5VNV | pdb_00005vnv

Crystal structure of Nb.b201

• PDB DOI: https://doi.org/10.2210/pdb5VNV/pdb

• Classification: DE NOVO PROTEIN
• Organism(s): synthetic construct
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2017-05-01 Released: 2018-02-21 
• Deposition Author(s): Kruse, A.C., McMahon, C.
• Funding Organization(s): Smith Family Foundation, National Institutes of Health/Office of the Director

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.214 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

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

• PubMed: 29434346 
• DOI: https://doi.org/10.1038/s41594-018-0028-6
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
Department of Neuroscience, University of Copenhagen, Copenhagen, Denmark.
Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA.
Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA.
Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA. [e-mail].
Department of Anesthesia and Perioperative Care, University of California San Francisco, San Francisco, CA, USA. [e-mail].
Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: light scattering

Macromolecule Content 

• Total Structure Weight: 14.27 kDa 
• Atom Count: 1,115 
• Modeled Residue Count: 120 
• Deposited Residue Count: 120 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nb.b201	A	120	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1PE	B [auth A], C [auth A], D [auth A]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
FMT	I [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
K	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 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.751	α = 90
b = 106.751	β = 90
c = 52.232	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-02-21 
Deposition Author(s): Kruse, A.C., McMahon, C.

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Funding Organization	Location	Grant Number
Smith Family Foundation	United States	--
National Institutes of Health/Office of the Director	United States	1DP5OD021345

Revision History  

• 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