7UGQ | pdb_00007ugq

Cryo-EM structure of BG24 Fabs with an inferred germline CDRL1 and 10-1074 Fabs in complex with HIV-1 Env 6405-SOSIP.664

PDB DOI: https://doi.org/10.2210/pdb7UGQ/pdb
EM Map EMD-26496: EMDB EMDataResource

Classification: VIRAL PROTEIN/IMMUNE SYSTEM
Organism(s): Human immunodeficiency virus 1, Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2022-03-25 Released: 2022-11-09
Deposition Author(s): Dam, K.A., Bjorkman, P.J.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Bill & Melinda Gates Foundation

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.40 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

HIV-1 CD4-binding site germline antibody-Env structures inform vaccine design.

Dam, K.A., Barnes, C.O., Gristick, H.B., Schoofs, T., Gnanapragasam, P.N.P., Nussenzweig, M.C., Bjorkman, P.J.

(2022) Nat Commun 13: 6123-6123

PubMed: 36253376 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-022-33860-2
Primary Citation Related Structures:
7UGM, 7UGN, 7UGO, 7UGP, 7UGQ

PubMed Abstract:
BG24, a VRC01-class broadly neutralizing antibody (bNAb) against HIV-1 Env with relatively few somatic hypermutations (SHMs), represents a promising target for vaccine strategies to elicit CD4-binding site (CD4bs) bNAbs. To understand how SHMs correlate with BG24 neutralization of HIV-1, we report 4.1 Å and 3.4 Å single-particle cryo-EM structures of two inferred germline (iGL) BG24 precursors complexed with engineered Env-based immunogens lacking CD4bs N-glycans. Structures reveal critical Env contacts by BG24 _iGL and identify antibody light chain structural features that impede Env recognition. In addition, biochemical data and cryo-EM structures of BG24 _iGL variants bound to Envs with CD4bs glycans present provide insights into N-glycan accommodation, including structural modes of light chain adaptations in the presence of the N276 _gp120 glycan. Together, these findings reveal Env regions critical for germline antibody recognition and potential sites to alter in immunogen design.

Organizational Affiliation

Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.

Macromolecule Content

Total Structure Weight: 375.09 kDa
Atom Count: 26,113
Modeled Residue Count: 3,138
Deposited Residue Count: 3,138
Unique protein chains: 6

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp120	A, B, C	447	Human immunodeficiency virus 1	Mutation(s): 0 Gene Names: env
UniProt
Find proteins for D7S1H2 (Human immunodeficiency virus type 1) Explore D7S1H2 Go to UniProtKB: D7S1H2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D7S1H2
Glycosylation
Glycosylation Sites: 19	Glycosylation Focus chain A Focus chain B Focus chain C
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp41	D, E, F	129	Human immunodeficiency virus 1	Mutation(s): 0 Gene Names: env

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
BG24 with an inferred germline CDRL1 Fab heavy chain	G, H, I	125	Homo sapiens	Mutation(s): 0

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
BG24 with an inferred germline CDRL1 Fab light chain	J, K, L	105	Homo sapiens	Mutation(s): 0

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
10-1074 Fab heavy chain	M, N, O	133	Homo sapiens	Mutation(s): 0

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| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
10-1074 Fab light chain	P, Q, R	107	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help

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	AB [auth 0], CA [auth c], EA [auth e], HA [auth h], OA [auth o], AB [auth 0], CA [auth c], EA [auth e], HA [auth h], OA [auth o], QA [auth q], S, TA [auth t], V	3		N-Glycosylation	Interactions Focus chain AB [auth 0] Focus chain CA [auth c] Focus chain EA [auth e] Focus chain HA [auth h] Focus chain OA [auth o] Focus chain QA [auth q] Focus chain S Focus chain TA [auth t] Focus chain V Interactions & Density Focus chain AB [auth 0] Focus chain CA [auth c] Focus chain EA [auth e] Focus chain HA [auth h] Focus chain OA [auth o] Focus chain QA [auth q] Focus chain S Focus chain TA [auth t] Focus chain V
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	AA [auth a], BA [auth b], FA [auth f], GA [auth g], JA [auth j], AA [auth a], BA [auth b], FA [auth f], GA [auth g], JA [auth j], KA [auth k], LA [auth l], MA [auth m], NA [auth n], RA [auth r], SA [auth s], T, U, VA [auth v], WA [auth w], X, XA [auth x], Y, YA [auth y], Z, ZA [auth z]	2		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain BA [auth b] Focus chain FA [auth f] Focus chain GA [auth g] Focus chain JA [auth j] Focus chain KA [auth k] Focus chain LA [auth l] Focus chain MA [auth m] Focus chain NA [auth n] Focus chain RA [auth r] Focus chain SA [auth s] Focus chain T Focus chain U Focus chain VA [auth v] 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 AA [auth a] Focus chain BA [auth b] Focus chain FA [auth f] Focus chain GA [auth g] Focus chain JA [auth j] Focus chain KA [auth k] Focus chain LA [auth l] Focus chain MA [auth m] Focus chain NA [auth n] Focus chain RA [auth r] Focus chain SA [auth s] Focus chain T Focus chain U Focus chain VA [auth v] 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: 9
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	IA [auth i], UA [auth u], W	5		N-Glycosylation	Interactions Focus chain IA [auth i] Focus chain UA [auth u] Focus chain W Interactions & Density Focus chain IA [auth i] Focus chain UA [auth u] Focus chain W
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Entity ID: 10
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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	BB [auth 1], DA [auth d]	9		N-Glycosylation	Interactions Focus chain BB [auth 1] Focus chain DA [auth d] Interactions & Density Focus chain BB [auth 1] Focus chain DA [auth d]
Glycosylation Resources
GlyTouCan: G68668TB GlyCosmos: G68668TB GlyGen: G68668TB

