7CZ0 | pdb_00007cz0

Crystal structure of a thermostable green fluorescent protein (TGP) with a synthetic nanobody (Sb92)

PDB DOI: https://doi.org/10.2210/pdb7CZ0/pdb

Classification: FLUORESCENT PROTEIN
Organism(s): Galaxea fascicularis, synthetic construct
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-09-06 Released: 2021-09-08
Deposition Author(s): Cai, H., Yao, H., Li, T., Hutter, C., Tang, Y., Li, Y., Seeger, M., Li, D.
Funding Organization(s): National Science Foundation (NSF, China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.77 Å
R-Value Free:
0.241 (Depositor), 0.241 (DCC)
R-Value Work:
0.202 (Depositor), 0.204 (DCC)
R-Value Observed:
0.204 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 3.1 of the entry. See complete history.

Literature

Structure-based design of covalent nanobody binders for a thermostable green fluorescence protein.

Yue, Z., Li, Y., Cai, H., Yao, H., Li, D., Ni, A., Li, T.

(2024) Acta Biochim Biophys Sin (Shanghai) 57: 1363-1370

PubMed: 39719878 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.3724/abbs.2024233
Primary Citation Related Structures:
7CZ0

PubMed Abstract:
The use of green fluorescence protein (GFP) has advanced numerous areas of life sciences. An ultra-thermostable GFP (TGP), engineered from a coral GFP, offers potential advantages over traditional jellyfish-derived GFP because of its high stability. However, owing to its later discovery, TGP lacks the extensive toolsets available for GFP, such as heavy chain-only antibody binders known as nanobodies. In this study, we report the crystal structure of TGP in complex with Sb92, a synthetic nanobody identified from a previous in vitro screening, revealing Sb92's precise three-dimensional epitope. This structural insight, alongside the previously characterized Sb44-TGP complex, allows us to rationally design disulfide bonds between the antigen and the antibody for tighter interactions. Using biochemical analysis, we identify two bridged complexes (TGP A18C-Sb44 V100C and TGP E118C-Sb92 S57C), with the TGP-Sb92 disulfide pair showing high resistance to reducing agents. Our study expands the toolkit available for TGP and should encourage its wider applications.

Organizational Affiliation

Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China.

Macromolecule Content

Total Structure Weight: 171.45 kDa
Atom Count: 10,620
Modeled Residue Count: 1,324
Deposited Residue Count: 1,504
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thermostable green fluorescent protein (TGP)	A, B, C, D	232	Galaxea fascicularis	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Synthetic nanobody (Sybody) 92 recognizing the thermostable green fluorescent protein (TGP)	E, F, G, H	144	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CAD Query on CAD Download:Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A] mmCIF format, chain L [auth A]	L [auth A]	CACODYLIC ACID C₂ H₇ As O₂ OGGXGZAMXPVRFZ-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]
CAC Query on CAC Download:Ideal Coordinates CCD File SDF format, chain U [auth D] MOL2 format, chain U [auth D] mmCIF format, chain U [auth D]	U [auth D]	CACODYLATE ION C₂ H₆ As O₂ OGGXGZAMXPVRFZ-UHFFFAOYSA-M		Interactions Focus chain U [auth D] Interactions & Density Focus chain U [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain V [auth D] SDF format, chain T [auth C] SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain M [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] MOL2 format, chain V [auth D] MOL2 format, chain T [auth C] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain M [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] mmCIF format, chain V [auth D] mmCIF format, chain T [auth C] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain M [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A]	I [auth A] J [auth A] K [auth A] M [auth A] N [auth B] I [auth A], J [auth A], K [auth A], M [auth A], N [auth B], O [auth B], Q [auth B], R [auth B], S [auth B], T [auth C], V [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth C] Focus chain V [auth D] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth C] Focus chain V [auth D]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain W [auth D] SDF format, chain P [auth B] MOL2 format, chain W [auth D] MOL2 format, chain P [auth B] mmCIF format, chain W [auth D] mmCIF format, chain P [auth B]	P [auth B], W [auth D]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain P [auth B] Focus chain W [auth D] Interactions & Density Focus chain P [auth B] Focus chain W [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CRQ Query on CRQ	A, B, C, D	L-PEPTIDE LINKING	C₁₆ H₁₆ N₄ O₅		GLN, TYR, GLY

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.77 Å
R-Value Free: 0.241 (Depositor), 0.241 (DCC)
R-Value Work: 0.202 (Depositor), 0.204 (DCC)
R-Value Observed: 0.204 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.245	α = 90
b = 130.154	β = 90
c = 171.453	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2021-09-08

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	31870726

Revision History (Full details and data files)

Version 1.0: 2021-09-08
Type: Initial release
Version 2.0: 2023-11-15
Changes: Atomic model, Data collection, Derived calculations
Version 2.1: 2023-11-29
Changes: Refinement description
Version 2.2: 2024-10-16
Changes: Structure summary
Version 3.0: 2026-03-18
Changes: Polymer sequence
Version 3.1: 2026-07-01
Changes: Database references