8TRS | pdb_00008trs

Structure of the EphA2 CRD bound to FabS1CE_C1, trigonal form

PDB DOI: https://doi.org/10.2210/pdb8TRS/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., 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: 1.90 Å
R-Value Free:
0.214 (Depositor), 0.216 (DCC)
R-Value Work:
0.180 (Depositor), 0.182 (DCC)
R-Value Observed:
0.182 (Depositor)

Starting Model: experimental
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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: 63.83 kDa
Atom Count: 4,598
Modeled Residue Count: 562
Deposited Residue Count: 569
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
S1CE variant of Fab C1 heavy chain	A	222	Homo sapiens	Mutation(s): 0

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
S1CE variant of Fab C1 light chain	B [auth G]	215	Homo sapiens	Mutation(s): 0

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Ephrin type-A receptor 2	C [auth D]	132	Homo sapiens	Mutation(s): 0 Gene Names: EPHA2, ECK EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P29317 (Homo sapiens) Explore P29317 Go to UniProtKB: P29317
PHAROS: P29317 GTEx: ENSG00000142627
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P29317
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain AA [auth G] SDF format, chain CA [auth G] SDF format, chain GA [auth G] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain Y [auth G] SDF format, chain Z [auth G] MOL2 format, chain AA [auth G] MOL2 format, chain CA [auth G] MOL2 format, chain GA [auth G] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain Y [auth G] MOL2 format, chain Z [auth G] mmCIF format, chain AA [auth G] mmCIF format, chain CA [auth G] mmCIF format, chain GA [auth G] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain Y [auth G] mmCIF format, chain Z [auth G]	AA [auth G] CA [auth G] GA [auth G] K [auth A] L [auth A] AA [auth G], CA [auth G], GA [auth G], K [auth A], L [auth A], Y [auth G], Z [auth G]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain AA [auth G] Focus chain CA [auth G] Focus chain GA [auth G] Focus chain K [auth A] Focus chain L [auth A] Focus chain Y [auth G] Focus chain Z [auth G] Interactions & Density Focus chain AA [auth G] Focus chain CA [auth G] Focus chain GA [auth G] Focus chain K [auth A] Focus chain L [auth A] Focus chain Y [auth G] Focus chain Z [auth G]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain BA [auth G] SDF format, chain D [auth A] SDF format, chain DA [auth G] SDF format, chain E [auth A] SDF format, chain EA [auth G] SDF format, chain F [auth A] SDF format, chain FA [auth G] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain HA [auth G] SDF format, chain I [auth A] SDF format, chain IA [auth G] SDF format, chain J [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain RA [auth D] SDF format, chain V [auth G] SDF format, chain W [auth G] SDF format, chain X [auth G] MOL2 format, chain BA [auth G] MOL2 format, chain D [auth A] MOL2 format, chain DA [auth G] MOL2 format, chain E [auth A] MOL2 format, chain EA [auth G] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth G] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth G] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth G] MOL2 format, chain J [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain RA [auth D] MOL2 format, chain V [auth G] MOL2 format, chain W [auth G] MOL2 format, chain X [auth G] mmCIF format, chain BA [auth G] mmCIF format, chain D [auth A] mmCIF format, chain DA [auth G] mmCIF format, chain E [auth A] mmCIF format, chain EA [auth G] mmCIF format, chain F [auth A] mmCIF format, chain FA [auth G] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth G] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth G] mmCIF format, chain J [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain RA [auth D] mmCIF format, chain V [auth G] mmCIF format, chain W [auth G] mmCIF format, chain X [auth G]	BA [auth G] D [auth A] DA [auth G] E [auth A] EA [auth G] BA [auth G], D [auth A], DA [auth G], E [auth A], EA [auth G], F [auth A], FA [auth G], G [auth A], H [auth A], HA [auth G], I [auth A], IA [auth G], J [auth A], M [auth A], N [auth A], RA [auth D], V [auth G], W [auth G], X [auth G]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain BA [auth G] Focus chain D [auth A] Focus chain DA [auth G] Focus chain E [auth A] Focus chain EA [auth G] Focus chain F [auth A] Focus chain FA [auth G] Focus chain G [auth A] Focus chain H [auth A] Focus chain HA [auth G] Focus chain I [auth A] Focus chain IA [auth G] Focus chain J [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain RA [auth D] Focus chain V [auth G] Focus chain W [auth G] Focus chain X [auth G] Interactions & Density Focus chain BA [auth G] Focus chain D [auth A] Focus chain DA [auth G] Focus chain E [auth A] Focus chain EA [auth G] Focus chain F [auth A] Focus chain FA [auth G] Focus chain G [auth A] Focus chain H [auth A] Focus chain HA [auth G] Focus chain I [auth A] Focus chain IA [auth G] Focus chain J [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain RA [auth D] Focus chain V [auth G] Focus chain W [auth G] Focus chain X [auth G]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain JA [auth G] SDF format, chain KA [auth G] SDF format, chain LA [auth G] SDF format, chain MA [auth G] SDF format, chain NA [auth G] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain PA [auth G] SDF format, chain Q [auth A] SDF format, chain QA [auth G] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain SA [auth D] SDF format, chain T [auth A] SDF format, chain TA [auth D] SDF format, chain U [auth A] SDF format, chain OA [auth G] MOL2 format, chain JA [auth G] MOL2 format, chain KA [auth G] MOL2 format, chain LA [auth G] MOL2 format, chain MA [auth G] MOL2 format, chain NA [auth G] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth G] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth G] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth D] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth D] MOL2 format, chain U [auth A] MOL2 format, chain OA [auth G] mmCIF format, chain JA [auth G] mmCIF format, chain KA [auth G] mmCIF format, chain LA [auth G] mmCIF format, chain MA [auth G] mmCIF format, chain NA [auth G] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth G] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth G] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain SA [auth D] mmCIF format, chain T [auth A] mmCIF format, chain TA [auth D] mmCIF format, chain U [auth A] mmCIF format, chain OA [auth G]	JA [auth G] KA [auth G] LA [auth G] MA [auth G] NA [auth G] JA [auth G], KA [auth G], LA [auth G], MA [auth G], NA [auth G], O [auth A], OA [auth G], P [auth A], PA [auth G], Q [auth A], QA [auth G], R [auth A], S [auth A], SA [auth D], T [auth A], TA [auth D], U [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain JA [auth G] Focus chain KA [auth G] Focus chain LA [auth G] Focus chain MA [auth G] Focus chain NA [auth G] Focus chain O [auth A] Focus chain OA [auth G] Focus chain P [auth A] Focus chain PA [auth G] Focus chain Q [auth A] Focus chain QA [auth G] Focus chain R [auth A] Focus chain S [auth A] Focus chain SA [auth D] Focus chain T [auth A] Focus chain TA [auth D] Focus chain U [auth A] Interactions & Density Focus chain JA [auth G] Focus chain KA [auth G] Focus chain LA [auth G] Focus chain MA [auth G] Focus chain NA [auth G] Focus chain O [auth A] Focus chain OA [auth G] Focus chain P [auth A] Focus chain PA [auth G] Focus chain Q [auth A] Focus chain QA [auth G] Focus chain R [auth A] Focus chain S [auth A] Focus chain SA [auth D] Focus chain T [auth A] Focus chain TA [auth D] Focus chain U [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain UA [auth D] MOL2 format, chain UA [auth D] mmCIF format, chain UA [auth D]	UA [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain UA [auth D] Interactions & Density Focus chain UA [auth D]