9ZG5 | pdb_00009zg5

Structure of superfolder GFP bound to nanobody 15


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 
    0.331 (Depositor), 0.331 (DCC) 
  • R-Value Work: 
    0.295 (Depositor), 0.295 (DCC) 
  • R-Value Observed: 
    0.297 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9ZG5

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Literature

Time-Resolved Native Mass Spectrometry for Direct Measurement of Biomolecular Kinetics.

James, V.K.Stover, L.Bahramimoghaddam, H.Khandelwal, T.Chang, J.Y.Downing, J.Scott, E.Bailey, K.O.Russell, D.H.Baker, L.A.Laganowsky, A.

(2026) J Am Chem Soc 148: 19567-19577

  • DOI: https://doi.org/10.1021/jacs.5c21842
  • Primary Citation Related Structures: 
    9ZG5

  • PubMed Abstract: 

    The functional outcomes of biomolecular interactions depend on the kinetics of association and dissociation between proteins and their binding partners, ranging from small molecules to other proteins, and are fundamental to understanding cooperativity, allostery, and drug action. However, existing kinetic methods, such as surface plasmon resonance and biolayer interferometry (BLI), require immobilization or labeling of one binding partner and are often indirect measurements. Here, we introduce a transformative time-resolved native mass spectrometry (MS) approach that enables direct, label-free, and immobilization-free quantification of biomolecular kinetics across diverse interactions within minutes using only picomolar sample amounts. We benchmarked the approach using well-characterized systems and obtained kinetic parameters that agreed with those measured by BLI. We further demonstrate the utility of time-resolved native MS in quantifying the kinetics of protein-small-molecule interactions, including those involving an irreversible inhibitor. By capturing the association and dissociation of biomolecular interactions in real time, time-resolved native MS overcomes longstanding limitations of conventional kinetic assays and transforms native MS from a static technique to a dynamic, quantitative tool for probing biomolecular kinetics and mechanisms that underpin therapeutic discovery.


  • Organizational Affiliation
    • Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States.

Macromolecule Content 

  • Total Structure Weight: 164.04 kDa 
  • Atom Count: 11,330 
  • Modeled Residue Count: 1,451 
  • Deposited Residue Count: 1,476 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Green fluorescent proteinA,
C [auth B],
E,
G
239Aequorea victoriaMutation(s): 1 
Gene Names: gfp
UniProt
Find proteins for A0A059PIQ0 (Aequorea victoria)
Explore A0A059PIQ0 
Go to UniProtKB:  A0A059PIQ0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A059PIQ0
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Nanobody 15B [auth C],
D,
F,
H
130Lama glamaMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free:  0.331 (Depositor), 0.331 (DCC) 
  • R-Value Work:  0.295 (Depositor), 0.295 (DCC) 
  • R-Value Observed: 0.297 (Depositor) 
Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 169.05α = 90
b = 169.05β = 90
c = 70.79γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesRM1GM145416

Revision History  (Full details and data files)

  • Version 1.0: 2026-06-03
    Type: Initial release