Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C7  (3D View)
Global Stoichiometry: Homo 7-mer - A7 

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

Macromolecule Content

• Total Structure Weight: 346.93 kDa 
• Atom Count: 24175 
• Residue Count: 3024 
• Unique protein chains: 1

3W9T

pore-forming CEL-III

• DOI: 10.2210/pdb3W9T/pdb

• Classification: TOXIN
• Organism(s): Cucumaria echinata
• Mutation(s): No 


• Deposited: 2013-04-16 Released: 2014-03-19 
• Deposition Author(s): Unno, H., Goda, S., Hatakeyama, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.273 
• R-Value Work: 0.239 
• R-Value Observed: 0.241 

Literature

Hemolytic lectin CEL-III heptamer reveals its transmembrane pore-formation mechanism

Unno, H., Goda, S., Hatakeyama, T.

(2014) J Biol Chem 

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemolytic lectin CEL-III	A, B, C, D, E, F, G	432	Cucumaria echinata	Mutation(s): 0  Gene Names: cel3
Find proteins for Q868M7 (Cucumaria echinata) Explore Q868M7  Go to UniProtKB:  Q868M7

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-galactopyranose-(1-4)-beta-D-fructofuranose	H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r	2		N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	A, B, C, D, E, F, G	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG	A, B, C, D, E, F, G	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA	A,B,C,D,E,F,G	L-PEPTIDE LINKING	C5 H7 N O3		GLN

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900038	H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r	lactulose	Oligosaccharide /  Water retention		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.273 
• R-Value Work: 0.239 
• R-Value Observed: 0.241 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 219.8	α = 90
b = 228.65	β = 127.13
c = 133.02	γ = 90

Software Package:

Software Name	Purpose
PHENIX	model building
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-04-16 
• Released Date: 2014-03-19 
Deposition Author(s): Unno, H., Goda, S., Hatakeyama, T.

Revision History 

• Version 1.0: 2014-03-19
  Type: Initial release
  
• Version 1.1: 2014-05-21
  Changes: Other
• Version 2.0: 2018-07-25
  Changes: Advisory, Data collection, Database references, Non-polymer description, Source and taxonomy, Structure summary
• Version 3.0: 2019-12-25
  Changes: Derived calculations, Polymer sequence
• Version 4.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary