8G4M | pdb_00008g4m

Vaccine-elicited human antibody 2C06 in complex with HIV-1 envelope trimer BG505 DS-SOSIP

PDB DOI: https://doi.org/10.2210/pdb8G4M/pdb
EM Map EMD-29725: EMDB EMDataResource

Classification: ANTIVIRAL PROTEIN
Organism(s): Human immunodeficiency virus 1, Homo sapiens
Expression System: Cricetulus griseus, Homo sapiens
Mutation(s): Yes

Deposited: 2023-02-10 Released: 2023-07-12
Deposition Author(s): Wang, S., Morano, N.C., Shapiro, L., 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: 2.95 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

HIV-1 neutralizing antibodies elicited in humans by a prefusion-stabilized envelope trimer form a reproducible class targeting fusion peptide.

Wang, S., Matassoli, F., Zhang, B., Liu, T., Shen, C.H., Bylund, T., Johnston, T., Henry, A.R., Teng, I.T., Tripathi, P., Becker, J.E., Changela, A., Chaudhary, R., Cheng, C., Gaudinski, M., Gorman, J., Harris, D.R., Lee, M., Morano, N.C., Novik, L., O'Dell, S., Olia, A.S., Parchment, D.K., Rawi, R., Roberts-Torres, J., Stephens, T., Tsybovsky, Y., Wang, D., Van Wazer, D.J., Zhou, T., Doria-Rose, N.A., Koup, R.A., Shapiro, L., Douek, D.C., McDermott, A.B., Kwong, P.D.

(2023) Cell Rep 42: 112755-112755

PubMed: 37436899 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.celrep.2023.112755
Primary Citation Related Structures:
8G4M, 8G4T

PubMed Abstract:
Elicitation of antibodies that neutralize the tier-2 neutralization-resistant isolates that typify HIV-1 transmission has been a long-sought goal. Success with prefusion-stabilized envelope trimers eliciting autologous neutralizing antibodies has been reported in multiple vaccine-test species, though not in humans. To investigate elicitation of HIV-1 neutralizing antibodies in humans, here, we analyze B cells from a phase I clinical trial of the "DS-SOSIP"-stabilized envelope trimer from strain BG505, identifying two antibodies, N751-2C06.01 and N751-2C09.01 (named for donor-lineage.clone), that neutralize the autologous tier-2 strain, BG505. Though derived from distinct lineages, these antibodies form a reproducible antibody class that targets the HIV-1 fusion peptide. Both antibodies are highly strain specific, which we attribute to their partial recognition of a BG505-specific glycan hole and to their binding requirements for a few BG505-specific residues. Prefusion-stabilized envelope trimers can thus elicit autologous tier-2 neutralizing antibodies in humans, with initially identified neutralizing antibodies recognizing the fusion-peptide site of vulnerability.

Organizational Affiliation

Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA.

Macromolecule Content

Total Structure Weight: 380.5 kDa
Atom Count: 20,584
Modeled Residue Count: 2,432
Deposited Residue Count: 3,228
Unique protein chains: 4

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp120	A [auth C], C [auth G], E [auth I]	473	Human immunodeficiency virus 1	Mutation(s): 4 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: 17	Glycosylation Focus chain A [auth C] Focus chain C [auth G] Focus chain E [auth I]
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp41	B [auth A], D [auth B], F	153	Human immunodeficiency virus 1	Mutation(s): 1 Gene Names: env
UniProt
Find proteins for Q2N0S7 (Human immunodeficiency virus type 1) Explore Q2N0S7 Go to UniProtKB: Q2N0S7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2N0S7
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain B [auth A] Focus chain D [auth B] Focus chain F
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
antibody heavy chain	G [auth D], I [auth H], 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 light chain	H [auth E], J [auth L], 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
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	AA [auth a], M, OA [auth o]	5		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain M Focus chain OA [auth o] Interactions & Density Focus chain AA [auth a] Focus chain M Focus chain OA [auth o]
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Entity ID: 6
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], CA [auth c], CB [auth 2], AB [auth 0], BA [auth b], BB [auth 1], CA [auth c], CB [auth 2], DA [auth d], FA [auth f], GA [auth g], HA [auth h], IA [auth i], JA [auth j], KA [auth k], LA [auth l], MA [auth m], N, NA [auth n], P, PA [auth p], QA [auth q], R, RA [auth r], S, SA [auth s], T, U, UA [auth u], V, VA [auth v], W, WA [auth w], X, XA [auth x], Y, YA [auth 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 CA [auth c] Focus chain CB [auth 2] Focus chain DA [auth d] Focus chain FA [auth f] Focus chain GA [auth g] Focus chain HA [auth h] Focus chain IA [auth i] Focus chain JA [auth j] Focus chain KA [auth k] Focus chain LA [auth l] Focus chain MA [auth m] Focus chain N Focus chain NA [auth n] Focus chain P Focus chain PA [auth p] Focus chain QA [auth q] Focus chain R Focus chain RA [auth r] Focus chain S Focus chain SA [auth s] Focus chain T Focus chain U Focus chain UA [auth u] Focus chain V Focus chain VA [auth v] Focus chain W Focus chain WA [auth w] Focus chain X Focus chain XA [auth x] Focus chain Y Focus chain YA [auth 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 CA [auth c] Focus chain CB [auth 2] Focus chain DA [auth d] Focus chain FA [auth f] Focus chain GA [auth g] Focus chain HA [auth h] Focus chain IA [auth i] Focus chain JA [auth j] Focus chain KA [auth k] Focus chain LA [auth l] Focus chain MA [auth m] Focus chain N Focus chain NA [auth n] Focus chain P Focus chain PA [auth p] Focus chain QA [auth q] Focus chain R Focus chain RA [auth r] Focus chain S Focus chain SA [auth s] Focus chain T Focus chain U Focus chain UA [auth u] Focus chain V Focus chain VA [auth v] Focus chain W Focus chain WA [auth w] Focus chain X Focus chain XA [auth x] Focus chain Y Focus chain YA [auth y] Focus chain Z Focus chain ZA [auth z]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

