7LUA | pdb_00007lua

Cryo-EM structure of DH898.1 Fab-dimer bound near the CD4 binding site of HIV-1 Env CH848 SOSIP trimer

PDB DOI: https://doi.org/10.2210/pdb7LUA/pdb
EM Map EMD-23519: EMDB EMDataResource

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

Deposited: 2021-02-21 Released: 2021-03-17
Deposition Author(s): Manne, K., Edwards, R.J., Acharya, P.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

Fab-dimerized glycan-reactive antibodies are a structural category of natural antibodies.

Williams, W.B., Meyerhoff, R.R., Edwards, R.J., Li, H., Manne, K., Nicely, N.I., Henderson, R., Zhou, Y., Janowska, K., Mansouri, K., Gobeil, S., Evangelous, T., Hora, B., Berry, M., Abuahmad, A.Y., Sprenz, J., Deyton, M., Stalls, V., Kopp, M., Hsu, A.L., Borgnia, M.J., Stewart-Jones, G.B.E., Lee, M.S., Bronkema, N., Moody, M.A., Wiehe, K., Bradley, T., Alam, S.M., Parks, R.J., Foulger, A., Oguin, T., Sempowski, G.D., Bonsignori, M., LaBranche, C.C., Montefiori, D.C., Seaman, M., Santra, S., Perfect, J., Francica, J.R., Lynn, G.M., Aussedat, B., Walkowicz, W.E., Laga, R., Kelsoe, G., Saunders, K.O., Fera, D., Kwong, P.D., Seder, R.A., Bartesaghi, A., Shaw, G.M., Acharya, P., Haynes, B.F.

(2021) Cell 184: 2955

PubMed: 34019795 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.cell.2021.04.042
Primary Citation Related Structures:
6VTU, 6XRJ, 7L02, 7L06, 7L09, 7L6M, 7L6O, 7LU9, 7LUA

PubMed Abstract:
Natural antibodies (Abs) can target host glycans on the surface of pathogens. We studied the evolution of glycan-reactive B cells of rhesus macaques and humans using glycosylated HIV-1 envelope (Env) as a model antigen. 2G12 is a broadly neutralizing Ab (bnAb) that targets a conserved glycan patch on Env of geographically diverse HIV-1 strains using a unique heavy-chain (V _H) domain-swapped architecture that results in fragment antigen-binding (Fab) dimerization. Here, we describe HIV-1 Env Fab-dimerized glycan (FDG)-reactive bnAbs without V _H-swapped domains from simian-human immunodeficiency virus (SHIV)-infected macaques. FDG Abs also recognized cell-surface glycans on diverse pathogens, including yeast and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike. FDG precursors were expanded by glycan-bearing immunogens in macaques and were abundant in HIV-1-naive humans. Moreover, FDG precursors were predominately mutated IgM ⁺IgD ⁺CD27 ⁺, thus suggesting that they originated from a pool of antigen-experienced IgM ⁺ or marginal zone B cells.

Organizational Affiliation

Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Medicine, Duke University, Durham, NC 27710, USA. Electronic address: wilton.williams@duke.edu.

Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Medicine, Duke University, Durham, NC 27710, USA.

Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.

Duke Human Vaccine Institute, Durham, NC 27710, USA.

Department of Computer Science, Duke University, Durham, NC 27708, USA.

Genome Integrity and Structural Biology Laboratory, NIEHS, NIH, Department of Health and Human Services, Research Triangle Park, NC 27709, USA.

Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA.

Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA.

Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, PA 19081, USA.

Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Immunology, Duke University, Durham, NC 27710, USA; Department of Pediatrics, Duke University, Durham, NC 27710, USA.

Department of Surgery, Duke University, Durham, NC 27710, USA.

Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Surgery, Duke University, Durham, NC 27710, USA.

Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA.

Department of Medicine, Duke University, Durham, NC 27710, USA.

Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA; Avidea Technologies, Inc., Baltimore, MD, USA.

Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.

Institute of Macromolecular Chemistry, Czech Academy of Sciences, Prague, Czech Republic.

Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Immunology, Duke University, Durham, NC 27710, USA.

Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Immunology, Duke University, Durham, NC 27710, USA; Department of Surgery, Duke University, Durham, NC 27710, USA.

Department of Computer Science, Duke University, Durham, NC 27708, USA; Department of Biochemistry, Duke University, Durham, NC 27705, USA; Department of Electrical and Computer Engineering, Duke University, Durham, NC 27708, USA.

Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Surgery, Duke University, Durham, NC 27710, USA. Electronic address: priyamvada.acharya@duke.edu.

Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Medicine, Duke University, Durham, NC 27710, USA; Department of Immunology, Duke University, Durham, NC 27710, USA. Electronic address: hayne002@mc.duke.edu.

