8TOX | pdb_00008tox

Cryo-EM structure of BG505 Env mutant A517E in complex with antibody ACS202 Fab

PDB DOI: https://doi.org/10.2210/pdb8TOX/pdb
EM Map EMD-41461: EMDB EMDataResource

Classification: VIRAL PROTEIN/ANTIVIRAL PROTEIN,IMMUNE SYSTEM
Organism(s): Human immunodeficiency virus 1, Homo sapiens
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2023-08-04 Released: 2024-08-14
Deposition Author(s): Wang, S., Kwong, P.D.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.30 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

Vaccine-elicited and naturally elicited antibodies differ in their recognition of the HIV-1 fusion peptide.

Reveiz, M., Xu, K., Lee, M., Wang, S., Olia, A.S., Harris, D.R., Liu, K., Liu, T., Schaub, A.J., Stephens, T., Wang, Y., Zhang, B., Huang, R., Tsybovsky, Y., Kwong, P.D., Rawi, R.

(2024) Front Immunol 15: 1484029-1484029

PubMed: 39611147 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.3389/fimmu.2024.1484029
Primary Citation Related Structures:
8TOX

PubMed Abstract:
Broadly neutralizing antibodies have been proposed as templates for HIV-1 vaccine design, but it has been unclear how similar vaccine-elicited antibodies are to their naturally elicited templates. To provide insight, here we compare the recognition of naturally elicited and vaccine-elicited antibodies targeting the HIV-1 fusion peptide, which comprises envelope (Env) residues 512-526, with the most common sequence being AVGIGAVFLGFLGAA. Naturally elicited antibodies bound peptides with substitutions to negatively charged amino acids at residue positions 517-520 substantially better than the most common sequence, despite these substitutions rarely appearing in HIV-1; by contrast, vaccine-elicited antibodies were less tolerant of sequence variation, with no substitution of residues 512-516 showing increased binding. Molecular dynamics analysis and cryo-EM structural analysis of the naturally elicited ACS202 antibody in complex with the HIV-1 Env trimer with an alanine 517 to glutamine substitution suggested enhanced binding to result from electrostatic interactions with positively charged antibody residues. Overall, vaccine-elicited antibodies appeared to be more fully optimized to bind the most common fusion peptide sequence, perhaps reflecting the immunization with fusion peptide of the vaccine-elicited antibodies.

Organizational Affiliation

Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States.

Macromolecule Content

Total Structure Weight: 389.08 kDa
Atom Count: 22,008
Modeled Residue Count: 2,490
Deposited Residue Count: 3,234
Unique protein chains: 4

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp41	A [auth B], C [auth A], E [auth F]	153	Human immunodeficiency virus 1	Mutation(s): 12 Gene Names: env
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus type 1) Explore Q2N0S6 Go to UniProtKB: Q2N0S6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2N0S6
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A [auth B] Focus chain C [auth A] Focus chain E [auth F]
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp120	B [auth G], D [auth C], F [auth I]	475	Human immunodeficiency virus 1	Mutation(s): 12 Gene Names: env
UniProt
Find proteins for Q2N0S6 (Human immunodeficiency virus type 1) Explore Q2N0S6 Go to UniProtKB: Q2N0S6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2N0S6
Glycosylation
Glycosylation Sites: 18	Glycosylation Focus chain B [auth G] Focus chain D [auth C] Focus chain F [auth I]
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
antibody ACS202 Fab heavy chain	G [auth H], I [auth D], K [auth J]	236	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
antibody ACS202 Fab light chain	H [auth L], J [auth E], L [auth K]	214	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

