5VNV

Crystal structure of Nb.b201


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Yeast surface display platform for rapid discovery of conformationally selective nanobodies.

McMahon, C.Baier, A.S.Pascolutti, R.Wegrecki, M.Zheng, S.Ong, J.X.Erlandson, S.C.Hilger, D.Rasmussen, S.G.F.Ring, A.M.Manglik, A.Kruse, A.C.

(2018) Nat Struct Mol Biol 25: 289-296

  • DOI: https://doi.org/10.1038/s41594-018-0028-6
  • Primary Citation of Related Structures:  
    5VNV, 5VNW

  • PubMed Abstract: 

    Camelid single-domain antibody fragments ('nanobodies') provide the remarkable specificity of antibodies within a single 15-kDa immunoglobulin V HH domain. This unique feature has enabled applications ranging from use as biochemical tools to therapeutic agents. Nanobodies have emerged as especially useful tools in protein structural biology, facilitating studies of conformationally dynamic proteins such as G-protein-coupled receptors (GPCRs). Nearly all nanobodies available to date have been obtained by animal immunization, a bottleneck restricting many applications of this technology. To solve this problem, we report a fully in vitro platform for nanobody discovery based on yeast surface display. We provide a blueprint for identifying nanobodies, demonstrate the utility of the library by crystallizing a nanobody with its antigen, and most importantly, we utilize the platform to discover conformationally selective nanobodies to two distinct human GPCRs. To facilitate broad deployment of this platform, the library and associated protocols are freely available for nonprofit research.


  • Organizational Affiliation

    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nb.b201120synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A]
PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
FMT
Query on FMT

Download Ideal Coordinates CCD File 
I [auth A]FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A],
H [auth A]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.751α = 90
b = 106.751β = 90
c = 52.232γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Smith Family FoundationUnited States--
National Institutes of Health/Office of the DirectorUnited States1DP5OD021345

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-21
    Type: Initial release
  • Version 1.1: 2018-03-14
    Changes: Database references
  • Version 1.2: 2018-04-18
    Changes: Data collection
  • Version 1.3: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-10-09
    Changes: Structure summary