Macromolecule Content

Total Structure Weight: 327.77 kDa
Atom Count: 22,390
Modeled Residue Count: 2,650
Deposited Residue Count: 2,710
Unique protein chains: 4

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CH848 SOSIP gp120	A [auth a], C [auth c], E [auth e]	466	Human immunodeficiency virus 1	Mutation(s): 0 Gene Names: env
UniProt
Find proteins for A0A1W6IPB2 (Human immunodeficiency virus type 1) Explore A0A1W6IPB2 Go to UniProtKB: A0A1W6IPB2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A1W6IPB2
Glycosylation
Glycosylation Sites: 13	Glycosylation Focus chain A [auth a] Focus chain C [auth c] Focus chain E [auth e]
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Env polyprotein	B [auth b], D [auth d], F [auth f]	146	Simian-Human immunodeficiency virus	Mutation(s): 0 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: 2	Glycosylation Focus chain B [auth b] Focus chain D [auth d] Focus chain F [auth f]
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DH898.1 light chain	G [auth g], J [auth j]	218	Homo sapiens	Mutation(s): 0
UniProt
Find proteins for A0A2K6CXN9 (Macaca nemestrina) Explore A0A2K6CXN9 Go to UniProtKB: A0A2K6CXN9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A2K6CXN9
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DH898.1 heavy chain	H [auth h], I [auth i]	219	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P01861 (Homo sapiens) Explore P01861 Go to UniProtKB: P01861
PHAROS: P01861 GTEx: ENSG00000211892
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01861
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 5
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	BA [auth R], DA [auth T], EA [auth U], GA [auth W], HA [auth X], BA [auth R], DA [auth T], EA [auth U], GA [auth W], HA [auth X], JA [auth Z], K [auth A], KA [auth k], LA [auth l], M [auth C], MA [auth m], O [auth E], OA [auth o], P [auth F], QA [auth q], R [auth H], RA [auth r], S [auth I], TA [auth t], U [auth K], UA [auth u], V [auth L], WA [auth w], XA [auth x], Y [auth O], Z [auth P]	3		N-Glycosylation, O-Glycosylation	Interactions Focus chain BA [auth R] Focus chain DA [auth T] Focus chain EA [auth U] Focus chain GA [auth W] Focus chain HA [auth X] Focus chain JA [auth Z] Focus chain K [auth A] Focus chain KA [auth k] Focus chain LA [auth l] Focus chain M [auth C] Focus chain MA [auth m] Focus chain O [auth E] Focus chain OA [auth o] Focus chain P [auth F] Focus chain QA [auth q] Focus chain R [auth H] Focus chain RA [auth r] Focus chain S [auth I] Focus chain TA [auth t] Focus chain U [auth K] Focus chain UA [auth u] Focus chain V [auth L] Focus chain WA [auth w] Focus chain XA [auth x] Focus chain Y [auth O] Focus chain Z [auth P] Interactions & Density Focus chain BA [auth R] Focus chain DA [auth T] Focus chain EA [auth U] Focus chain GA [auth W] Focus chain HA [auth X] Focus chain JA [auth Z] Focus chain K [auth A] Focus chain KA [auth k] Focus chain LA [auth l] Focus chain M [auth C] Focus chain MA [auth m] Focus chain O [auth E] Focus chain OA [auth o] Focus chain P [auth F] Focus chain QA [auth q] Focus chain R [auth H] Focus chain RA [auth r] Focus chain S [auth I] Focus chain TA [auth t] Focus chain U [auth K] Focus chain UA [auth u] Focus chain V [auth L] Focus chain WA [auth w] Focus chain XA [auth x] Focus chain Y [auth O] Focus chain Z [auth P]
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

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	AA [auth Q], FA [auth V], IA [auth Y], L [auth B], NA [auth n], AA [auth Q], FA [auth V], IA [auth Y], L [auth B], NA [auth n], Q [auth G], SA [auth s], T [auth J], VA [auth v]	2		N-Glycosylation	Interactions Focus chain AA [auth Q] Focus chain FA [auth V] Focus chain IA [auth Y] Focus chain L [auth B] Focus chain NA [auth n] Focus chain Q [auth G] Focus chain SA [auth s] Focus chain T [auth J] Focus chain VA [auth v] Interactions & Density Focus chain AA [auth Q] Focus chain FA [auth V] Focus chain IA [auth Y] Focus chain L [auth B] Focus chain NA [auth n] Focus chain Q [auth G] Focus chain SA [auth s] Focus chain T [auth J] Focus chain VA [auth v]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 7
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 S], N [auth D], PA [auth p], X [auth N]	5		N-Glycosylation	Interactions Focus chain CA [auth S] Focus chain N [auth D] Focus chain PA [auth p] Focus chain X [auth N] Interactions & Density Focus chain CA [auth S] Focus chain N [auth D] Focus chain PA [auth p] Focus chain X [auth N]
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-6)-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	W [auth M]	6		N/A	Interactions Focus chain W [auth M] Interactions & Density Focus chain W [auth M]
Glycosylation Resources
GlyTouCan: G34442SS GlyCosmos: G34442SS GlyGen: G34442SS

