Crystal structure of in vitro folded Chitoporin VhChip from Vibrio harveyi (crystal form I)

Experimental Data Snapshot

  • Resolution: 1.95 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.167 

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Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 7EQM


Structural basis for chitin acquisition by marine Vibrio species.

Aunkham, A.Zahn, M.Kesireddy, A.Pothula, K.R.Schulte, A.Basle, A.Kleinekathofer, U.Suginta, W.van den Berg, B.

(2018) Nat Commun 9: 220-220

  • DOI: https://doi.org/10.1038/s41467-017-02523-y
  • Primary Citation of Related Structures:  
    5MDO, 5MDP, 5MDQ, 5MDR, 5MDS

  • PubMed Abstract: 

    Chitin, an insoluble polymer of N-acetylglucosamine, is one of the most abundant biopolymers on Earth. By degrading chitin, chitinolytic bacteria such as Vibrio harveyi are critical for chitin recycling and maintenance of carbon and nitrogen cycles in the world's oceans. A decisive step in chitin degradation is the uptake of chito-oligosaccharides by an outer membrane protein channel named chitoporin (ChiP). Here, we report X-ray crystal structures of ChiP from V. harveyi in the presence and absence of chito-oligosaccharides. Structures without bound sugar reveal a trimeric assembly with an unprecedented closing of the transport pore by the N-terminus of a neighboring subunit. Substrate binding ejects the pore plug to open the transport channel. Together with molecular dynamics simulations, electrophysiology and in vitro transport assays our data provide an explanation for the exceptional affinity of ChiP for chito-oligosaccharides and point to an important role of the N-terminal gate in substrate transport.

  • Organizational Affiliation

    Biochemistry-Electrochemistry Research Unit, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D, E
A, B, C, D, E, F
352Vibrio harveyiMutation(s): 0 
Gene Names: chiP
Membrane Entity: Yes 
Find proteins for L0RVU0 (Vibrio harveyi)
Explore L0RVU0 
Go to UniProtKB:  L0RVU0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupL0RVU0
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on C8E

Download Ideal Coordinates CCD File 
CA [auth D]
DA [auth D]
EA [auth D]
IA [auth E]
J [auth A]
CA [auth D],
DA [auth D],
EA [auth D],
IA [auth E],
J [auth A],
JA [auth E],
K [auth A],
KA [auth E],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
OA [auth F],
P [auth A],
T [auth B],
U [auth B],
Y [auth C]
C16 H34 O5
Query on NA

Download Ideal Coordinates CCD File 
AA [auth D]
BA [auth D]
FA [auth E]
G [auth A]
GA [auth E]
AA [auth D],
BA [auth D],
FA [auth E],
G [auth A],
GA [auth E],
H [auth A],
HA [auth E],
I [auth A],
LA [auth F],
MA [auth F],
NA [auth F],
Q [auth B],
R [auth B],
S [auth B],
V [auth C],
W [auth C],
X [auth C],
Z [auth D]
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on MSE
A, B, C, D, E
A, B, C, D, E, F
Experimental Data & Validation

Experimental Data

  • Resolution: 1.95 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.167 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 146.884α = 90
b = 123.379β = 117.89
c = 147.026γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-20
    Type: Initial release
  • Version 1.1: 2018-01-24
    Changes: Database references