Oligosaccharides

Help

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	AB [auth 0], BA [auth b], BB [auth 1], DA [auth d], EA [auth e], AB [auth 0], BA [auth b], BB [auth 1], DA [auth d], EA [auth e], EB [auth 4], FB [auth 5], GA [auth g], GB [auth 6], HB [auth 7], IA [auth i], JA [auth j], JB [auth 9], KA [auth k], M, N, NA [auth n], OA [auth o], P, PA [auth p], QA [auth q], R, S, SA [auth s], T, UA [auth u], VA [auth v], W, X, XA [auth x], Y, Z, ZA [auth z]	2		N-Glycosylation	Interactions Focus chain AB [auth 0] Focus chain BA [auth b] Focus chain BB [auth 1] Focus chain DA [auth d] Focus chain EA [auth e] Focus chain EB [auth 4] Focus chain FB [auth 5] Focus chain GA [auth g] Focus chain GB [auth 6] Focus chain HB [auth 7] Focus chain IA [auth i] Focus chain JA [auth j] Focus chain JB [auth 9] Focus chain KA [auth k] Focus chain M Focus chain N Focus chain NA [auth n] Focus chain OA [auth o] Focus chain P Focus chain PA [auth p] Focus chain QA [auth q] Focus chain R Focus chain S Focus chain SA [auth s] Focus chain T Focus chain UA [auth u] Focus chain VA [auth v] Focus chain W Focus chain X Focus chain XA [auth x] Focus chain Y Focus chain Z Focus chain ZA [auth z] Interactions & Density Focus chain AB [auth 0] Focus chain BA [auth b] Focus chain BB [auth 1] Focus chain DA [auth d] Focus chain EA [auth e] Focus chain EB [auth 4] Focus chain FB [auth 5] Focus chain GA [auth g] Focus chain GB [auth 6] Focus chain HB [auth 7] Focus chain IA [auth i] Focus chain JA [auth j] Focus chain JB [auth 9] Focus chain KA [auth k] Focus chain M Focus chain N Focus chain NA [auth n] Focus chain OA [auth o] Focus chain P Focus chain PA [auth p] Focus chain QA [auth q] Focus chain R Focus chain S Focus chain SA [auth s] Focus chain T Focus chain UA [auth u] Focus chain VA [auth v] Focus chain W Focus chain X Focus chain XA [auth x] Focus chain Y Focus chain Z Focus chain ZA [auth z]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	CA [auth c], DB [auth 3], FA [auth f], KB [auth AA], MA [auth m], CA [auth c], DB [auth 3], FA [auth f], KB [auth AA], MA [auth m], O, TA [auth t], V, WA [auth w]	5		N-Glycosylation	Interactions Focus chain CA [auth c] Focus chain DB [auth 3] Focus chain FA [auth f] Focus chain KB [auth AA] Focus chain MA [auth m] Focus chain O Focus chain TA [auth t] Focus chain V Focus chain WA [auth w] Interactions & Density Focus chain CA [auth c] Focus chain DB [auth 3] Focus chain FA [auth f] Focus chain KB [auth AA] Focus chain MA [auth m] Focus chain O Focus chain TA [auth t] Focus chain V Focus chain WA [auth w]
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	AA [auth a], HA [auth h], IB [auth 8], Q, RA [auth r], AA [auth a], HA [auth h], IB [auth 8], Q, RA [auth r], YA [auth y]	3		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain HA [auth h] Focus chain IB [auth 8] Focus chain Q Focus chain RA [auth r] Focus chain YA [auth y] Interactions & Density Focus chain AA [auth a] Focus chain HA [auth h] Focus chain IB [auth 8] Focus chain Q Focus chain RA [auth r] Focus chain YA [auth y]
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	CB [auth 2], LA [auth l], U	6		N-Glycosylation	Interactions Focus chain CB [auth 2] Focus chain LA [auth l] Focus chain U Interactions & Density Focus chain CB [auth 2] Focus chain LA [auth l] Focus chain U
Glycosylation Resources
GlyTouCan: G56014GC GlyCosmos: G56014GC GlyGen: G56014GC

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG (Subject of Investigation/LOI) Query on NAG Download:Ideal Coordinates CCD File SDF format, chain NB [auth G] SDF format, chain WB [auth I] SDF format, chain VB [auth I] SDF format, chain UB [auth I] SDF format, chain TB [auth F] SDF format, chain SB [auth C] SDF format, chain RB [auth C] SDF format, chain QB [auth C] SDF format, chain PB [auth A] SDF format, chain OB [auth G] SDF format, chain MB [auth G] SDF format, chain LB [auth B] MOL2 format, chain NB [auth G] MOL2 format, chain WB [auth I] MOL2 format, chain VB [auth I] MOL2 format, chain UB [auth I] MOL2 format, chain TB [auth F] MOL2 format, chain SB [auth C] MOL2 format, chain RB [auth C] MOL2 format, chain QB [auth C] MOL2 format, chain PB [auth A] MOL2 format, chain OB [auth G] MOL2 format, chain MB [auth G] MOL2 format, chain LB [auth B] mmCIF format, chain NB [auth G] mmCIF format, chain WB [auth I] mmCIF format, chain VB [auth I] mmCIF format, chain UB [auth I] mmCIF format, chain TB [auth F] mmCIF format, chain SB [auth C] mmCIF format, chain RB [auth C] mmCIF format, chain QB [auth C] mmCIF format, chain PB [auth A] mmCIF format, chain OB [auth G] mmCIF format, chain MB [auth G] mmCIF format, chain LB [auth B]	LB [auth B] MB [auth G] NB [auth G] OB [auth G] PB [auth A] LB [auth B], MB [auth G], NB [auth G], OB [auth G], PB [auth A], QB [auth C], RB [auth C], SB [auth C], TB [auth F], UB [auth I], VB [auth I], WB [auth I]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain LB [auth B] Focus chain MB [auth G] Focus chain NB [auth G] Focus chain OB [auth G] Focus chain PB [auth A] Focus chain QB [auth C] Focus chain RB [auth C] Focus chain SB [auth C] Focus chain TB [auth F] Focus chain UB [auth I] Focus chain VB [auth I] Focus chain WB [auth I] Interactions & Density Focus chain LB [auth B] Focus chain MB [auth G] Focus chain NB [auth G] Focus chain OB [auth G] Focus chain PB [auth A] Focus chain QB [auth C] Focus chain RB [auth C] Focus chain SB [auth C] Focus chain TB [auth F] Focus chain UB [auth I] Focus chain VB [auth I] Focus chain WB [auth I]