9U78 | pdb_00009u78

Single Chain Protein of De Novo Designed Helix Bundles-4EH2 with KDPV Loop


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.199 (Depositor), 0.198 (DCC) 
  • R-Value Work: 
    0.176 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 
    0.178 (Depositor) 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 9U78

This is version 1.2 of the entry. See complete history

Literature

A Designed Zn 2+ Sensor Domain Transmits Binding Information to Transmembrane Histidine Kinases.

Hatstat, A.K.Kormos, R.Xu, V.Du, G.Liu, L.Zhang, S.Q.DeGrado, W.F.

(2025) J Am Chem Soc 147: 18770-18782

  • DOI: https://doi.org/10.1021/jacs.5c02273
  • Primary Citation Related Structures: 
    9U78

  • PubMed Abstract: 

    Generating stimulus-responsive allosteric signaling de novo is a significant challenge in protein design. In natural systems like bacterial histidine kinases (HKs), signal transduction occurs when ligand binding initiates a signal that is amplified across biological membranes over long distances to induce large-scale rearrangements and phosphorylation relays. Here, we ask whether our understanding of protein design and multidomain, intramolecular signaling has progressed sufficiently to enable engineering of a HK with tunable de novo components. We generated de novo metal-binding sensor domains and substituted them for the native sensor domain of a transmembrane HK, affording chimeras that transduce signals initiated from a de novo sensor. Signaling depended on the designed sensor's stability and the interdomain linker's phase and length. These results show the usefulness of de novo design to elucidate the biochemical mechanisms and principles of transmembrane signaling.


  • Organizational Affiliation
    • Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158-9001, United States.

Macromolecule Content 

  • Total Structure Weight: 29.19 kDa 
  • Atom Count: 2,295 
  • Modeled Residue Count: 236 
  • Deposited Residue Count: 236 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Single Chain Protein of De Novo Designed Helix Bundles-4EH2 with KDPV Loop
A, B
118synthetic constructMutation(s): 0 

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL

Query on GOL



Download:Ideal Coordinates CCD File
H [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
(Subject of Investigation/LOI)

Query on ZN



Download:Ideal Coordinates CCD File
C [auth A],
I [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
D [auth A],
J [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
FMT

Query on FMT



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A],
G [auth A],
K [auth B]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.199 (Depositor), 0.198 (DCC) 
  • R-Value Work:  0.176 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 0.178 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.748α = 90
b = 69.748β = 104.8
c = 55.048γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China22177113
National Key R&D Program of ChinaChina2024YFA0916800

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-09
    Type: Initial release
  • Version 1.1: 2025-06-11
    Changes: Database references
  • Version 1.2: 2025-06-18
    Changes: Database references