5MDR

Crystal structure of in vitro folded Chitoporin VhChip from Vibrio harveyi in complex with chitohexaose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.172 

Starting Model: experimental
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This is version 2.2 of the entry. See complete history


Literature

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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chitoporin
A, B, C, D, E
A, B, C, D, E, F
352Vibrio harveyiMutation(s): 0 
Gene Names: chiP
Membrane Entity: Yes 
UniProt
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
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
G, H, I, J, K
G, H, I, J, K, L
6N/A
Glycosylation Resources
GlyTouCan:  G36414FS
GlyCosmos:  G36414FS
GlyGen:  G36414FS
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
C8E
Query on C8E

Download Ideal Coordinates CCD File 
BA [auth C]
EA [auth D]
FA [auth D]
GA [auth D]
LA [auth E]
BA [auth C],
EA [auth D],
FA [auth D],
GA [auth D],
LA [auth E],
M [auth A],
MA [auth E],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
QA [auth F],
R [auth A],
W [auth B],
X [auth B]
(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE
C16 H34 O5
FEOZZFHAVXYAMB-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
AA [auth B]
CA [auth C]
DA [auth C]
HA [auth D]
IA [auth D]
AA [auth B],
CA [auth C],
DA [auth C],
HA [auth D],
IA [auth D],
JA [auth D],
KA [auth D],
NA [auth E],
OA [auth E],
PA [auth E],
RA [auth F],
S [auth A],
SA [auth F],
T [auth A],
U [auth A],
V [auth A],
Y [auth B],
Z [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E
A, B, C, D, E, F
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.172 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 146.552α = 90
b = 121.941β = 117.92
c = 147.155γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

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
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-01-17
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 2.2: 2024-10-16
    Changes: Structure summary