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	O	3		N-Glycosylation	Interactions Focus chain O Interactions & Density Focus chain O
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	Q, TA [auth t]	6		N-Glycosylation	Interactions Focus chain Q Focus chain TA [auth t] Interactions & Density Focus chain Q Focus chain TA [auth t]
Glycosylation Resources
GlyTouCan: G56014GC GlyCosmos: G56014GC GlyGen: G56014GC

Entity ID: 9
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	EA [auth e]	5		N-Glycosylation	Interactions Focus chain EA [auth e] Interactions & Density Focus chain EA [auth e]
Glycosylation Resources
GlyTouCan: G42227JK GlyCosmos: G42227JK GlyGen: G42227JK

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 OB [auth F] SDF format, chain NB [auth F] SDF format, chain MB [auth I] SDF format, chain LB [auth I] SDF format, chain KB [auth B] SDF format, chain JB [auth G] SDF format, chain IB [auth G] SDF format, chain HB [auth G] SDF format, chain GB [auth A] SDF format, chain FB [auth C] SDF format, chain EB [auth C] SDF format, chain DB [auth C] MOL2 format, chain OB [auth F] MOL2 format, chain NB [auth F] MOL2 format, chain MB [auth I] MOL2 format, chain LB [auth I] MOL2 format, chain KB [auth B] MOL2 format, chain JB [auth G] MOL2 format, chain IB [auth G] MOL2 format, chain HB [auth G] MOL2 format, chain GB [auth A] MOL2 format, chain FB [auth C] MOL2 format, chain EB [auth C] MOL2 format, chain DB [auth C] mmCIF format, chain OB [auth F] mmCIF format, chain NB [auth F] mmCIF format, chain MB [auth I] mmCIF format, chain LB [auth I] mmCIF format, chain KB [auth B] mmCIF format, chain JB [auth G] mmCIF format, chain IB [auth G] mmCIF format, chain HB [auth G] mmCIF format, chain GB [auth A] mmCIF format, chain FB [auth C] mmCIF format, chain EB [auth C] mmCIF format, chain DB [auth C]	DB [auth C] EB [auth C] FB [auth C] GB [auth A] HB [auth G] DB [auth C], EB [auth C], FB [auth C], GB [auth A], HB [auth G], IB [auth G], JB [auth G], KB [auth B], LB [auth I], MB [auth I], NB [auth F], OB [auth F]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain DB [auth C] Focus chain EB [auth C] Focus chain FB [auth C] Focus chain GB [auth A] Focus chain HB [auth G] Focus chain IB [auth G] Focus chain JB [auth G] Focus chain KB [auth B] Focus chain LB [auth I] Focus chain MB [auth I] Focus chain NB [auth F] Focus chain OB [auth F] Interactions & Density Focus chain DB [auth C] Focus chain EB [auth C] Focus chain FB [auth C] Focus chain GB [auth A] Focus chain HB [auth G] Focus chain IB [auth G] Focus chain JB [auth G] Focus chain KB [auth B] Focus chain LB [auth I] Focus chain MB [auth I] Focus chain NB [auth F] Focus chain OB [auth F]