9CQS | pdb_00009cqs

Human OxyHb (C1 symmetry) obtained using the SPT Labtech chameleon In the presence of 5 mM sodium dithionite under Al's oil


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.52 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Preparation of oxygen-sensitive proteins for high-resolution cryoEM structure determination using blot-free vitrification.

Cook, B.D.Narehood, S.M.McGuire, K.L.Li, Y.Akif Tezcan, F.Herzik Jr., M.A.

(2025) Nat Commun 16: 3528-3528

  • DOI: https://doi.org/10.1038/s41467-025-58243-1
  • Primary Citation of Related Structures:  
    9CQM, 9CQN, 9CQO, 9CQP, 9CQQ, 9CQR, 9CQS, 9CQT, 9CQU, 9CQV, 9CQW, 9CQX, 9CQY, 9CQZ, 9CR0, 9MLY, 9MLZ, 9MM0, 9MM1

  • PubMed Abstract: 

    High-quality grid preparation for single-particle cryogenic electron microscopy (cryoEM) remains a bottleneck for routinely obtaining high-resolution structures. The issues that arise from traditional grid preparation workflows are particularly exacerbated for oxygen-sensitive proteins, including metalloproteins, whereby oxygen-induced damage and alteration of oxidation states can result in protein inactivation, denaturation, and/or aggregation. Indeed, 99% of the current structures in the EMBD were prepared aerobically and limited successes for anaerobic cryoEM grid preparation exist. Current practices for anaerobic grid preparation involve a vitrification device located in an anoxic chamber, which presents significant challenges including temperature and humidity control, optimization of freezing conditions, costs for purchase and operation, as well as accessibility. Here, we present a streamlined approach that allows for the vitrification of oxygen-sensitive proteins in reduced states using an automated blot-free grid vitrification device - the SPT Labtech chameleon. This robust workflow allows for high-resolution structure determination of dynamic, oxygen-sensitive proteins, of varying complexity and molecular weight.


  • Organizational Affiliation
    • Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hemoglobin subunit alpha
A, C
139Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P69905 (Homo sapiens)
Explore P69905 
Go to UniProtKB:  P69905
PHAROS:  P69905
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP69905
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Hemoglobin subunit beta
B, D
145Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P68871 (Homo sapiens)
Explore P68871 
Go to UniProtKB:  P68871
PHAROS:  P68871
GTEx:  ENSG00000244734 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68871
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM (Subject of Investigation/LOI)
Query on HEM

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B],
I [auth C],
K [auth D]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
OXY (Subject of Investigation/LOI)
Query on OXY

Download Ideal Coordinates CCD File 
F [auth A],
H [auth B],
J [auth C],
L [auth D]
OXYGEN MOLECULE
O2
MYMOFIZGZYHOMD-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.52 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTPHENIX1.21.1_5286

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 States5R35GM138206
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States5R01GM148607-02
Other privateSearle Scholars

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-30
    Type: Initial release
  • Version 1.1: 2025-08-20
    Changes: Data collection, Experimental preparation