7VTZ | pdb_00007vtz

Chitoporin from Escherichia coli

• PDB DOI: https://doi.org/10.2210/pdb7VTZ/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTM


• Deposited: 2021-11-01 Released: 2022-11-09 
• Deposition Author(s): Amornloetwattana, R., Soysa, H.S.M., Suginta, W., van den Berg, B.
• Funding Organization(s): European Union (EU)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.286 (Depositor), 0.287 (DCC) 
• R-Value Work: 
  0.236 (Depositor), 0.238 (DCC) 
• R-Value Observed: 
  0.239 (Depositor) 

Literature

Structure-based classification of bacterial chitooligosaccharide-specific outer membrane porins (ChiPs).

Amornloetwattana, R., Bunkum, P., Soysa, H.S.M., Basle, A., Aunkham, A., Robinson, R.C., van den Berg, B., Suginta, W.

(2026) J Biol Chem : 113441-113441

• PubMed: 42586430 
• DOI: https://doi.org/10.1016/j.jbc.2026.113441
• Primary Citation Related Structures: 
  7VTZ, 7VU0, 7VU1, 7VU2, 7VU3


• PubMed Abstract: 
  

  Chitoporins (ChiPs) are chitooligosaccharide-specific outer membrane porins found in various Gram-negative bacteria and are critical for marine species that use chitin as a carbon and nitrogen source. Vibrio spp. ChiPs, exemplified by VhChiP from V. harveyi, are trimeric OmpC-like 16-stranded β-barrels with a long pore-confining loop L3 that interacts exclusively with long chain chitooligosaccharides. Here, using crystallography and electrophysiology, we show that two atypical ChiPs, Escherichia coli ChiP (EcChiP) and Serratia marcescens ChiP (SmChiP), are monomeric 18-stranded β-barrels with shorter L3 loops, which display weaker and less selective substrate interactions compared with their Vibrio counterparts. Structure-based phylogenetic analysis of bacterial ChiPs resolves three clades: monomeric ChiPs; clade A, trimeric ChiPs with an N-plug; and clade B, trimeric ChiPs lacking the characterized helical N-plug. These architectural differences likely reflect environmental selection. Marine Vibrio spp., living in chitin-rich environments, possess trimeric ChiPs that enable rapid chitin uptake, whereas soil-borne S. marcescens and multi-habitat E. coli encode monomeric ChiPs that we speculate are more suited to variable substrate availability.

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Organizational Affiliation: 
• School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology, (VISTEC), Wangchan Valley 555 Moo 1 Payupnai, Rayong 21210, Thailand.
School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology, (VISTEC), Wangchan Valley 555 Moo 1 Payupnai, Rayong 21210, Thailand; Department of Physical Sciences and Technology, Faculty of Applied Sciences, Sabaragamuwa University of Sri Lanka, Belihuloya, 70140 Sri Lanka.
Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom.
Program of Environmental Health, School of Health Science, Mae Fah Luang University, Chiang Rai 57100, Thailand.
School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology, (VISTEC), Wangchan Valley 555 Moo 1 Payupnai, Rayong 21210, Thailand. Electronic address: [e-mail].
Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom,. Electronic address: [e-mail].
School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology, (VISTEC), Wangchan Valley 555 Moo 1 Payupnai, Rayong 21210, Thailand. Electronic address: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 51.63 kDa 
• Atom Count: 3,666 
• Modeled Residue Count: 435 
• Deposited Residue Count: 442 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chitoporin	A	442	Escherichia coli K-12	Mutation(s): 0  Gene Names: chiP, ybfM, b0681, JW0667 Membrane Entity: Yes
UniProt
Find proteins for P75733 (Escherichia coli (strain K12)) Explore P75733  Go to UniProtKB:  P75733

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LMT	F [auth A]	DODECYL-BETA-D-MALTOSIDE C24 H46 O11 NLEBIOOXCVAHBD-QKMCSOCLSA-N
PT (Subject of Investigation/LOI)	B [auth A], C [auth A], D [auth A], E [auth A]	PLATINUM (II) ION Pt HRGDZIGMBDGFTC-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.286 (Depositor), 0.287 (DCC) 
• R-Value Work:  0.236 (Depositor), 0.238 (DCC) 
• R-Value Observed: 0.239 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.913	α = 90
b = 58.673	β = 110.384
c = 95.028	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
Aimless	data scaling
AutoSol	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-11-09 
Deposition Author(s): Amornloetwattana, R., Soysa, H.S.M., Suginta, W., van den Berg, B.

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Funding Organization	Location	Grant Number
European Union (EU)	European Union	--

Revision History  

• Version 1.0: 2022-11-09
  Type: Initial release
  
• Version 2.0: 2023-10-11
  Type: Coordinate replacement
  Reason: Ligand identity
  Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Derived calculations, Non-polymer description, Refinement description, Source and taxonomy, Structure summary
• Version 2.1: 2026-09-09
  Changes: Database references, Structure summary