4ZMJ | pdb_00004zmj

Crystal Structure of Ligand-Free BG505 SOSIP.664 HIV-1 Env Trimer

PDB DOI: https://doi.org/10.2210/pdb4ZMJ/pdb

Classification: VIRAL PROTEIN
Organism(s): Human immunodeficiency virus 1
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2015-05-04 Released: 2015-06-24
Deposition Author(s): Kwon, Y.D., Kwong, P.D.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.31 Å
R-Value Free:
0.285 (Depositor), 0.291 (DCC)
R-Value Work:
0.266 (Depositor), 0.273 (DCC)
R-Value Observed:
0.268 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Crystal structure, conformational fixation and entry-related interactions of mature ligand-free HIV-1 Env.

Do Kwon, Y., Pancera, M., Acharya, P., Georgiev, I.S., Crooks, E.T., Gorman, J., Joyce, M.G., Guttman, M., Ma, X., Narpala, S., Soto, C., Terry, D.S., Yang, Y., Zhou, T., Ahlsen, G., Bailer, R.T., Chambers, M., Chuang, G.Y., Doria-Rose, N.A., Druz, A., Hallen, M.A., Harned, A., Kirys, T., Louder, M.K., O'Dell, S., Ofek, G., Osawa, K., Prabhakaran, M., Sastry, M., Stewart-Jones, G.B., Stuckey, J., Thomas, P.V., Tittley, T., Williams, C., Zhang, B., Zhao, H., Zhou, Z., Donald, B.R., Lee, L.K., Zolla-Pazner, S., Baxa, U., Schon, A., Freire, E., Shapiro, L., Lee, K.K., Arthos, J., Munro, J.B., Blanchard, S.C., Mothes, W., Binley, J.M., McDermott, A.B., Mascola, J.R., Kwong, P.D.

(2015) Nat Struct Mol Biol 22: 522-531

PubMed: 26098315 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/nsmb.3051
Primary Citation Related Structures:
4ZMJ

PubMed Abstract:
As the sole viral antigen on the HIV-1-virion surface, trimeric Env is a focus of vaccine efforts. Here we present the structure of the ligand-free HIV-1-Env trimer, fix its conformation and determine its receptor interactions. Epitope analyses revealed trimeric ligand-free Env to be structurally compatible with broadly neutralizing antibodies but not poorly neutralizing ones. We coupled these compatibility considerations with binding antigenicity to engineer conformationally fixed Envs, including a 201C 433C (DS) variant specifically recognized by broadly neutralizing antibodies. DS-Env retained nanomolar affinity for the CD4 receptor, with which it formed an asymmetric intermediate: a closed trimer bound by a single CD4 without the typical antigenic hallmarks of CD4 induction. Antigenicity-guided structural design can thus be used both to delineate mechanism and to fix conformation, with DS-Env trimers in virus-like-particle and soluble formats providing a new generation of vaccine antigens.

Organizational Affiliation

Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA.

San Diego Biomedical Research Institute, San Diego, California, USA.

Department of Medicinal Chemistry, University of Washington, Seattle, Washington, USA.

Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut, USA.

Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, New York, USA.

1] Department of Biochemistry &Molecular Biophysics, Columbia University, New York, New York, USA. [2] Department of Systems Biology, Columbia University, New York, New York, USA.

1] Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA. [2] Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, USA.

Electron Microscopy Laboratory, Cancer Research Technology Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA.

New York University School of Medicine, New York, New York, USA.

1] Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, USA. [2] Department of Chemistry, Duke University, Durham, North Carolina, USA. [3] Department of Computer Science, Duke University, Durham, North Carolina, USA.

Structural and Computational Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia.

1] New York University School of Medicine, New York, New York, USA. [2] New York Veterans Affairs Harbor Healthcare System, New York, New York, USA.

Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA.

1] Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA. [2] Department of Biochemistry &Molecular Biophysics, Columbia University, New York, New York, USA.

Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA.

1] Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut, USA. [2] Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, USA.

Macromolecule Content

Total Structure Weight: 76.45 kDa
Atom Count: 4,856
Modeled Residue Count: 573
Deposited Residue Count: 634
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp160	A [auth G]	481	Human immunodeficiency virus 1	Mutation(s): 2 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: 15	Glycosylation Focus chain A [auth G]
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein gp160	B	153	Human immunodeficiency virus 1	Mutation(s): 2 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: 3	Glycosylation Focus chain B
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 3
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	C [auth A]	6		N-Glycosylation	Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
Glycosylation Resources
GlyTouCan: G56014GC GlyCosmos: G56014GC GlyGen: G56014GC

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth C], E [auth D]	2		N-Glycosylation	Interactions Focus chain D [auth C] Focus chain E [auth D] Interactions & Density Focus chain D [auth C] Focus chain E [auth D]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

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 F [auth G] SDF format, chain G SDF format, chain H [auth G] SDF format, chain I [auth G] SDF format, chain J [auth G] SDF format, chain K [auth G] SDF format, chain L [auth G] SDF format, chain M [auth G] SDF format, chain N [auth G] SDF format, chain O [auth G] SDF format, chain P [auth G] SDF format, chain Q [auth G] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] MOL2 format, chain F [auth G] MOL2 format, chain G MOL2 format, chain H [auth G] MOL2 format, chain I [auth G] MOL2 format, chain J [auth G] MOL2 format, chain K [auth G] MOL2 format, chain L [auth G] MOL2 format, chain M [auth G] MOL2 format, chain N [auth G] MOL2 format, chain O [auth G] MOL2 format, chain P [auth G] MOL2 format, chain Q [auth G] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] mmCIF format, chain F [auth G] mmCIF format, chain G mmCIF format, chain H [auth G] mmCIF format, chain I [auth G] mmCIF format, chain J [auth G] mmCIF format, chain K [auth G] mmCIF format, chain L [auth G] mmCIF format, chain M [auth G] mmCIF format, chain N [auth G] mmCIF format, chain O [auth G] mmCIF format, chain P [auth G] mmCIF format, chain Q [auth G] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B]	F [auth G] G H [auth G] I [auth G] J [auth G] F [auth G], G, H [auth G], I [auth G], J [auth G], K [auth G], L [auth G], M [auth G], N [auth G], O [auth G], P [auth G], Q [auth G], R [auth B], S [auth B], T [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain F [auth G] Focus chain G Focus chain H [auth G] Focus chain I [auth G] Focus chain J [auth G] Focus chain K [auth G] Focus chain L [auth G] Focus chain M [auth G] Focus chain N [auth G] Focus chain O [auth G] Focus chain P [auth G] Focus chain Q [auth G] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Interactions & Density Focus chain F [auth G] Focus chain G Focus chain H [auth G] Focus chain I [auth G] Focus chain J [auth G] Focus chain K [auth G] Focus chain L [auth G] Focus chain M [auth G] Focus chain N [auth G] Focus chain O [auth G] Focus chain P [auth G] Focus chain Q [auth G] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.31 Å
R-Value Free: 0.285 (Depositor), 0.291 (DCC)
R-Value Work: 0.266 (Depositor), 0.273 (DCC)
R-Value Observed: 0.268 (Depositor)

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.18	α = 90
b = 107.18	β = 90
c = 103.06	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2015-06-24

Deposition Author(s):

Kwon, Y.D.

Kwong, P.D.

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

Revision History (Full details and data files)

Version 1.0: 2015-06-24
Type: Initial release
Version 1.1: 2015-07-08
Changes: Database references
Version 1.2: 2015-07-29
Changes: Database references
Version 1.3: 2017-09-27
Changes: Author supporting evidence, Derived calculations, Source and taxonomy
Version 1.4: 2019-12-11
Changes: Author supporting evidence
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
Version 2.2: 2024-10-16
Changes: Structure summary