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 ZA [auth a] SDF format, chain YA [auth a] SDF format, chain OB [auth f] SDF format, chain NB [auth f] SDF format, chain MB [auth e] SDF format, chain LB [auth e] SDF format, chain KB [auth e] SDF format, chain JB [auth d] SDF format, chain IB [auth d] SDF format, chain HB [auth c] SDF format, chain GB [auth c] SDF format, chain FB [auth c] SDF format, chain EB [auth c] SDF format, chain DB [auth b] SDF format, chain CB [auth b] SDF format, chain BB [auth a] SDF format, chain AB [auth a] MOL2 format, chain ZA [auth a] MOL2 format, chain YA [auth a] MOL2 format, chain OB [auth f] MOL2 format, chain NB [auth f] MOL2 format, chain MB [auth e] MOL2 format, chain LB [auth e] MOL2 format, chain KB [auth e] MOL2 format, chain JB [auth d] MOL2 format, chain IB [auth d] MOL2 format, chain HB [auth c] MOL2 format, chain GB [auth c] MOL2 format, chain FB [auth c] MOL2 format, chain EB [auth c] MOL2 format, chain DB [auth b] MOL2 format, chain CB [auth b] MOL2 format, chain BB [auth a] MOL2 format, chain AB [auth a] mmCIF format, chain ZA [auth a] mmCIF format, chain YA [auth a] mmCIF format, chain OB [auth f] mmCIF format, chain NB [auth f] mmCIF format, chain MB [auth e] mmCIF format, chain LB [auth e] mmCIF format, chain KB [auth e] mmCIF format, chain JB [auth d] mmCIF format, chain IB [auth d] mmCIF format, chain HB [auth c] mmCIF format, chain GB [auth c] mmCIF format, chain FB [auth c] mmCIF format, chain EB [auth c] mmCIF format, chain DB [auth b] mmCIF format, chain CB [auth b] mmCIF format, chain BB [auth a] mmCIF format, chain AB [auth a]	AB [auth a] BB [auth a] CB [auth b] DB [auth b] EB [auth c] AB [auth a], BB [auth a], CB [auth b], DB [auth b], EB [auth c], FB [auth c], GB [auth c], HB [auth c], IB [auth d], JB [auth d], KB [auth e], LB [auth e], MB [auth e], NB [auth f], OB [auth f], YA [auth a], ZA [auth a]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AB [auth a] Focus chain BB [auth a] Focus chain CB [auth b] Focus chain DB [auth b] Focus chain EB [auth c] Focus chain FB [auth c] Focus chain GB [auth c] Focus chain HB [auth c] Focus chain IB [auth d] Focus chain JB [auth d] Focus chain KB [auth e] Focus chain LB [auth e] Focus chain MB [auth e] Focus chain NB [auth f] Focus chain OB [auth f] Focus chain YA [auth a] Focus chain ZA [auth a] Interactions & Density Focus chain AB [auth a] Focus chain BB [auth a] Focus chain CB [auth b] Focus chain DB [auth b] Focus chain EB [auth c] Focus chain FB [auth c] Focus chain GB [auth c] Focus chain HB [auth c] Focus chain IB [auth d] Focus chain JB [auth d] Focus chain KB [auth e] Focus chain LB [auth e] Focus chain MB [auth e] Focus chain NB [auth f] Focus chain OB [auth f] Focus chain YA [auth a] Focus chain ZA [auth a]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 4.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	Coot
MODEL REFINEMENT	PHENIX
MODEL REFINEMENT	ISOLDE
RECONSTRUCTION	cryoSPARC

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2021-03-17

Deposition Author(s):

Manne, K.

Edwards, R.J.

Acharya, P.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI145687

Revision History (Full details and data files)

Version 1.0: 2021-03-17
Type: Initial release
Version 1.1: 2021-06-02
Changes: Database references
Version 1.2: 2021-06-09
Changes: Database references
Version 1.3: 2024-11-06
Changes: Data collection, Database references, Structure summary

7LUA | pdb_00007lua

Cryo-EM structure of DH898.1 Fab-dimer bound near the CD4 binding site of HIV-1 Env CH848 SOSIP trimer

Literature

Fab-dimerized glycan-reactive antibodies are a structural category of natural antibodies.

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Glycosylation

Sequence Annotations

Expand

Entity ID: 2

UniProt

Entity Groups

Glycosylation

Sequence Annotations

Expand

Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

Expand

Entity ID: 4

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Oligosaccharides

Entity ID: 5

Glycosylation Resources

Entity ID: 6

Glycosylation Resources

Entity ID: 7

Glycosylation Resources

Entity ID: 8

Glycosylation Resources

Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Entry History

Deposition Data

Revision History (Full details and data files)