8VUI | pdb_00008vui

Structure of FabS1CE-EPR-1, an elbow-locked Fab, in complex with the erythropoeitin receptor

PDB DOI: https://doi.org/10.2210/pdb8VUI/pdb

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

Deposited: 2024-01-29 Released: 2024-07-10
Deposition Author(s): Singer, A.U., Bruce, H.A., Blazer, L., Adams, J.J., Sidhu, S.S.
Funding Organization(s): Canadian Institutes of Health Research (CIHR), Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.240 (Depositor), 0.241 (DCC)
R-Value Work:
0.197 (Depositor), 0.200 (DCC)
R-Value Observed:
0.199 (Depositor)

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Antigen-binding fragments with improved crystal lattice packing and enhanced conformational flexibility at the elbow region as crystallization chaperones.

Bruce, H.A., Singer, A.U., Blazer, L.L., Luu, K., Ploder, L., Pavlenco, A., Kurinov, I., Adams, J.J., Sidhu, S.S.

(2024) Protein Sci 33: e5081-e5081

PubMed: 38924648 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/pro.5081
Primary Citation Related Structures:
8VTP, 8VTR, 8VU1, 8VU4, 8VUA, 8VUC, 8VUI, 8VVM, 8VVO

PubMed Abstract:
It has been shown previously that a set of three modifications-termed S1, Crystal Kappa, and elbow-act synergistically to improve the crystallizability of an antigen-binding fragment (Fab) framework. Here, we prepared a phage-displayed library and performed crystallization screenings to identify additional substitutions-located near the heavy-chain elbow region-which cooperate with the S1, Crystal Kappa, and elbow modifications to increase expression and improve crystallizability of the Fab framework even further. One substitution (K141Q) supports the signature Crystal Kappa-mediated Fab:Fab crystal lattice packing interaction. Another substitution (E172G) improves the compatibility of the elbow modification with the Fab framework by alleviating some of the strain incurred by the shortened and bulkier elbow linker region. A third substitution (F170W) generates a split-Fab conformation, resulting in a powerful crystal lattice packing interaction comprising the biological interaction interface between the variable heavy and light chain domains. In sum, we have used K141Q, E172G, and F170W substitutions-which complement the S1, Crystal Kappa, and elbow modifications-to generate a set of highly crystallizable Fab frameworks that can be used as chaperones to enable facile elucidation of Fab:antigen complex structures by x-ray crystallography.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 73.71 kDa
Atom Count: 5,016
Modeled Residue Count: 626
Deposited Residue Count: 668
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-EPR-1 heavy chain	A	224	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-EPR-1 light chain	B [auth G]	212	Homo sapiens	Mutation(s): 0

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Erythropoietin receptor	C [auth D]	232	Homo sapiens	Mutation(s): 0 Gene Names: EPOR
UniProt & NIH Common Fund Data Resources
Find proteins for P19235 (Homo sapiens) Explore P19235 Go to UniProtKB: P19235
PHAROS: P19235 GTEx: ENSG00000187266
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P19235
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain C [auth D]	Go to GlyGen: P19235-1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain N [auth D] MOL2 format, chain N [auth D] mmCIF format, chain N [auth D]	N [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain N [auth D] Interactions & Density Focus chain N [auth D]
CIT Query on CIT Download:Ideal Coordinates CCD File SDF format, chain O [auth D] MOL2 format, chain O [auth D] mmCIF format, chain O [auth D]	O [auth D]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain O [auth D] Interactions & Density Focus chain O [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain I [auth G] SDF format, chain J [auth G] MOL2 format, chain D [auth A] MOL2 format, chain I [auth G] MOL2 format, chain J [auth G] mmCIF format, chain D [auth A] mmCIF format, chain I [auth G] mmCIF format, chain J [auth G]	D [auth A], I [auth G], J [auth G]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain I [auth G] Focus chain J [auth G] Interactions & Density Focus chain D [auth A] Focus chain I [auth G] Focus chain J [auth G]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain M [auth G] SDF format, chain Q [auth D] SDF format, chain R [auth D] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain M [auth G] MOL2 format, chain Q [auth D] MOL2 format, chain R [auth D] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain M [auth G] mmCIF format, chain Q [auth D] mmCIF format, chain R [auth D]	G [auth A], H [auth A], M [auth G], Q [auth D], R [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth G] Focus chain Q [auth D] Focus chain R [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth G] Focus chain Q [auth D] Focus chain R [auth D]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain K [auth G] SDF format, chain L [auth G] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain K [auth G] MOL2 format, chain L [auth G] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain K [auth G] mmCIF format, chain L [auth G]	E [auth A], F [auth A], K [auth G], L [auth G]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain K [auth G] Focus chain L [auth G] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain K [auth G] Focus chain L [auth G]
NH4 Query on NH4 Download:Ideal Coordinates CCD File SDF format, chain P [auth D] MOL2 format, chain P [auth D] mmCIF format, chain P [auth D]	P [auth D]	AMMONIUM ION H₄ N QGZKDVFQNNGYKY-UHFFFAOYSA-O		Interactions Focus chain P [auth D] Interactions & Density Focus chain P [auth D]