5ESV | pdb_00005esv

Crystal Structure of Broadly Neutralizing Antibody CH03, Isolated from Donor CH0219, in Complex with Scaffolded Trimeric HIV-1 Env V1V2 Domain from the Clade C Superinfecting Strain of Donor CAP256.

• PDB DOI: https://doi.org/10.2210/pdb5ESV/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Haemophilus influenzae Rd KW20, Human immunodeficiency virus 1
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2015-11-17 Released: 2015-12-16 
• Deposition Author(s): Gorman, J., Yang, M., Kwong, P.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 
  0.259 (Depositor), 0.261 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Starting Models: experimental

Literature

Structures of HIV-1 Env V1V2 with broadly neutralizing antibodies reveal commonalities that enable vaccine design.

Gorman, J., Soto, C., Yang, M.M., Davenport, T.M., Guttman, M., Bailer, R.T., Chambers, M., Chuang, G.Y., DeKosky, B.J., Doria-Rose, N.A., Druz, A., Ernandes, M.J., Georgiev, I.S., Jarosinski, M.C., Joyce, M.G., Lemmin, T.M., Leung, S., Louder, M.K., McDaniel, J.R., Narpala, S., Pancera, M., Stuckey, J., Wu, X., Yang, Y., Zhang, B., Zhou, T., Program, N.C., Mullikin, J.C., Baxa, U., Georgiou, G., McDermott, A.B., Bonsignori, M., Haynes, B.F., Moore, P.L., Morris, L., Lee, K.K., Shapiro, L., Mascola, J.R., Kwong, P.D.

(2016) Nat Struct Mol Biol 23: 81-90

• PubMed: 26689967 
• DOI: https://doi.org/10.1038/nsmb.3144
• Primary Citation Related Structures: 
  5ESV, 5ESZ


• PubMed Abstract: 
  

  Broadly neutralizing antibodies (bNAbs) against HIV-1 Env V1V2 arise in multiple donors. However, atomic-level interactions had previously been determined only with antibodies from a single donor, thus making commonalities in recognition uncertain. Here we report the cocrystal structure of V1V2 with antibody CH03 from a second donor and model Env interactions of antibody CAP256-VRC26 from a third donor. These V1V2-directed bNAbs used strand-strand interactions between a protruding antibody loop and a V1V2 strand but differed in their N-glycan recognition. Ontogeny analysis indicated that protruding loops develop early, and glycan interactions mature over time. Altogether, the multidonor information suggested that V1V2-directed bNAbs form an 'extended class', for which we engineered ontogeny-specific antigens: Env trimers with chimeric V1V2s that interacted with inferred ancestor and intermediate antibodies. The ontogeny-based design of vaccine antigens described here may provide a general means for eliciting antibodies of a desired class.

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Organizational Affiliation: 
• Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, Maryland, USA.
Department of Medicinal Chemistry, University of Washington, Seattle, Washington, USA.
Department of Chemical Engineering, University of Texas at Austin, Austin, Texas, USA.
Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, USA.
NIH Intramural Sequencing Center (NISC), National Human Genome Research Institute, NIH, Bethesda, Maryland, USA.
Electron Microscopy Laboratory, Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA.
Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA.
Center for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.
Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Congella, South Africa.
Department of Biochemistry &Molecular Biophysics, Columbia University, New York, New York, USA.
Department of Systems Biology, Columbia University, New York, New York, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 9-mer - A3B3C3 Pseudo Symmetry: Cyclic - C3  (Explore in 3D)
Pseudo Stoichiometry: Hetero 9-mer - A6B3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 230.24 kDa 
• Atom Count: 15,044 
• Modeled Residue Count: 1,872 
• Deposited Residue Count: 2,010 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CH03 Heavy Chain	A, C, H	244	Homo sapiens	Mutation(s): 0
UniProt
Find proteins for S6BGE0 (Homo sapiens) Explore S6BGE0  Go to UniProtKB:  S6BGE0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CH03 Light Chain	B, D, I [auth L]	215	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P01834 (Homo sapiens) Explore P01834  Go to UniProtKB:  P01834
PHAROS:  P01834

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase,Envelope glycoprotein gp160	E, F, G	211	Haemophilus influenzae Rd KW20, Human immunodeficiency virus 1	Mutation(s): 0  Gene Names: ispF, HI_0671, env EC: 4.6.1.12
UniProt
Find proteins for P44815 (Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)) Explore P44815  Go to UniProtKB:  P44815
Find proteins for W6ICC0 (Human immunodeficiency virus type 1) Explore W6ICC0  Go to UniProtKB:  W6ICC0
UniProt Groups	W6ICC0P44815
Glycosylation
Glycosylation Sites: 4

Oligosaccharides

Help  

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	J [auth I]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 5
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	K [auth J]	5		N-Glycosylation
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-[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	L [auth K], M, P, Q, T	7		N-Glycosylation
Glycosylation Resources
GlyTouCan: G55220VL GlyCosmos: G55220VL GlyGen: G55220VL

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	N, O	3		N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 8
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	R, S	6		N-Glycosylation
Glycosylation Resources
GlyTouCan: G09724ZC GlyCosmos: G09724ZC GlyGen: G09724ZC

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	W [auth G]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
ZN	U [auth E], V [auth F], X [auth G]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free:  0.259 (Depositor), 0.261 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 162.693	α = 90
b = 98.211	β = 112.82
c = 170.629	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-12-16 
Deposition Author(s): Gorman, J., Yang, M., Kwong, P.D.

Revision History  

• Version 1.0: 2015-12-16
  Type: Initial release
  
• Version 1.1: 2016-01-06
  Changes: Database references
• Version 1.2: 2016-01-13
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, 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: 2024-11-20
  Changes: Structure summary