8TS5 | pdb_00008ts5

Structure of the apo FabS1C_C1

PDB DOI: https://doi.org/10.2210/pdb8TS5/pdb

Classification: SIGNALING PROTEIN/IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2023-08-10 Released: 2023-11-22
Deposition Author(s): Singer, A.U., Bruce, H.A., Blazer, L.L., Adams, J.J., Sicheri, F., Sidhu, S.S.
Funding Organization(s): Celgene Corporation, Bristol-Myers Squibb (BMS) Research

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.264 (Depositor), 0.264 (DCC)
R-Value Work:
0.220 (Depositor), 0.223 (DCC)
R-Value Observed:
0.222 (Depositor)

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Engineered antigen-binding fragments for enhanced crystallization of antibody:antigen complexes.

Bruce, H.A., Singer, A.U., Filippova, E.V., Blazer, L.L., Adams, J.J., Enderle, L., Ben-David, M., Radley, E.H., Mao, D.Y.L., Pau, V., Orlicky, S., Sicheri, F., Kurinov, I., Atwell, S., Kossiakoff, A.A., Sidhu, S.S.

(2024) Protein Sci 33: e4824-e4824

PubMed: 37945533 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/pro.4824
Primary Citation Related Structures:
8T58, 8T6I, 8T7F, 8T7G, 8T7I, 8T8I, 8T9Y, 8TRS, 8TRT, 8TS5

PubMed Abstract:
The atomic-resolution structural information that X-ray crystallography can provide on the binding interface between a Fab and its cognate antigen is highly valuable for understanding the mechanism of interaction. However, many Fab:antigen complexes are recalcitrant to crystallization, making the endeavor a considerable effort with no guarantee of success. Consequently, there have been significant steps taken to increase the likelihood of Fab:antigen complex crystallization by altering the Fab framework. In this investigation, we applied the surface entropy reduction strategy coupled with phage-display technology to identify a set of surface substitutions that improve the propensity of a human Fab framework to crystallize. In addition, we showed that combining these surface substitutions with previously reported Crystal Kappa and elbow substitutions results in an extraordinary improvement in Fab and Fab:antigen complex crystallizability, revealing a strong synergistic relationship between these sets of substitutions. Through comprehensive Fab and Fab:antigen complex crystallization screenings followed by structure determination and analysis, we defined the roles that each of these substitutions play in facilitating crystallization and how they complement each other in the process.

Organizational Affiliation

School of Pharmacy, University of Waterloo, Waterloo, Canada.

Macromolecule Content

Total Structure Weight: 97.09 kDa
Atom Count: 7,063
Modeled Residue Count: 848
Deposited Residue Count: 876
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
S1C variant of Fab C1 heavy chain	A, C [auth B]	223	Homo sapiens	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
S1C variant of Fab C1 light chain	B [auth G], D [auth C]	215	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BTB Query on BTB Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain W [auth G] MOL2 format, chain E [auth A] MOL2 format, chain W [auth G] mmCIF format, chain E [auth A] mmCIF format, chain W [auth G]	E [auth A], W [auth G]	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₈ H₁₉ N O₅ OWMVSZAMULFTJU-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain W [auth G] Interactions & Density Focus chain E [auth A] Focus chain W [auth G]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain CA [auth G] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain HA [auth G] SDF format, chain IA [auth B] SDF format, chain K [auth A] SDF format, chain V [auth G] SDF format, chain X [auth G] SDF format, chain Y [auth G] SDF format, chain F [auth A] MOL2 format, chain CA [auth G] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth G] MOL2 format, chain IA [auth B] MOL2 format, chain K [auth A] MOL2 format, chain V [auth G] MOL2 format, chain X [auth G] MOL2 format, chain Y [auth G] MOL2 format, chain F [auth A] mmCIF format, chain CA [auth G] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth G] mmCIF format, chain IA [auth B] mmCIF format, chain K [auth A] mmCIF format, chain V [auth G] mmCIF format, chain X [auth G] mmCIF format, chain Y [auth G] mmCIF format, chain F [auth A]	CA [auth G] F [auth A] G [auth A] H [auth A] HA [auth G] CA [auth G], F [auth A], G [auth A], H [auth A], HA [auth G], IA [auth B], K [auth A], V [auth G], X [auth G], Y [auth G]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain CA [auth G] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain HA [auth G] Focus chain IA [auth B] Focus chain K [auth A] Focus chain V [auth G] Focus chain X [auth G] Focus chain Y [auth G] Interactions & Density Focus chain CA [auth G] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain HA [auth G] Focus chain IA [auth B] Focus chain K [auth A] Focus chain V [auth G] Focus chain X [auth G] Focus chain Y [auth G]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain AA [auth G] SDF format, chain BA [auth G] SDF format, chain DA [auth G] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain L [auth A] SDF format, chain N [auth A] SDF format, chain NA [auth C] SDF format, chain Z [auth G] SDF format, chain M [auth A] MOL2 format, chain AA [auth G] MOL2 format, chain BA [auth G] MOL2 format, chain DA [auth G] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain L [auth A] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth C] MOL2 format, chain Z [auth G] MOL2 format, chain M [auth A] mmCIF format, chain AA [auth G] mmCIF format, chain BA [auth G] mmCIF format, chain DA [auth G] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain L [auth A] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth C] mmCIF format, chain Z [auth G] mmCIF format, chain M [auth A]	AA [auth G] BA [auth G] DA [auth G] I [auth A] J [auth A] AA [auth G], BA [auth G], DA [auth G], I [auth A], J [auth A], L [auth A], M [auth A], N [auth A], NA [auth C], Z [auth G]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth G] Focus chain BA [auth G] Focus chain DA [auth G] Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth C] Focus chain Z [auth G] Interactions & Density Focus chain AA [auth G] Focus chain BA [auth G] Focus chain DA [auth G] Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth C] Focus chain Z [auth G]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain KA [auth B] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain JA [auth B] MOL2 format, chain KA [auth B] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain JA [auth B] mmCIF format, chain KA [auth B] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain JA [auth B]	JA [auth B], KA [auth B], O [auth A], P [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain JA [auth B] Focus chain KA [auth B] Focus chain O [auth A] Focus chain P [auth A] Interactions & Density Focus chain JA [auth B] Focus chain KA [auth B] Focus chain O [auth A] Focus chain P [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain GA [auth G] SDF format, chain U [auth A] MOL2 format, chain GA [auth G] MOL2 format, chain U [auth A] mmCIF format, chain GA [auth G] mmCIF format, chain U [auth A]	GA [auth G], U [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain GA [auth G] Focus chain U [auth A] Interactions & Density Focus chain GA [auth G] Focus chain U [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain FA [auth G] SDF format, chain LA [auth B] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain MA [auth B] SDF format, chain EA [auth G] MOL2 format, chain FA [auth G] MOL2 format, chain LA [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain MA [auth B] MOL2 format, chain EA [auth G] mmCIF format, chain FA [auth G] mmCIF format, chain LA [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A] mmCIF format, chain MA [auth B] mmCIF format, chain EA [auth G]	EA [auth G] FA [auth G] LA [auth B] MA [auth B] Q [auth A] EA [auth G], FA [auth G], LA [auth B], MA [auth B], Q [auth A], R [auth A], S [auth A], T [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain EA [auth G] Focus chain FA [auth G] Focus chain LA [auth B] Focus chain MA [auth B] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Interactions & Density Focus chain EA [auth G] Focus chain FA [auth G] Focus chain LA [auth B] Focus chain MA [auth B] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A]