6MPG | pdb_00006mpg

Cryo-EM structure at 3.2 A resolution of HIV-1 fusion peptide-directed antibody, A12V163-b.01, elicited by vaccination of Rhesus macaques, in complex with stabilized HIV-1 Env BG505 DS-SOSIP, which was also bound to antibodies VRC03 and PGT122

PDB DOI: https://doi.org/10.2210/pdb6MPG/pdb
EM Map EMD-8977: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Macaca mulatta, Human immunodeficiency virus 1, Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2018-10-06 Released: 2019-07-24
Deposition Author(s): Acharya, P., Kwong, P.D.

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.20 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Literature

Antibody Lineages with Vaccine-Induced Antigen-Binding Hotspots Develop Broad HIV Neutralization.

Kong, R., Duan, H., Sheng, Z., Xu, K., Acharya, P., Chen, X., Cheng, C., Dingens, A.S., Gorman, J., Sastry, M., Shen, C.H., Zhang, B., Zhou, T., Chuang, G.Y., Chao, C.W., Gu, Y., Jafari, A.J., Louder, M.K., O'Dell, S., Rowshan, A.P., Viox, E.G., Wang, Y., Choi, C.W., Corcoran, M.M., Corrigan, A.R., Dandey, V.P., Eng, E.T., Geng, H., Foulds, K.E., Guo, Y., Kwon, Y.D., Lin, B., Liu, K., Mason, R.D., Nason, M.C., Ohr, T.Y., Ou, L., Rawi, R., Sarfo, E.K., Schon, A., Todd, J.P., Wang, S., Wei, H., Wu, W., Mullikin, J.C., Bailer, R.T., Doria-Rose, N.A., Karlsson Hedestam, G.B., Scorpio, D.G., Overbaugh, J., Bloom, J.D., Carragher, B., Potter, C.S., Shapiro, L., Kwong, P.D., Mascola, J.R.

(2019) Cell 178: 567-584.e19

PubMed: 31348886 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.cell.2019.06.030
Primary Citation Related Structures:
6MPG, 6MPH, 6MQC, 6MQE, 6MQM, 6MQR, 6MQS, 6N16, 6N1V, 6N1W, 6NF2, 6OSY, 6OT1

PubMed Abstract:
The vaccine-mediated elicitation of antibodies (Abs) capable of neutralizing diverse HIV-1 strains has been a long-standing goal. To understand how broadly neutralizing antibodies (bNAbs) can be elicited, we identified, characterized, and tracked five neutralizing Ab lineages targeting the HIV-1-fusion peptide (FP) in vaccinated macaques over time. Genetic and structural analyses revealed two of these lineages to belong to a reproducible class capable of neutralizing up to 59% of 208 diverse viral strains. B cell analysis indicated each of the five lineages to have been initiated and expanded by FP-carrier priming, with envelope (Env)-trimer boosts inducing cross-reactive neutralization. These Abs had binding-energy hotspots focused on FP, whereas several FP-directed Abs induced by immunization with Env trimer-only were less FP-focused and less broadly neutralizing. Priming with a conserved subregion, such as FP, can thus induce Abs with binding-energy hotspots coincident with the target subregion and capable of broad neutralization.

Organizational Affiliation

Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA.

Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA.

Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA; National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA; Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA.

Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98195, USA; Molecular and Cellular Biology PhD Program, University of Washington, Seattle, WA 98195, USA; Division of Human Biology and Epidemiology Program, Seattle, WA 98195, USA.

Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm 17177, Sweden.

National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA.

Biostatistics Research Branch, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA.

Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA.

NIH Intramural Sequencing Center, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA.

Division of Human Biology and Epidemiology Program, Seattle, WA 98195, USA.

Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98195, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA.

Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA; Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.

Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA. Electronic address: pdkwong@nih.gov.

Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA. Electronic address: jmascola@nih.gov.

