9N4G | pdb_00009n4g

YehD Receptor Binding Domain

• PDB DOI: https://doi.org/10.2210/pdb9N4G/pdb

• Classification: CELL ADHESION
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-02-02 Released: 2025-11-26 
• Deposition Author(s): Klein, R.D., Tamadonfar, K.O., Pinkner, J.S., Hultgren, S.J.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.256 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.235 (Depositor), 0.238 (DCC) 
• R-Value Observed: 
  0.236 (Depositor) 

Literature

The Yeh pilus, tipped by an adhesin equipped with a mobile alpha-helical flap motif, mediates GI colonization via pectin adherence.

Tamadonfar, K.O., Klein, R.D., Lopatto, E., Zimmerman, M.I., Azimzadeh, P., Porter, J., Bazan Villicana, J., Pinkner, J.S., Birchenough, G., Dodson, K.W., Bowman, G.R., Hultgren, S.J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 37.11 kDa 
• Atom Count: 2,646 
• Modeled Residue Count: 345 
• Deposited Residue Count: 346 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YehD protein	A, B	173	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P33340 (Escherichia coli (strain K12)) Explore P33340  Go to UniProtKB:  P33340

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.256 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.235 (Depositor), 0.238 (DCC) 
• R-Value Observed: 0.236 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.787	α = 90
b = 50.486	β = 90
c = 71.877	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data scaling
AutoSol	phasing
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-26 
Deposition Author(s): Klein, R.D., Tamadonfar, K.O., Pinkner, J.S., Hultgren, S.J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R37AI048689
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01AI029549
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	T32 AI007172-40

Revision History  

• Version 1.0: 2025-11-26
  Type: Initial release