.204 (DCC)
R-Value Observed: 0.205 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.262	α = 90
b = 87.262	β = 90
c = 42.341	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-10-29

Deposition Author(s):

Glockshuber, R.

Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	--

Revision History (Full details and data files)

Version 1.0: 2025-10-29
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.