3RU8

Structure of an HIV epitope scaffold in complex with neutralizing antibody b12 Fab

• PDB DOI: https://doi.org/10.2210/pdb3RU8/pdb

• Classification: DE NOVO PROTEIN, IMMUNE SYSTEM
• Organism(s): Human immunodeficiency virus, synthetic construct, Thermobifida fusca, Homo sapiens
• Expression System: Escherichia coli, Homo sapiens
• Mutation(s): No 


• Deposited: 2011-05-04 Released: 2011-11-02 
• Deposition Author(s): Carrico, C.T.D., Strong, R.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free: 0.203 
• R-Value Work: 0.168 
• R-Value Observed: 0.170 

Literature

Computation-guided backbone grafting of a discontinuous motif onto a protein scaffold.

Azoitei, M.L., Correia, B.E., Ban, Y.E., Carrico, C., Kalyuzhniy, O., Chen, L., Schroeter, A., Huang, P.S., McLellan, J.S., Kwong, P.D., Baker, D., Strong, R.K., Schief, W.R.

(2011) Science 334: 373-376

• PubMed: 22021856 
• DOI: https://doi.org/10.1126/science.1209368
• Primary Citation of Related Structures:  
  3RPT, 3RU8


• PubMed Abstract: 
  

  The manipulation of protein backbone structure to control interaction and function is a challenge for protein engineering. We integrated computational design with experimental selection for grafting the backbone and side chains of a two-segment HIV gp120 epitope, targeted by the cross-neutralizing antibody b12, onto an unrelated scaffold protein. The final scaffolds bound b12 with high specificity and with affinity similar to that of gp120, and crystallographic analysis of a scaffold bound to b12 revealed high structural mimicry of the gp120-b12 complex structure. The method can be generalized to design other functional proteins through backbone grafting.

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Organizational Affiliation: 

Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

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

Macromolecule Content

• Total Structure Weight: 79.06 kDa 
• Atom Count: 5,881 
• Modelled Residue Count: 715 
• Deposited Residue Count: 727 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Epitope Scaffold 2bodx43	A [auth X]	282	Human immunodeficiency virus, synthetic construct, Thermobifida fusca This entity is chimeric	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody b12, Heavy Chain	B [auth H]	230	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody b12, Light Chain	C [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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth X], E [auth X], F [auth L], G [auth L]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.07 Å
• R-Value Free: 0.203 
• R-Value Work: 0.168 
• R-Value Observed: 0.170 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.453	α = 90
b = 93.097	β = 90
c = 94.373	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-11-02 
Deposition Author(s): Carrico, C.T.D., Strong, R.K.

Revision History  

• Version 1.0: 2011-11-02
  Type: Initial release
  
• Version 1.1: 2012-02-22
  Changes: Database references
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description