Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - ABCD Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer -A2BC 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - ABCD Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer -A2BC 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 174810.55 
• Atom Count: 12046 
• Residue Count: 1566 
• Unique protein chains: 4

1YYL

crystal structure of CD4M33, a scorpion-toxin mimic of CD4, in complex with HIV-1 YU2 gp120 envelope glycoprotein and anti-HIV-1 antibody 17b

• DOI: 10.2210/pdb1YYL/pdb

• Classification: Viral protein/Immune system
• Organism(s): Human immunodeficiency virus type 1 group M subtype B
• Expression System: Mus musculus, Drosophila melanogaster


• 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: 2.75 Å
• R-Value Free: 0.275 
• R-Value Work: 0.202 

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: 10.1016/j.str.2005.03.006
• Primary Citation of Related Structures:  
  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.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Exterior membrane glycoprotein(GP120),Exterior membrane glycoprotein(GP120),Exterior membrane glycoprotein(GP120)	G, P	313	Human immunodeficiency virus type 1 group M subtype B	Mutation(s): 0  Gene Names: env
Find proteins for P35961 (Human immunodeficiency virus type 1 group M subtype B) Go to UniProtKB:  P35961

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
antibody 17b light chain	L, Q	214	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
antibody 17b heavy chain	H, R	229	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
CD4M33, scorpion-toxin mimic of CD4	M, S	27	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
NDG	G	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE C8 H15 N O6 OVRNDRQMDRJTHS-PVFLNQBWSA-N
NAG	G, P	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Modified Residues  3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
BIF	M, S	L-PEPTIDE LINKING	C15 H15 N O2		PHE
MPT	M, S	NON-POLYMER	C3 H6 O2 S		--
VLM	M, S	L-PEPTIDE LINKING	C5 H12 N2 O		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.275 
• R-Value Work: 0.202 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 51.516	α = 90.00
b = 157.841	β = 93.55
c = 109.920	γ = 90.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-02-25 
• 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
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Non-polymer description, Version format compliance
• Version 1.3: 2017-06-14
  Type: Database references, Source and taxonomy, Structure summary