Macromolecule Content

Total Structure Weight: 502.65 kDa
Atom Count: 32,085
Modeled Residue Count: 3,846
Deposited Residue Count: 4,272
Unique protein chains: 8

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
A12V163-b.01 Light Chain	A [auth B], K [auth 4], X [auth Y]	113	Macaca mulatta	Mutation(s): 0

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp41	B [auth U], P [auth A], R [auth D]	153	Human immunodeficiency virus 1	Mutation(s): 0 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: 1	Glycosylation Focus chain B [auth U] Focus chain P [auth A] Focus chain R [auth D]
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp120	C [auth V], I [auth 2], Q [auth C]	473	Human immunodeficiency virus 1	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: 16	Glycosylation Focus chain C [auth V] Focus chain I [auth 2] Focus chain Q [auth C]
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
A12V163-b.01 Heavy Chain	D [auth W], J [auth 3], W [auth X]	117	Macaca mulatta	Mutation(s): 0

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
PGT122 Heavy chain	E [auth m], L [auth 5], S [auth M]	132	Homo sapiens	Mutation(s): 0

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| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
PGT122 Light chain	F [auth n], M [auth 6], T [auth N]	107	Homo sapiens	Mutation(s): 0

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| 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
VRC03 heavy chain	G [auth q], O [auth 8], U [auth Q]	227	Homo sapiens	Mutation(s): 0

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| 3D Structure

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
VRC03 Light chain	H [auth r], N [auth 7], V [auth R]	102	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 9
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 G], AB [auth t], BA [auth H], CA [auth I], CB [auth v], AA [auth G], AB [auth t], BA [auth H], CA [auth I], CB [auth v], DB [auth w], EA [auth K], EB [auth x], FA [auth L], GB [auth z], HB [auth 0], JA [auth T], LB [auth BA], MA [auth b], OA [auth d], PA [auth e], QA [auth f], SA [auth h], TA [auth i], XA [auth o], Y [auth E]	2		N-Glycosylation	Interactions Focus chain AA [auth G] Focus chain AB [auth t] Focus chain BA [auth H] Focus chain CA [auth I] Focus chain CB [auth v] Focus chain DB [auth w] Focus chain EA [auth K] Focus chain EB [auth x] Focus chain FA [auth L] Focus chain GB [auth z] Focus chain HB [auth 0] Focus chain JA [auth T] Focus chain LB [auth BA] Focus chain MA [auth b] Focus chain OA [auth d] Focus chain PA [auth e] Focus chain QA [auth f] Focus chain SA [auth h] Focus chain TA [auth i] Focus chain XA [auth o] Focus chain Y [auth E] Interactions & Density Focus chain AA [auth G] Focus chain AB [auth t] Focus chain BA [auth H] Focus chain CA [auth I] Focus chain CB [auth v] Focus chain DB [auth w] Focus chain EA [auth K] Focus chain EB [auth x] Focus chain FA [auth L] Focus chain GB [auth z] Focus chain HB [auth 0] Focus chain JA [auth T] Focus chain LB [auth BA] Focus chain MA [auth b] Focus chain OA [auth d] Focus chain PA [auth e] Focus chain QA [auth f] Focus chain SA [auth h] Focus chain TA [auth i] Focus chain XA [auth o] Focus chain Y [auth E]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 10
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
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	BB [auth u], HA [auth P], JB [auth 9], KA [auth Z], MB [auth CA], BB [auth u], HA [auth P], JB [auth 9], KA [auth Z], MB [auth CA], NA [auth c], VA [auth k], YA [auth p], Z [auth F]	4		N-Glycosylation	Interactions Focus chain BB [auth u] Focus chain HA [auth P] Focus chain JB [auth 9] Focus chain KA [auth Z] Focus chain MB [auth CA] Focus chain NA [auth c] Focus chain VA [auth k] Focus chain YA [auth p] Focus chain Z [auth F] Interactions & Density Focus chain BB [auth u] Focus chain HA [auth P] Focus chain JB [auth 9] Focus chain KA [auth Z] Focus chain MB [auth CA] Focus chain NA [auth c] Focus chain VA [auth k] Focus chain YA [auth p] Focus chain Z [auth F]
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Entity ID: 11
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	DA [auth J], FB [auth y], RA [auth g]	5		N-Glycosylation	Interactions Focus chain DA [auth J] Focus chain FB [auth y] Focus chain RA [auth g] Interactions & Density Focus chain DA [auth J] Focus chain FB [auth y] Focus chain RA [auth g]
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Entity ID: 12
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	GA [auth O], IB [auth 1], LA [auth a], NB [auth DA], UA [auth j], GA [auth O], IB [auth 1], LA [auth a], NB [auth DA], UA [auth j], ZA [auth s]	3		N-Glycosylation	Interactions Focus chain GA [auth O] Focus chain IB [auth 1] Focus chain LA [auth a] Focus chain NB [auth DA] Focus chain UA [auth j] Focus chain ZA [auth s] Interactions & Density Focus chain GA [auth O] Focus chain IB [auth 1] Focus chain LA [auth a] Focus chain NB [auth DA] Focus chain UA [auth j] Focus chain ZA [auth s]
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 13
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	IA [auth S], KB [auth AA], WA [auth l]	9		N-Glycosylation	Interactions Focus chain IA [auth S] Focus chain KB [auth AA] Focus chain WA [auth l] Interactions & Density Focus chain IA [auth S] Focus chain KB [auth AA] Focus chain WA [auth l]
Glycosylation Resources
GlyTouCan: G68668TB GlyCosmos: G68668TB GlyGen: G68668TB

