9J1F | pdb_00009j1f

Dimeric Structure of ConA/M2P-Man


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 
    0.257 (Depositor), 0.261 (DCC) 
  • R-Value Work: 
    0.209 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 
    0.211 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Liquid Phase Exfoliation of Protein Parent Crystals into Nanosheets and Fibrils Based on Orthogonal Supramolecular Interactions.

Li, L.Ye, L.Shi, Y.Yin, L.Chen, G.

(2024) J Am Chem Soc 146: 31992-32002

  • DOI: https://doi.org/10.1021/jacs.4c11921
  • Primary Citation Related Structures: 
    8WMG, 8WMK, 9J1A, 9J1B, 9J1C, 9J1D, 9J1F

  • PubMed Abstract: 

    Proteins are attractive building blocks for fabricating diverse and precise nanomaterials. However, the facile fabrication of multidimensional artificial assemblies is highly challenging. Here, inspired by the large-scale production technique of inorganic nanomaterials, we demonstrate the application of liquid phase exfoliation (LPE) on native protein ConA by the design of synthetic ligands. These ligands provide distinct in-plane and out-of-plane supramolecular interactions, allowing the generation of multidimensional architectures based on the same protein by dissociating a single interaction in solution, including 3D porous protein crystals, 2D sizable nanosheets, and 1D fibrils. Importantly, the exfoliated 2D sheets were dozens of times larger than the self-assembled nanosheets, resulting in a dramatic enhancement of the intrinsic bioactivity of the building blocks by receptor clustering and less endocytosis. These findings enable the successful application of LPE on biomacromolecules and open up an alternative avenue to generate advanced multidimensional nanomaterials, without the need for complex protein design and careful adjustment of self-assembly conditions.


  • Organizational Affiliation
    • The State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science, Fudan University, Shanghai 200433, China.

Macromolecule Content 

  • Total Structure Weight: 104.4 kDa 
  • Atom Count: 7,417 
  • Modeled Residue Count: 948 
  • Deposited Residue Count: 948 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Concanavalin-A
A, B, C, D
237Canavalia ensiformisMutation(s): 0 
UniProt
Find proteins for P02866 (Canavalia ensiformis)
Explore P02866 
Go to UniProtKB:  P02866
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02866
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1EAW
(Subject of Investigation/LOI)

Query on A1EAW



Download:Ideal Coordinates CCD File
G [auth B],
J [auth C]
~{N}2,~{N}9-bis[2-[2-[(2~{S},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxyethoxy]ethyl]-1,10-phenanthroline-2,9-dicarboxamide
C34 H46 N4 O16
OKAYCRSCTNGBEC-RYKYLIPQSA-N
MN

Query on MN



Download:Ideal Coordinates CCD File
E [auth A],
H [auth B],
K [auth C],
M [auth D]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
F [auth A],
I [auth B],
L [auth C],
N [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free:  0.257 (Depositor), 0.261 (DCC) 
  • R-Value Work:  0.209 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 0.211 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.216α = 90
b = 79.07β = 117.2
c = 87.917γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-04
    Type: Initial release
  • Version 1.1: 2025-10-15
    Changes: Structure summary
  • Version 1.2: 2026-07-29
    Changes: Database references