6NSJ

CryoEM structure of Helicobacter pylori urea channel in closed state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: 2D ARRAY 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 6NSK


Literature

pH-dependent gating mechanism of theHelicobacter pyloriurea channel revealed by cryo-EM.

Cui, Y.Zhou, K.Strugatsky, D.Wen, Y.Sachs, G.Zhou, Z.H.Munson, K.

(2019) Sci Adv 5: eaav8423-eaav8423

  • DOI: https://doi.org/10.1126/sciadv.aav8423
  • Primary Citation of Related Structures:  
    6NSJ, 6NSK

  • PubMed Abstract: 

    The urea channel of Helicobacter pylori ( Hp UreI) is an ideal drug target for preventing gastric cancer but incomplete understanding of its gating mechanism has hampered development of inhibitors for the eradication of H. pylori . Here, we present the cryo-EM structures of Hp UreI in closed and open conformations, both at a resolution of 2.7 Å. Our hexameric structures of this small membrane protein (~21 kDa/protomer) resolve its periplasmic loops and carboxyl terminus that close and open the channel, and define a gating mechanism that is pH dependent and requires cooperativity between protomers in the hexamer. Gating is further associated with well-resolved changes in the channel-lining residues that modify the shape and length of the urea pore. Site-specific mutations in the periplasmic domain and urea pore identified key residues important for channel function. Drugs blocking the urea pore based on our structures should lead to a new strategy for H. pylori eradication.


  • Organizational Affiliation

    California NanoSystems Institute, University California Los Angeles, Los Angeles, CA 90095, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Acid-activated urea channel
A, B, C, D, E
A, B, C, D, E, F
201Helicobacter pylori J99Mutation(s): 0 
Gene Names: ureIjhp_0066
Membrane Entity: Yes 
UniProt
Find proteins for P56874 (Helicobacter pylori (strain J99 / ATCC 700824))
Explore P56874 
Go to UniProtKB:  P56874
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56874
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
XP4
Query on XP4

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
J [auth B]
K [auth B]
G [auth A],
H [auth A],
I [auth A],
J [auth B],
K [auth B],
L [auth B],
M [auth C],
N [auth C],
O [auth C],
P [auth D],
Q [auth D],
R [auth D],
S [auth E],
T [auth E],
U [auth E],
V [auth F],
W [auth F],
X [auth F]
1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHATE
C31 H60 O8 P
OZSITQMWYBNPMW-GDLZYMKVSA-M
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: 2D ARRAY 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION2.0
MODEL REFINEMENTPHENIX1.14

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Center for Research Resources (NIH/NCRR)United StatesR01GM071940/AI094386/DE025567
National Institutes of Health/National Center for Research Resources (NIH/NCRR)United StatesR01DK46917/DK53462/DK58333

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-03
    Type: Initial release
  • Version 1.1: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.2: 2024-03-20
    Changes: Data collection, Database references, Refinement description