6LZ2 | pdb_00006lz2

Crystal structure of a thermostable green fluorescent protein (TGP) with a synthetic nanobody (Sb44)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 
    0.215 (Depositor), 0.219 (DCC) 
  • R-Value Work: 
    0.175 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 
    0.176 (Depositor) 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6LZ2

This is version 3.0 of the entry. See complete history

Literature

An improved fluorescent tag and its nanobodies for membrane protein expression, stability assay, and purification.

Cai, H.Yao, H.Li, T.Hutter, C.A.J.Li, Y.Tang, Y.Seeger, M.A.Li, D.

(2020) Commun Biol 3: 753-753

  • DOI: https://doi.org/10.1038/s42003-020-01478-z
  • Primary Citation Related Structures: 
    6LZ2

  • PubMed Abstract: 

    Green fluorescent proteins (GFPs) are widely used to monitor membrane protein expression, purification, and stability. An ideal reporter should be stable itself and provide high sensitivity and yield. Here, we demonstrate that a coral (Galaxea fascicularis) thermostable GFP (TGP) is by such reasons an improved tag compared to the conventional jellyfish GFPs. TGP faithfully reports membrane protein stability at temperatures near 90 °C (20-min heating). By contrast, the limit for the two popular GFPs is 64 °C and 74 °C. Replacing GFPs with TGP increases yield for all four test membrane proteins in four expression systems. To establish TGP as an affinity tag for membrane protein purification, several high-affinity synthetic nanobodies (sybodies), including a non-competing pair, are generated, and the crystal structure of one complex is solved. Given these advantages, we anticipate that TGP becomes a widely used tool for membrane protein structural studies.


  • Organizational Affiliation
    • University of Chinese Academy of Sciences, National Center for Protein Science Shanghai, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 320 Yueyang Road, 200031, Shanghai, China.

Macromolecule Content 

  • Total Structure Weight: 85.12 kDa 
  • Atom Count: 5,990 
  • Modeled Residue Count: 670 
  • Deposited Residue Count: 752 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Thermostable green fluorescent protein
A, C
232Galaxea fascicularisMutation(s): 0 
Gene Names: Green fluorescent GFP-like protein
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
synthetic nanobody (sybody) 44 against the thermostable green fluorescent protein (TGP)
B, D
144Lama glamaMutation(s): 0 

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TRS

Query on TRS



Download:Ideal Coordinates CCD File
J [auth C]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
GOL

Query on GOL



Download:Ideal Coordinates CCD File
I [auth C],
K [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
G [auth B],
H [auth C],
L [auth D],
M [auth D]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
NA

Query on NA



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CRQ
Query on CRQ
A, C
L-PEPTIDE LINKINGC16 H16 N4 O5GLN, TYR, GLY

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free:  0.215 (Depositor), 0.219 (DCC) 
  • R-Value Work:  0.175 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 0.176 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.61α = 90
b = 83.486β = 90
c = 184.562γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, China)China31870726

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-23
    Type: Initial release
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Database references, Derived calculations
  • Version 2.1: 2023-11-29
    Changes: Refinement description
  • Version 2.2: 2024-11-13
    Changes: Structure summary
  • Version 3.0: 2026-03-18
    Changes: Polymer sequence