8FWF | pdb_00008fwf

Crystal structure of Apo form Fab235

PDB DOI: https://doi.org/10.2210/pdb8FWF/pdb

Classification: IMMUNE SYSTEM
Organism(s): Mus musculus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-01-21 Released: 2023-10-11
Deposition Author(s): Tan, K., Kim, M., Reinherz, E.L.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free:
0.206 (Depositor), 0.208 (DCC)
R-Value Work:
0.171 (Depositor), 0.171 (DCC)
R-Value Observed:
0.172 (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

Inadequate structural constraint on Fab approach rather than paratope elicitation limits HIV-1 MPER vaccine utility.

Tan, K., Chen, J., Kaku, Y., Wang, Y., Donius, L., Khan, R.A., Li, X., Richter, H., Seaman, M.S., Walz, T., Hwang, W., Reinherz, E.L., Kim, M.

(2023) Nat Commun 14: 7218-7218

PubMed: 37940661 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-023-42097-6
Primary Citation Related Structures:
8FWF, 8FXJ, 8FYM, 8FZ2

PubMed Abstract:
Broadly neutralizing antibodies (bnAbs) against HIV-1 target conserved envelope (Env) epitopes to block viral replication. Here, using structural analyses, we provide evidence to explain why a vaccine targeting the membrane-proximal external region (MPER) of HIV-1 elicits antibodies with human bnAb-like paratopes paradoxically unable to bind HIV-1. Unlike in natural infection, vaccination with MPER/liposomes lacks a necessary structure-based constraint to select for antibodies with an adequate approach angle. Consequently, the resulting Abs cannot physically access the MPER crawlspace on the virion surface. By studying naturally arising Abs, we further reveal that flexibility of the human IgG3 hinge mitigates the epitope inaccessibility and additionally facilitates Env spike protein crosslinking. Our results suggest that generation of IgG3 subtype class-switched B cells is a strategy for anti-MPER bnAb induction. Moreover, the findings illustrate the need to incorporate topological features of the target epitope in immunogen design.

Organizational Affiliation

Structural Biology Center, X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Lemont, IL, USA.

Macromolecule Content

Total Structure Weight: 50.58 kDa
Atom Count: 3,830
Modeled Residue Count: 446
Deposited Residue Count: 448
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab235, light chain	A [auth L]	220	Mus musculus	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab235, heavy chain	B [auth H]	228	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain P [auth H] SDF format, chain O [auth H] SDF format, chain E [auth L] SDF format, chain D [auth L] MOL2 format, chain P [auth H] MOL2 format, chain O [auth H] MOL2 format, chain E [auth L] MOL2 format, chain D [auth L] mmCIF format, chain P [auth H] mmCIF format, chain O [auth H] mmCIF format, chain E [auth L] mmCIF format, chain D [auth L]	D [auth L], E [auth L], O [auth H], P [auth H]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain D [auth L] Focus chain E [auth L] Focus chain O [auth H] Focus chain P [auth H] Interactions & Density Focus chain D [auth L] Focus chain E [auth L] Focus chain O [auth H] Focus chain P [auth H]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain Z [auth H] SDF format, chain Y [auth H] SDF format, chain X [auth H] SDF format, chain K [auth L] SDF format, chain J [auth L] SDF format, chain I [auth L] SDF format, chain H [auth L] SDF format, chain G [auth L] SDF format, chain BA [auth H] SDF format, chain AA [auth H] MOL2 format, chain Z [auth H] MOL2 format, chain Y [auth H] MOL2 format, chain X [auth H] MOL2 format, chain K [auth L] MOL2 format, chain J [auth L] MOL2 format, chain I [auth L] MOL2 format, chain H [auth L] MOL2 format, chain G [auth L] MOL2 format, chain BA [auth H] MOL2 format, chain AA [auth H] mmCIF format, chain Z [auth H] mmCIF format, chain Y [auth H] mmCIF format, chain X [auth H] mmCIF format, chain K [auth L] mmCIF format, chain J [auth L] mmCIF format, chain I [auth L] mmCIF format, chain H [auth L] mmCIF format, chain G [auth L] mmCIF format, chain BA [auth H] mmCIF format, chain AA [auth H]	AA [auth H] BA [auth H] G [auth L] H [auth L] I [auth L] AA [auth H], BA [auth H], G [auth L], H [auth L], I [auth L], J [auth L], K [auth L], X [auth H], Y [auth H], Z [auth H]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth H] Focus chain BA [auth H] Focus chain G [auth L] Focus chain H [auth L] Focus chain I [auth L] Focus chain J [auth L] Focus chain K [auth L] Focus chain X [auth H] Focus chain Y [auth H] Focus chain Z [auth H] Interactions & Density Focus chain AA [auth H] Focus chain BA [auth H] Focus chain G [auth L] Focus chain H [auth L] Focus chain I [auth L] Focus chain J [auth L] Focus chain K [auth L] Focus chain X [auth H] Focus chain Y [auth H] Focus chain Z [auth H]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain W [auth H] SDF format, chain V [auth H] SDF format, chain F [auth L] MOL2 format, chain W [auth H] MOL2 format, chain V [auth H] MOL2 format, chain F [auth L] mmCIF format, chain W [auth H] mmCIF format, chain V [auth H] mmCIF format, chain F [auth L]	F [auth L], V [auth H], W [auth H]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth L] Focus chain V [auth H] Focus chain W [auth H] Interactions & Density Focus chain F [auth L] Focus chain V [auth H] Focus chain W [auth H]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain S [auth H] SDF format, chain R [auth H] SDF format, chain Q [auth H] MOL2 format, chain S [auth H] MOL2 format, chain R [auth H] MOL2 format, chain Q [auth H] mmCIF format, chain S [auth H] mmCIF format, chain R [auth H] mmCIF format, chain Q [auth H]	Q [auth H], R [auth H], S [auth H]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain Q [auth H] Focus chain R [auth H] Focus chain S [auth H] Interactions & Density Focus chain Q [auth H] Focus chain R [auth H] Focus chain S [auth H]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain U [auth H] SDF format, chain T [auth H] MOL2 format, chain U [auth H] MOL2 format, chain T [auth H] mmCIF format, chain U [auth H] mmCIF format, chain T [auth H]	T [auth H], U [auth H]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain T [auth H] Focus chain U [auth H] Interactions & Density Focus chain T [auth H] Focus chain U [auth H]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain N [auth H] SDF format, chain M [auth H] SDF format, chain L [auth H] SDF format, chain C [auth L] MOL2 format, chain N [auth H] MOL2 format, chain M [auth H] MOL2 format, chain L [auth H] MOL2 format, chain C [auth L] mmCIF format, chain N [auth H] mmCIF format, chain M [auth H] mmCIF format, chain L [auth H] mmCIF format, chain C [auth L]	C [auth L], L [auth H], M [auth H], N [auth H]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth L] Focus chain L [auth H] Focus chain M [auth H] Focus chain N [auth H] Interactions & Density Focus chain C [auth L] Focus chain L [auth H] Focus chain M [auth H] Focus chain N [auth H]