6CDX | pdb_00006cdx

High-resolution crystal structure of fluoropropylated cystine knot, binding to alpha-5 beta-6 integrin

• PDB DOI: https://doi.org/10.2210/pdb6CDX/pdb

• Classification: PROTEIN BINDING
• Organism(s): Momordica cochinchinensis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-02-09 Released: 2019-08-14 
• Deposition Author(s): Kimura, R., Nix, J., Bongura, C., Chakraborti, S., Gambhir, S., Filipp, F.V.
• Funding Organization(s): German Federal Ministry for Education and Research, National Institutes of Health/National Cancer Institute (NIH/NCI), The University Grants Committee, Research Grants Council (RGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Free: 
  0.226 (Depositor), 0.223 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Models: experimental

Literature

Evaluation of integrin alpha v beta6cystine knot PET tracers to detect cancer and idiopathic pulmonary fibrosis.

Kimura, R.H., Wang, L., Shen, B., Huo, L., Tummers, W., Filipp, F.V., Guo, H.H., Haywood, T., Abou-Elkacem, L., Baratto, L., Habte, F., Devulapally, R., Witney, T.H., Cheng, Y., Tikole, S., Chakraborti, S., Nix, J., Bonagura, C.A., Hatami, N., Mooney, J.J., Desai, T., Turner, S., Gaster, R.S., Otte, A., Visser, B.C., Poultsides, G.A., Norton, J., Park, W., Stolowitz, M., Lau, K., Yang, E., Natarajan, A., Ilovich, O., Srinivas, S., Srinivasan, A., Paulmurugan, R., Willmann, J., Chin, F.T., Cheng, Z., Iagaru, A., Li, F., Gambhir, S.S.

(2019) Nat Commun 10: 4673-4673

• PubMed: 31611594 
• DOI: https://doi.org/10.1038/s41467-019-11863-w
• Primary Citation Related Structures: 
  6CDX


• PubMed Abstract: 
  

  Advances in precision molecular imaging promise to transform our ability to detect, diagnose and treat disease. Here, we describe the engineering and validation of a new cystine knot peptide (knottin) that selectively recognizes human integrin αvβ ₆ with single-digit nanomolar affinity. We solve its 3D structure by NMR and x-ray crystallography and validate leads with 3 different radiolabels in pre-clinical models of cancer. We evaluate the lead tracer's safety, biodistribution and pharmacokinetics in healthy human volunteers, and show its ability to detect multiple cancers (pancreatic, cervical and lung) in patients at two study locations. Additionally, we demonstrate that the knottin PET tracers can also detect fibrotic lung disease in idiopathic pulmonary fibrosis patients. Our results indicate that these cystine knot PET tracers may have potential utility in multiple disease states that are associated with upregulation of integrin α _v β ₆ .

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Organizational Affiliation: 
• Department of Radiology, Stanford University, Stanford, CA, 94305, USA.
Department of Nuclear Medicine, Peking Union Medical College, Beijing, 100730, China.
Cancer Systems Biology, Institute of Computational Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, D-85764, München, Germany.
School of Life Sciences Weihenstephan, Technical University München, Maximus-von-Imhof-Forum 3, D-85354, Freising, Germany.
Department of Chemistry, Mississippi State University, Mississippi State, MS, 39762, USA.
Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
Art Robbins Instruments, Sunnyvale, CA, 94089, USA.
Department of Medicine, Stanford University, Stanford, CA, 94305, USA.
Department of Internal Medicine, Stanford University, Stanford, CA, 94305, USA.
Pliant Therapeutics, Redwood City, CA, 94063, USA.
Department of Surgery, Stanford University, Stanford, CA, 94305, USA.
Department of Pathology, Stanford University, Stanford, CA, 95305, USA.
Department of Radiology, Stanford University, Stanford, CA, 94305, USA. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 7.83 kDa 
• Atom Count: 589 
• Modeled Residue Count: 73 
• Deposited Residue Count: 74 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cystine knot (fluoropropylated)	A, B	37	Momordica cochinchinensis	Mutation(s): 0
UniProt
Find proteins for P82408 (Momordica cochinchinensis) Explore P82408  Go to UniProtKB:  P82408

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Free:  0.226 (Depositor), 0.223 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 16.95	α = 90
b = 44.25	β = 90
c = 66.41	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-08-14 
Deposition Author(s): Kimura, R., Nix, J., Bongura, C., Chakraborti, S., Gambhir, S., Filipp, F.V.

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Funding Organization	Location	Grant Number
German Federal Ministry for Education and Research	Germany	DJUSA
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	CA154887
The University Grants Committee, Research Grants Council (RGC)	United States	CRN-17-427258

Revision History  

• Version 1.0: 2019-08-14
  Type: Initial release
  
• Version 1.1: 2019-12-04
  Changes: Author supporting evidence
• Version 1.2: 2020-02-26
  Changes: Database references
• Version 1.3: 2020-09-23
  Changes: Database references
• Version 1.4: 2023-10-04
  Changes: Data collection, Database references, Refinement description
• Version 1.5: 2024-10-23
  Changes: Structure summary