9KUE | pdb_00009kue

Crystal structure of the soluble green pigment protein from Tettigonia cantans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 
    0.267 (Depositor), 0.264 (DCC) 
  • R-Value Work: 
    0.223 (Depositor), 0.228 (DCC) 
  • R-Value Observed: 
    0.225 (Depositor) 

Starting Model: in silico
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

A green dichromophoric protein enabling foliage mimicry in arthropods.

Egorkin, N.A.Aleksin, A.M.Sedlov, I.A.Zhiganov, N.I.Bodunova, D.V.Varfolomeeva, L.A.Slonimskiy, Y.B.Ziganshin, R.H.Popov, V.O.Boyko, K.M.Vassilevski, A.A.Maksimov, E.G.Sluchanko, N.N.

(2025) Proc Natl Acad Sci U S A 122: e2502567122-e2502567122

  • DOI: https://doi.org/10.1073/pnas.2502567122
  • Primary Citation of Related Structures:  
    9KUE

  • PubMed Abstract: 

    Molecular mechanisms underlying the green insect camouflage have puzzled researchers for over a century. Here, we isolated and identified a green water-soluble protein from the integument of bush-cricket Tettigonia cantans . De novo sequencing and cloning revealed a severely fragmented form of vitellogenins, ubiquitous and multifunctional, but still largely enigmatic glycolipoproteins essential for embryonic development and lacking structural characterization. The distinctive color of the identified chromoprotein results from binding of a remarkable combination of farnesylated bilins (recently identified, tentative heme A catabolites) and xanthophylls, which commensurably absorb light in the 600 to 700 nm and 400 to 550 nm spectral regions and thereby produce a hue that perfectly mimics foliage. The high-resolution crystal structure of this unique ~80 kDa dichromophoric protein, which we named "dibilinoxanthinin" (DBXN), revealed two DBXN protomers, each consisting of three polypeptides, with a novel fold enclosing a large hydrophobic cavity that accommodates two bilins, two luteins, and four phosphatidylcholines, all anchored by hydrogen bonds and giving DBXN unique biochemical and optical properties. Among the green insects tested, some contained yellow and blue chromophores in separate fractions, while others had green proteins similar to DBXN, although not necessarily of the same size. Surprisingly, we isolated and identified a larger vitellogenin proteoform with DBXN-like absorption, from the green huntsman spider Micrommata virescens . These data illustrate striking variations in the DBXN-related pigmentation mechanism among different green arthropods and suggest that vitellogenins may have undergone neofunctionalization, reflecting their potential for functional diversification.


  • Organizational Affiliation
    • Laboratory of Protein-Protein Interactions, A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology, Russian Academy of Sciences, Moscow 119071, Russia.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dibilinoxanthinin (DBXN)
A, D
114Tettigonia cantansMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Dibilinoxanthinin (DBXN)
B, E
67Tettigonia cantansMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Dibilinoxanthinin (DBXN)
C, F
172Tettigonia cantansMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1L6M (Subject of Investigation/LOI)
Query on A1L6M

Download Ideal Coordinates CCD File 
K [auth C],
T [auth F]
3-[5-[(~{Z})-(3-ethyl-4-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-2-[(~{Z})-[4-(hydroxymethyl)-3-(3-hydroxy-3-oxopropyl)-5-[(~{Z})-[3-methyl-5-oxidanylidene-4-[(1~{S},4~{E},8~{Z})-5,9,13-trimethyl-1-oxidanyl-tetradeca-4,8,12-trienyl]pyrrol-2-ylidene]methyl]pyrrol-2-ylidene]methyl]-4-methyl-1~{H}-pyrrol-3-yl]propanoic acid
C48 H62 N4 O8
XIZXJTXQUCTMIQ-OYUVAKGFSA-N
PLC (Subject of Investigation/LOI)
Query on PLC

Download Ideal Coordinates CCD File 
J [auth C],
L [auth C],
O [auth D],
S [auth F]
DIUNDECYL PHOSPHATIDYL CHOLINE
C32 H65 N O8 P
IJFVSSZAOYLHEE-SSEXGKCCSA-O
LUT (Subject of Investigation/LOI)
Query on LUT

Download Ideal Coordinates CCD File 
G [auth A],
N [auth D]
(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
C40 H56 O2
KBPHJBAIARWVSC-NSIPBSJQSA-N
AZI
Query on AZI

Download Ideal Coordinates CCD File 
H [auth A]
I [auth B]
M [auth C]
P [auth D]
Q [auth E]
H [auth A],
I [auth B],
M [auth C],
P [auth D],
Q [auth E],
R [auth E]
AZIDE ION
N3
IVRMZWNICZWHMI-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSD
Query on CSD
A, D
L-PEPTIDE LINKINGC3 H7 N O4 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free:  0.267 (Depositor), 0.264 (DCC) 
  • R-Value Work:  0.223 (Depositor), 0.228 (DCC) 
  • R-Value Observed: 0.225 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.57α = 90
b = 87.256β = 90
c = 167.609γ = 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
Ministry of Science and Higher Education of the Russian FederationRussian Federation--

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-23
    Type: Initial release
  • Version 1.1: 2025-09-10
    Changes: Database references