7UGN | pdb_00007ugn

Cryo-EM structure of BG24 inferred germline Fabs with germline CDR3s and 10-1074 Fabs in complex with HIV-1 Env immunogen BG505-SOSIPv4.1-GT1 - Class 1

PDB DOI: https://doi.org/10.2210/pdb7UGN/pdb
EM Map EMD-26490: 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: 2022-10-26
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: 368.23 kDa
Atom Count: 25,698
Modeled Residue Count: 3,150
Deposited Residue Count: 3,153
Unique protein chains: 6

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp120	A, B, C	451	Human immunodeficiency virus 1	Mutation(s): 0 Gene Names: env
UniProt
Find proteins for Q2N0S5 (Human immunodeficiency virus type 1) Explore Q2N0S5 Go to UniProtKB: Q2N0S5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2N0S5
Glycosylation
Glycosylation Sites: 12	Glycosylation Focus chain A Focus chain B Focus chain C
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 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
UniProt
Find proteins for Q2N0S5 (Human immunodeficiency virus type 1) Explore Q2N0S5 Go to UniProtKB: Q2N0S5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2N0S5
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain D Focus chain E Focus chain F
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
BG24 inferred germline Fab with germline CDR3s heavy chain	G, H, I	125	Homo sapiens	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
BG24 inferred germline Fab with germline CDR3s light chain	J, K, L	106	Homo sapiens	Mutation(s): 0

Find similar proteins by:

| 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

Find similar proteins by:

| 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
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	AA [auth a], BA [auth b], DA [auth d], EA [auth e], GA [auth g], AA [auth a], BA [auth b], DA [auth d], EA [auth e], GA [auth g], HA [auth h], IA [auth i], JA [auth j], LA [auth l], MA [auth m], OA [auth o], PA [auth p], S, T, V, W, Y, Z	2		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain BA [auth b] Focus chain DA [auth d] Focus chain EA [auth e] Focus chain GA [auth g] Focus chain HA [auth h] Focus chain IA [auth i] Focus chain JA [auth j] Focus chain LA [auth l] Focus chain MA [auth m] Focus chain OA [auth o] Focus chain PA [auth p] Focus chain S Focus chain T Focus chain V Focus chain W Focus chain Y Focus chain Z Interactions & Density Focus chain AA [auth a] Focus chain BA [auth b] Focus chain DA [auth d] Focus chain EA [auth e] Focus chain GA [auth g] Focus chain HA [auth h] Focus chain IA [auth i] Focus chain JA [auth j] Focus chain LA [auth l] Focus chain MA [auth m] Focus chain OA [auth o] Focus chain PA [auth p] Focus chain S Focus chain T Focus chain V Focus chain W Focus chain Y Focus chain Z
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 8
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], KA [auth k], U	5		N-Glycosylation	Interactions Focus chain CA [auth c] Focus chain KA [auth k] Focus chain U Interactions & Density Focus chain CA [auth c] Focus chain KA [auth k] Focus chain U
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Entity ID: 9
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-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	NA [auth n], X	7		N-Glycosylation	Interactions Focus chain NA [auth n] Focus chain X Interactions & Density Focus chain NA [auth n] Focus chain X
Glycosylation Resources
GlyTouCan: G11052OE GlyCosmos: G11052OE GlyGen: G11052OE

Entity ID: 10
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[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	FA [auth f]	6		N-Glycosylation	Interactions Focus chain FA [auth f] Interactions & Density Focus chain FA [auth f]
Glycosylation Resources
GlyTouCan: G09724ZC GlyCosmos: G09724ZC GlyGen: G09724ZC

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain RA [auth A] SDF format, chain UA [auth B] SDF format, chain WA [auth B] SDF format, chain ZA [auth C] SDF format, chain YA [auth C] SDF format, chain XA [auth B] SDF format, chain VA [auth B] SDF format, chain TA [auth A] SDF format, chain SA [auth A] SDF format, chain QA [auth A] SDF format, chain EB [auth F] SDF format, chain DB [auth E] SDF format, chain CB [auth D] SDF format, chain BB [auth C] SDF format, chain AB [auth C] MOL2 format, chain RA [auth A] MOL2 format, chain UA [auth B] MOL2 format, chain WA [auth B] MOL2 format, chain ZA [auth C] MOL2 format, chain YA [auth C] MOL2 format, chain XA [auth B] MOL2 format, chain VA [auth B] MOL2 format, chain TA [auth A] MOL2 format, chain SA [auth A] MOL2 format, chain QA [auth A] MOL2 format, chain EB [auth F] MOL2 format, chain DB [auth E] MOL2 format, chain CB [auth D] MOL2 format, chain BB [auth C] MOL2 format, chain AB [auth C] mmCIF format, chain RA [auth A] mmCIF format, chain UA [auth B] mmCIF format, chain WA [auth B] mmCIF format, chain ZA [auth C] mmCIF format, chain YA [auth C] mmCIF format, chain XA [auth B] mmCIF format, chain VA [auth B] mmCIF format, chain TA [auth A] mmCIF format, chain SA [auth A] mmCIF format, chain QA [auth A] mmCIF format, chain EB [auth F] mmCIF format, chain DB [auth E] mmCIF format, chain CB [auth D] mmCIF format, chain BB [auth C] mmCIF format, chain AB [auth C]	AB [auth C] BB [auth C] CB [auth D] DB [auth E] EB [auth F] AB [auth C], BB [auth C], CB [auth D], DB [auth E], EB [auth F], QA [auth A], RA [auth A], SA [auth A], TA [auth A], UA [auth B], VA [auth B], WA [auth B], XA [auth B], YA [auth C], ZA [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AB [auth C] Focus chain BB [auth C] Focus chain CB [auth D] Focus chain DB [auth E] Focus chain EB [auth F] Focus chain QA [auth A] Focus chain RA [auth A] Focus chain SA [auth A] Focus chain TA [auth A] Focus chain UA [auth B] Focus chain VA [auth B] Focus chain WA [auth B] Focus chain XA [auth B] Focus chain YA [auth C] Focus chain ZA [auth C] Interactions & Density Focus chain AB [auth C] Focus chain BB [auth C] Focus chain CB [auth D] Focus chain DB [auth E] Focus chain EB [auth F] Focus chain QA [auth A] Focus chain RA [auth A] Focus chain SA [auth A] Focus chain TA [auth A] Focus chain UA [auth B] Focus chain VA [auth B] Focus chain WA [auth B] Focus chain XA [auth B] Focus chain YA [auth C] Focus chain ZA [auth C]
MAN Query on MAN Download:Ideal Coordinates CCD File SDF format, chain FB [auth Q] MOL2 format, chain FB [auth Q] mmCIF format, chain FB [auth Q]	FB [auth Q]	alpha-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PQMKYFCFSA-N		Interactions Focus chain FB [auth Q] Interactions & Density Focus chain FB [auth Q]

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: 2022-10-26

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