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 SB [auth 2] SDF format, chain TB [auth 2] SDF format, chain XB [auth C] SDF format, chain ZB [auth D] SDF format, chain YB [auth C] SDF format, chain WB [auth C] SDF format, chain VB [auth A] SDF format, chain UB [auth 2] SDF format, chain RB [auth V] SDF format, chain QB [auth V] SDF format, chain PB [auth V] SDF format, chain OB [auth U] MOL2 format, chain SB [auth 2] MOL2 format, chain TB [auth 2] MOL2 format, chain XB [auth C] MOL2 format, chain ZB [auth D] MOL2 format, chain YB [auth C] MOL2 format, chain WB [auth C] MOL2 format, chain VB [auth A] MOL2 format, chain UB [auth 2] MOL2 format, chain RB [auth V] MOL2 format, chain QB [auth V] MOL2 format, chain PB [auth V] MOL2 format, chain OB [auth U] mmCIF format, chain SB [auth 2] mmCIF format, chain TB [auth 2] mmCIF format, chain XB [auth C] mmCIF format, chain ZB [auth D] mmCIF format, chain YB [auth C] mmCIF format, chain WB [auth C] mmCIF format, chain VB [auth A] mmCIF format, chain UB [auth 2] mmCIF format, chain RB [auth V] mmCIF format, chain QB [auth V] mmCIF format, chain PB [auth V] mmCIF format, chain OB [auth U]	OB [auth U] PB [auth V] QB [auth V] RB [auth V] SB [auth 2] OB [auth U], PB [auth V], QB [auth V], RB [auth V], SB [auth 2], TB [auth 2], UB [auth 2], VB [auth A], WB [auth C], XB [auth C], YB [auth C], ZB [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain OB [auth U] Focus chain PB [auth V] Focus chain QB [auth V] Focus chain RB [auth V] Focus chain SB [auth 2] Focus chain TB [auth 2] Focus chain UB [auth 2] Focus chain VB [auth A] Focus chain WB [auth C] Focus chain XB [auth C] Focus chain YB [auth C] Focus chain ZB [auth D] Interactions & Density Focus chain OB [auth U] Focus chain PB [auth V] Focus chain QB [auth V] Focus chain RB [auth V] Focus chain SB [auth 2] Focus chain TB [auth 2] Focus chain UB [auth 2] Focus chain VB [auth A] Focus chain WB [auth C] Focus chain XB [auth C] Focus chain YB [auth C] Focus chain ZB [auth D]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.20 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2019-07-24

Deposition Author(s):

Acharya, P.

Kwong, P.D.

Revision History (Full details and data files)

Version 1.0: 2019-07-24
Type: Initial release
Version 1.1: 2020-02-05
Changes: Data collection, Database references
Version 1.2: 2020-07-01
Changes: Refinement description
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary
Version 2.1: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

6MPG | pdb_00006mpg

Cryo-EM structure at 3.2 A resolution of HIV-1 fusion peptide-directed antibody, A12V163-b.01, elicited by vaccination of Rhesus macaques, in complex with stabilized HIV-1 Env BG505 DS-SOSIP, which was also bound to antibodies VRC03 and PGT122

Literature

Antibody Lineages with Vaccine-Induced Antigen-Binding Hotspots Develop Broad HIV Neutralization.

Biological Assembly 1

Macromolecules

Entity ID: 1

Entity ID: 2

UniProt

Entity Groups

Glycosylation

Sequence Annotations

Expand

Entity ID: 3

UniProt

Entity Groups

Glycosylation

Sequence Annotations

Expand

Entity ID: 4

Entity ID: 5

Entity ID: 6

Entity ID: 7

Entity ID: 8

Oligosaccharides

Entity ID: 9

Glycosylation Resources

Entity ID: 10

Glycosylation Resources

Entity ID: 11

Glycosylation Resources

Entity ID: 12

Glycosylation Resources

Entity ID: 13

Glycosylation Resources

Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Entry History

Deposition Data

Revision History (Full details and data files)