Entity ID: 11
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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	PA [auth p]	8		N-Glycosylation	Interactions Focus chain PA [auth p] Interactions & Density Focus chain PA [auth p]
Glycosylation Resources
GlyTouCan: G83582BK GlyCosmos: G83582BK GlyGen: G83582BK

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain CB [auth A] SDF format, chain DB [auth A] SDF format, chain EB [auth A] SDF format, chain FB [auth A] SDF format, chain GB [auth A] SDF format, chain HB [auth A] SDF format, chain IB [auth A] SDF format, chain JB [auth B] SDF format, chain KB [auth B] SDF format, chain NB [auth B] SDF format, chain OB [auth B] SDF format, chain PB [auth B] SDF format, chain QB [auth C] SDF format, chain RB [auth C] SDF format, chain SB [auth C] SDF format, chain UB [auth C] SDF format, chain VB [auth C] SDF format, chain WB [auth C] SDF format, chain XB [auth D] SDF format, chain ZB [auth F] SDF format, chain YB [auth E] SDF format, chain TB [auth C] SDF format, chain MB [auth B] SDF format, chain LB [auth B] MOL2 format, chain CB [auth A] MOL2 format, chain DB [auth A] MOL2 format, chain EB [auth A] MOL2 format, chain FB [auth A] MOL2 format, chain GB [auth A] MOL2 format, chain HB [auth A] MOL2 format, chain IB [auth A] MOL2 format, chain JB [auth B] MOL2 format, chain KB [auth B] MOL2 format, chain NB [auth B] MOL2 format, chain OB [auth B] MOL2 format, chain PB [auth B] MOL2 format, chain QB [auth C] MOL2 format, chain RB [auth C] MOL2 format, chain SB [auth C] MOL2 format, chain UB [auth C] MOL2 format, chain VB [auth C] MOL2 format, chain WB [auth C] MOL2 format, chain XB [auth D] MOL2 format, chain ZB [auth F] MOL2 format, chain YB [auth E] MOL2 format, chain TB [auth C] MOL2 format, chain MB [auth B] MOL2 format, chain LB [auth B] mmCIF format, chain CB [auth A] mmCIF format, chain DB [auth A] mmCIF format, chain EB [auth A] mmCIF format, chain FB [auth A] mmCIF format, chain GB [auth A] mmCIF format, chain HB [auth A] mmCIF format, chain IB [auth A] mmCIF format, chain JB [auth B] mmCIF format, chain KB [auth B] mmCIF format, chain NB [auth B] mmCIF format, chain OB [auth B] mmCIF format, chain PB [auth B] mmCIF format, chain QB [auth C] mmCIF format, chain RB [auth C] mmCIF format, chain SB [auth C] mmCIF format, chain UB [auth C] mmCIF format, chain VB [auth C] mmCIF format, chain WB [auth C] mmCIF format, chain XB [auth D] mmCIF format, chain ZB [auth F] mmCIF format, chain YB [auth E] mmCIF format, chain TB [auth C] mmCIF format, chain MB [auth B] mmCIF format, chain LB [auth B]	CB [auth A] DB [auth A] EB [auth A] FB [auth A] GB [auth A] CB [auth A], DB [auth A], EB [auth A], FB [auth A], GB [auth A], HB [auth A], IB [auth A], JB [auth B], KB [auth B], LB [auth B], MB [auth B], NB [auth B], OB [auth B], PB [auth B], QB [auth C], RB [auth C], SB [auth C], TB [auth C], UB [auth C], VB [auth C], WB [auth C], XB [auth D], YB [auth E], ZB [auth F]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain CB [auth A] Focus chain DB [auth A] Focus chain EB [auth A] Focus chain FB [auth A] Focus chain GB [auth A] Focus chain HB [auth A] Focus chain IB [auth A] Focus chain JB [auth B] Focus chain KB [auth B] Focus chain LB [auth B] Focus chain MB [auth B] Focus chain NB [auth B] Focus chain OB [auth B] Focus chain PB [auth B] Focus chain QB [auth C] Focus chain RB [auth C] Focus chain SB [auth C] Focus chain TB [auth C] Focus chain UB [auth C] Focus chain VB [auth C] Focus chain WB [auth C] Focus chain XB [auth D] Focus chain YB [auth E] Focus chain ZB [auth F] Interactions & Density Focus chain CB [auth A] Focus chain DB [auth A] Focus chain EB [auth A] Focus chain FB [auth A] Focus chain GB [auth A] Focus chain HB [auth A] Focus chain IB [auth A] Focus chain JB [auth B] Focus chain KB [auth B] Focus chain LB [auth B] Focus chain MB [auth B] Focus chain NB [auth B] Focus chain OB [auth B] Focus chain PB [auth B] Focus chain QB [auth C] Focus chain RB [auth C] Focus chain SB [auth C] Focus chain TB [auth C] Focus chain UB [auth C] Focus chain VB [auth C] Focus chain WB [auth C] Focus chain XB [auth D] Focus chain YB [auth E] Focus chain ZB [auth F]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.40 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-11-09

Deposition Author(s):

Dam, K.A.

Bjorkman, P.J.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HIVRAD P01 AI100148
Bill & Melinda Gates Foundation	United States	CAVD INV-002143