6ITP

Crystal structure of cortisol complexed with its nanobody at pH 3.5

• PDB DOI: https://doi.org/10.2210/pdb6ITP/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Camelus bactrianus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-11-24 Released: 2019-07-24 
• Deposition Author(s): Ding, Y., Ding, L.L., Wang, Z.Y., Zhong, P.Y.
• Funding Organization(s): National Science Foundation (China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free: 0.223 
• R-Value Work: 0.195 
• R-Value Observed: 0.196 

Literature

Structural insights into the mechanism of single domain VHH antibody binding to cortisol.

Ding, L., Wang, Z., Zhong, P., Jiang, H., Zhao, Z., Zhang, Y., Ren, Z., Ding, Y.

(2019) FEBS Lett 593: 1248-1256

• PubMed: 31049949 
• DOI: https://doi.org/10.1002/1873-3468.13398
• Primary Citation of Related Structures:  
  6ITP, 6ITQ


• PubMed Abstract: 
  

  To date, few structural models of VHH antibody binding to low molecular weight haptens have been reported. Here, we report the crystal structure of cortisol binding to its VHH antibody NbCor at pH 3.5 and 10.5. Cortisol binds to NbCor mainly by burying itself under the tunnel formed by the complementarity determining region 1 (CDR1) of NbCor. The affinity of NbCor binding to cortisol and similar compounds was also verified by a microscale thermophoresis assay. Combining our findings with several previously reported structures of hapten-VHH antibody complexes, we propose that VHH antibodies exhibit a special mechanism of binding small haptens by encapsulating them in a tunnel formed by CDR1. Our findings provide useful structural information for the further development and optimization of hapten-specific VHH antibodies.

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Organizational Affiliation: 

Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration, isothermal titration calorimetry

Macromolecule Content

• Total Structure Weight: 28.29 kDa 
• Atom Count: 2,319 
• Modelled Residue Count: 250 
• Deposited Residue Count: 254 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
anti-cortisol camelid antibody	A, B	127	Camelus bactrianus	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HCY (Subject of Investigation/LOI)	C [auth A], D [auth B]	(11alpha,14beta)-11,17,21-trihydroxypregn-4-ene-3,20-dione C21 H30 O5 JYGXADMDTFJGBT-VWUMJDOOSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
HCY	Binding MOAD:  6ITP	Kd: 2.24e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free: 0.223 
• R-Value Work: 0.195 
• R-Value Observed: 0.196 
• Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.043	α = 90
b = 95.043	β = 90
c = 95.043	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-07-24 
Deposition Author(s): Ding, Y., Ding, L.L., Wang, Z.Y., Zhong, P.Y.

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Funding Organization	Location	Grant Number
National Science Foundation (China)	China	31470764
National Science Foundation (China)	China	91527305

Revision History  

• Version 1.0: 2019-07-24
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description