8SFX | pdb_00008sfx

High Affinity nanobodies against GFP

PDB DOI: https://doi.org/10.2210/pdb8SFX/pdb

Classification: IMMUNE SYSTEM
Organism(s): Aequorea victoria, Lama glama
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2023-04-11 Released: 2024-05-22
Deposition Author(s): Ketaren, N.E., Rout, M.P., Bonanno, J.B., Almo, S.C.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.228 (Depositor), 0.230 (DCC)
R-Value Work:
0.210 (Depositor), 0.210 (DCC)
R-Value Observed:
0.211 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Unique mechanisms to increase structural stability and enhance antigen binding in nanobodies.

Ketaren, N.E., Fridy, P.C., Malashkevich, V., Sanyal, T., Brillantes, M., Thompson, M.K., Oren, D.A., Bonanno, J.B., Sali, A., Almo, S.C., Chait, B.T., Rout, M.P.

(2025) Structure 33: 677-690.e5

PubMed: 39938509 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1016/j.str.2025.01.019
Primary Citation of Related Structures:
8G0I, 8SFS, 8SFV, 8SFX, 8SFZ, 8SG3, 8SLC

PubMed Abstract:
Nanobodies are single domain antibody variants proving themselves to be compelling tools for research, disease diagnostics, and as therapeutics targeting a myriad of disease agents. However, despite this potential, their mechanisms of paratope presentation and structural stabilization have not been fully explored. Here, we show that unlike monoclonal antibodies, a nanobody repertoire maximizes sampling of an antigen surface by binding a single antigen in at least three different orientations, which are correlated with their paratope composition. Structure-guided reengineering of several nanobodies reveals that a single point mutation within the paratope or a highly conserved region of a nanobody's framework 3 (FR3) can markedly improve antigen affinity, nanobody stability, or both. Conversely, we show the negative impact on antigen affinity when "over-stabilizing" nanobodies. Collectively our results provide a universal strategy to tune a nanobody's affinity by modifying specific residues that can readily be applied to guide nanobody optimization and functionalization.

Organizational Affiliation

Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065, USA. Electronic address: nketaren@rockefeller.edu.

Macromolecule Content

Total Structure Weight: 90.36 kDa
Atom Count: 5,688
Modeled Residue Count: 694
Deposited Residue Count: 790
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Green fluorescent protein	A, B	253	Aequorea victoria	Mutation(s): 1 Gene Names: GFP
UniProt
Find proteins for P42212 (Aequorea victoria) Explore P42212 Go to UniProtKB: P42212
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P42212
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
LaG21	C [auth D], D [auth C]	142	Lama glama	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MLT Query on MLT Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain P [auth B] MOL2 format, chain G [auth A] MOL2 format, chain P [auth B] mmCIF format, chain G [auth A] mmCIF format, chain P [auth B]	G [auth A], P [auth B]	D-MALATE C₄ H₆ O₅ BJEPYKJPYRNKOW-UWTATZPHSA-N		Interactions Focus chain G [auth A] Focus chain P [auth B] Interactions & Density Focus chain G [auth A] Focus chain P [auth B]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain EA [auth D] SDF format, chain FA [auth D] SDF format, chain KA [auth C] SDF format, chain L [auth A] SDF format, chain M [auth A] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain EA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain KA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain EA [auth D] mmCIF format, chain FA [auth D] mmCIF format, chain KA [auth C] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A]	AA [auth B] BA [auth B] EA [auth D] FA [auth D] KA [auth C] AA [auth B], BA [auth B], EA [auth D], FA [auth D], KA [auth C], L [auth A], M [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain KA [auth C] Focus chain L [auth A] Focus chain M [auth A] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain KA [auth C] Focus chain L [auth A] Focus chain M [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain GA [auth C] SDF format, chain N [auth B] SDF format, chain O [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain GA [auth C] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain GA [auth C] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B]	E [auth A], F [auth A], GA [auth C], N [auth B], O [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain GA [auth C] Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain GA [auth C] Focus chain N [auth B] Focus chain O [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain H [auth A] SDF format, chain HA [auth C] SDF format, chain I [auth A] SDF format, chain IA [auth C] SDF format, chain J [auth A] SDF format, chain JA [auth C] SDF format, chain K [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] mmCIF format, chain CA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth C] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth C] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B]	CA [auth D] DA [auth D] H [auth A] HA [auth C] I [auth A] CA [auth D], DA [auth D], H [auth A], HA [auth C], I [auth A], IA [auth C], J [auth A], JA [auth C], K [auth A], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Focus chain DA [auth D] Focus chain H [auth A] Focus chain HA [auth C] Focus chain I [auth A] Focus chain IA [auth C] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain CA [auth D] Focus chain DA [auth D] Focus chain H [auth A] Focus chain HA [auth C] Focus chain I [auth A] Focus chain IA [auth C] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]