5GHU | pdb_00005ghu

Crystal structure of YadV chaperone at 1.63 Angstrom

• PDB DOI: https://doi.org/10.2210/pdb5GHU/pdb

• Classification: CHAPERONE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-06-20 Released: 2017-06-28 
• Deposition Author(s): Pandey, N.K., Bhavesh, N.S.
• Funding Organization(s): Department of Biotechnology

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free: 
  0.186 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.173 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

Starting Models: experimental

Literature

Crystal structure of the usher chaperone YadV reveals a monomer with the proline lock in closed conformation suggestive of an intermediate state.

Pandey, N.K., Verma, G., Kushwaha, G.S., Suar, M., Bhavesh, N.S.

(2020) FEBS Lett 

• PubMed: 32649775 
• DOI: https://doi.org/10.1002/1873-3468.13883
• Primary Citation Related Structures: 
  5GHU


• PubMed Abstract: 
  

  Cell surface pili assembled by the chaperone-usher (CU) pathway play a crucial role in the adhesion of uropathogenic Escherichia coli. YadV is the chaperone component of the CU pathway of Yad pili. Here, we report the crystal structure of YadV from E. coli. In contrast to major usher chaperones, YadV is a monomer in solution as well as in the crystallographic symmetry, and the monomeric form is a preferred state for interacting with pilus subunits. Moreover, we observed a closed conformation for the proline lock, a crucial structural element for chaperone-pilus subunit interaction. MD simulation shows that the closed state of the proline lock is not energetically stable. Thus, the structure of monomeric YadV with its closed proline lock may serve as an intermediate state to provide suitable access to pilus subunits.

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Organizational Affiliation: 
• Transcription Regulation Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India.
School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), (Deemed to be University), Bhubaneswar, India.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 24.84 kDa 
• Atom Count: 1,840 
• Modeled Residue Count: 201 
• Deposited Residue Count: 222 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable fimbrial chaperone YadV	A	222	Escherichia coli K-12	Mutation(s): 0  Gene Names: ecpD
UniProt
Find proteins for P33128 (Escherichia coli (strain K12)) Explore P33128  Go to UniProtKB:  P33128

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGE	F [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
ACT	C [auth A], D [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
FMT	E [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free:  0.186 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.173 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.28	α = 90
b = 127.56	β = 90
c = 45.84	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data collection
SCALA	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
iMOSFLM	data processing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-06-28 
Deposition Author(s): Pandey, N.K., Bhavesh, N.S.

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Funding Organization	Location	Grant Number
Department of Biotechnology	India	BT/PR6400/BRB/10/113

Revision History  

• Version 1.0: 2017-06-28
  Type: Initial release
  
• Version 1.1: 2020-07-22
  Changes: Database references, Structure summary
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Refinement description