9NS1 | pdb_00009ns1

Intermediate state of Src kinase domain

• PDB DOI: https://doi.org/10.2210/pdb9NS1/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-03-15 Released: 2026-01-21 
• Deposition Author(s): Cui, Y., Ali, R., Clay, M., Rossi, P., Liu, A., Yang, D., Gough, N., Geiger, T., Kalodimos, C.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: target function 

Literature

Conformational landscape adaptations enable processive phosphorylation by Src family kinases.

Cui, Y., Ali, R., Clay, M., Rossi, P., Liu, A., Yang, D., Gough, N.R., Geiger, T., Kalodimos, C.G.

(2025) Science 390: eadw8310-eadw8310

• PubMed: 41411430 
• DOI: https://doi.org/10.1126/science.adw8310
• Primary Citation of Related Structures:  
  9NS0, 9NS1


• PubMed Abstract: 
  

  Processive phosphorylation by kinases enables the rapid multisite modification of signaling hubs, serving to integrate signals during time-sensitive cellular events. To achieve processivity, multiple catalytic cycles must occur before substrate dissociation, making rapid turnover rates essential. Src family kinases processively phosphorylate multisite substrates. Using nuclear magnetic resonance spectroscopy, we identified a transient intermediate state within the Src conformational ensemble, positioned between its active and inactive states. This intermediate state facilitates the rapid release of adenosine diphosphate following adenosine triphosphate hydrolysis, ensuring efficient catalytic turnover. Depletion of the intermediate state abrogated processive phosphorylation by Src, Lck, and Hck, impairing function. These findings reveal that the conformational ensemble of Src family kinases has evolved to incorporate a transient state that underpins their capacity for processive substrate phosphorylation.

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Organizational Affiliation: 
• Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA.

Biological Assembly 1  

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

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

Biological Assembly Evidence: NMR Distance Restraints

Macromolecule Content 

• Total Structure Weight: 32.74 kDa 
• Atom Count: 2,298 
• Modeled Residue Count: 286 
• Deposited Residue Count: 286 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proto-oncogene tyrosine-protein kinase Src	A	286	Homo sapiens	Mutation(s): 0  Gene Names: SRC, SRC1 EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P12931 (Homo sapiens) Explore P12931  Go to UniProtKB:  P12931
PHAROS:  P12931 GTEx:  ENSG00000197122

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: target function 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2026-01-21 
Deposition Author(s): Cui, Y., Ali, R., Clay, M., Rossi, P., Liu, A., Yang, D., Gough, N., Geiger, T., Kalodimos, C.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35 GM122462

Revision History  

• Version 1.0: 2026-01-21
  Type: Initial release