6VRQ | pdb_00006vrq

Crystal structure of gl12A21 Fab in complex with anti-idiotypic iv12 Fab

PDB DOI: https://doi.org/10.2210/pdb6VRQ/pdb

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

Deposited: 2020-02-08 Released: 2021-02-17
Deposition Author(s): Aljedani, S.S., Weidle, C., Pancera, M.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.57 Å
R-Value Free:
0.241 (Depositor), 0.242 (DCC)
R-Value Work:
0.189 (Depositor), 0.188 (DCC)
R-Value Observed:
0.191 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Development of a VRC01-class germline targeting immunogen derived from anti-idiotypic antibodies.

Seydoux, E., Wan, Y.H., Feng, J., Wall, A., Aljedani, S., Homad, L.J., MacCamy, A.J., Weidle, C., Gray, M.D., Brumage, L., Taylor, J.J., Pancera, M., Stamatatos, L., McGuire, A.T.

(2021) Cell Rep 35: 109084-109084

PubMed: 33951425 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.celrep.2021.109084
Primary Citation Related Structures:
6VRQ, 6XOC, 7JLK, 7JLN

PubMed Abstract:
An effective HIV-1 vaccine will likely need to elicit broadly neutralizing antibodies (bNAbs). Broad and potent VRC01-class bNAbs have been isolated from multiple infected individuals, suggesting that they could be reproducibly elicited by vaccination. Several HIV-1 envelope-derived germline-targeting immunogens have been designed to engage naive VRC01-class precursor B cells. However, they also present off-target epitopes that could hinder development of VRC01-class bNAbs. We characterize a panel of anti-idiotypic monoclonal antibodies (ai-mAbs) raised against inferred-germline (iGL) VRC01-class antibodies. By leveraging binding, structural, and B cell sorting data, we engineered a bispecific molecule derived from two ai-mAbs; one specific for VRC01-class heavy chains and one specific for VRC01-class light chains. The bispecific molecule preferentially activates iGL-VRC01 B cells in vitro and induces specific antibody responses in a murine adoptive transfer model with a diverse polyclonal B cell repertoire. This molecule represents an alternative non-envelope-derived germline-targeting immunogen that can selectively activate VRC01-class precursors in vivo.

Organizational Affiliation

Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA 98109, USA.

Macromolecule Content

Total Structure Weight: 96.64 kDa
Atom Count: 6,809
Modeled Residue Count: 856
Deposited Residue Count: 882
Unique protein chains: 4

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
iv12 Fab Heavy Chain	A [auth H]	224	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
iv12 Fab Light Chain	B [auth L]	214	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
gl12A21 Fab Heavy Chain	C [auth A]	234	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
gl12A21 Fab Light Chain	D [auth B]	210	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
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 S [auth A] SDF format, chain R [auth A] SDF format, chain I [auth L] SDF format, chain G [auth H] MOL2 format, chain S [auth A] MOL2 format, chain R [auth A] MOL2 format, chain I [auth L] MOL2 format, chain G [auth H] mmCIF format, chain S [auth A] mmCIF format, chain R [auth A] mmCIF format, chain I [auth L] mmCIF format, chain G [auth H]	G [auth H], I [auth L], R [auth A], S [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain G [auth H] Focus chain I [auth L] Focus chain R [auth A] Focus chain S [auth A] Interactions & Density Focus chain G [auth H] Focus chain I [auth L] Focus chain R [auth A] Focus chain S [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain T [auth B] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain F [auth H] SDF format, chain E [auth H] MOL2 format, chain T [auth B] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain F [auth H] MOL2 format, chain E [auth H] mmCIF format, chain T [auth B] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain F [auth H] mmCIF format, chain E [auth H]	E [auth H], F [auth H], N [auth A], O [auth A], T [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth H] Focus chain F [auth H] Focus chain N [auth A] Focus chain O [auth A] Focus chain T [auth B] Interactions & Density Focus chain E [auth H] Focus chain F [auth H] Focus chain N [auth A] Focus chain O [auth A] Focus chain T [auth B]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain V [auth B] SDF format, chain U [auth B] SDF format, chain Q [auth A] SDF format, chain P [auth A] SDF format, chain H [auth L] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain P [auth A] MOL2 format, chain H [auth L] mmCIF format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain P [auth A] mmCIF format, chain H [auth L]	H [auth L], P [auth A], Q [auth A], U [auth B], V [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain H [auth L] Focus chain P [auth A] Focus chain Q [auth A] Focus chain U [auth B] Focus chain V [auth B] Interactions & Density Focus chain H [auth L] Focus chain P [auth A] Focus chain Q [auth A] Focus chain U [auth B] Focus chain V [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A]	J [auth A], K [auth A], L [auth A], M [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A]