1YYM

crystal structure of F23, a scorpion-toxin mimic of CD4, in complex with HIV-1 YU2 gp120 envelope glycoprotein and anti-HIV-1 antibody 17b

• PDB DOI:  https://doi.org/10.2210/pdb1YYM/pdb

• Classification: Viral protein/Immune system
• Organism(s): Human immunodeficiency virus 1, Homo sapiens, synthetic construct
• Expression System: Drosophila melanogaster, Mus musculus
• Mutation(s): No 


• Deposited: 2005-02-25 Released: 2005-05-03 
• Deposition Author(s): Huang, C.C., Stricher, F., Martin, L., Decker, J.M., Majeed, S., Barthe, P., Hendrickson, W.A., Robinson, J., Roumestand, C., Sodroski, J., Wyatt, R., Shaw, G.M., Vita, C., Kwong, P.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.268 
• R-Value Work: 0.209 
• R-Value Observed: 0.209 

Literature

Scorpion-toxin mimics of CD4 in complex with human immunodeficiency virus gp120 crystal structures, molecular mimicry, and neutralization breadth.

Huang, C.C., Stricher, F., Martin, L., Decker, J.M., Majeed, S., Barthe, P., Hendrickson, W.A., Robinson, J., Roumestand, C., Sodroski, J., Wyatt, R., Shaw, G.M., Vita, C., Kwong, P.D.

(2005) Structure 13: 755-768

• PubMed: 15893666 
• DOI: https://doi.org/10.1016/j.str.2005.03.006
• Primary Citation of Related Structures:  
  1YYL, 1YYM


• PubMed Abstract: 
  

The binding surface on CD4 for the HIV-1 gp120 envelope glycoprotein has been transplanted previously onto a scorpion-toxin scaffold. Here, we use X-ray crystallography to characterize atomic-level details of gp120 with this transplant, CD4M33. Despite known envelope flexibility, the conformation of gp120 induced by CD4M33 was so similar to that induced by CD4 that localized measures were required to distinguish ligand-induced differences from lattice variation. To investigate relationships between structure, function, and mimicry, an F23 analog of CD4M33 was devised. Structural and thermodynamic analyses showed F23 to be a better molecular mimic of CD4 than CD4M33. F23 also showed increased neutralization breadth, against diverse isolates of HIV-1, HIV-2, and SIVcpz. Our results lend insight into the stability of the CD4 bound conformation of gp120, define measures that quantify molecular mimicry as a function of evolutionary distance, and suggest how such evaluations might be useful in developing mimetic antagonists with increased neutralization breadth.

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Organizational Affiliation: 

Vaccine Research Center, National Institutes of Health, Bethesda, Maryland 20892, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 174.9 kDa 
• Atom Count: 12,823 
• Modelled Residue Count: 1,540 
• Deposited Residue Count: 1,566 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Exterior membrane glycoprotein(GP120),Exterior membrane glycoprotein(GP120),Exterior membrane glycoprotein(GP120)	A [auth G], E [auth P]	313	Human immunodeficiency virus 1	Mutation(s): 0
UniProt
Find proteins for P35961 (Human immunodeficiency virus type 1 group M subtype B (isolate YU-2)) Explore P35961  Go to UniProtKB:  P35961

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
antibody 17b light chain	B [auth L], F [auth Q]	214	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
antibody 17b heavy chain	C [auth H], G [auth R]	229	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
F23, scorpion-toxin mimic of CD4	D [auth M], H [auth S]	27	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	AA [auth P], I [auth G], J [auth G], K [auth G], L [auth G], M [auth G], N [auth G], O [auth G], P [auth G], T [auth P], U [auth P], V [auth P], W [auth P], X [auth P], Y [auth P], Z [auth P]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
EDO	Q [auth G], S [auth M]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
IPA	BA [auth P], R [auth G]	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.268 
• R-Value Work: 0.209 
• R-Value Observed: 0.209 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.62	α = 90
b = 157.041	β = 93.45
c = 108.929	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-05-03 
Deposition Author(s): Huang, C.C., Stricher, F., Martin, L., Decker, J.M., Majeed, S., Barthe, P., Hendrickson, W.A., Robinson, J., Roumestand, C., Sodroski, J., Wyatt, R., Shaw, G.M., Vita, C., Kwong, P.D.

Revision History  

• Version 1.0: 2005-05-03
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2017-06-14
  Changes: Database references, Source and taxonomy, Structure summary
• Version 1.4: 2019-12-11
  Changes: Derived calculations
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary