8EMT

Cryo-EM analysis of the human aldehyde oxidase from liver

  • Classification: OXIDOREDUCTASE
  • Organism(s): Homo sapiens
  • Mutation(s): No 

  • Deposited: 2022-09-28 Released: 2023-05-10 
  • Deposition Author(s): Su, C., Lyu, M., Zhang, Z., Yu, E.W.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.92 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

High-resolution structural-omics of human liver enzymes.

Su, C.C.Lyu, M.Zhang, Z.Miyagi, M.Huang, W.Taylor, D.J.Yu, E.W.

(2023) Cell Rep 42: 112609-112609

  • DOI: https://doi.org/10.1016/j.celrep.2023.112609
  • Primary Citation of Related Structures:  
    7UZM, 8EKW, 8EKY, 8EM2, 8EMR, 8EMS, 8EMT, 8ENE, 8EOJ, 8EOR

  • PubMed Abstract: 

    We applied raw human liver microsome lysate to a holey carbon grid and used cryo-electron microscopy (cryo-EM) to define its composition. From this sample we identified and simultaneously determined high-resolution structural information for ten unique human liver enzymes involved in diverse cellular processes. Notably, we determined the structure of the endoplasmic bifunctional protein H6PD, where the N- and C-terminal domains independently possess glucose-6-phosphate dehydrogenase and 6-phosphogluconolactonase enzymatic activity, respectively. We also obtained the structure of heterodimeric human GANAB, an ER glycoprotein quality-control machinery that contains a catalytic α subunit and a noncatalytic β subunit. In addition, we observed a decameric peroxidase, PRDX4, which directly contacts a disulfide isomerase-related protein, ERp46. Structural data suggest that several glycosylations, bound endogenous compounds, and ions associate with these human liver enzymes. These results highlight the importance of cryo-EM in facilitating the elucidation of human organ proteomics at the atomic level.


  • Organizational Affiliation

    Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aldehyde oxidaseA [auth B],
B [auth A]
1,338Homo sapiensMutation(s): 0 
EC: 1.2.3.1 (PDB Primary Data), 1.17.3 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q06278 (Homo sapiens)
Explore Q06278 
Go to UniProtKB:  Q06278
PHAROS:  Q06278
GTEx:  ENSG00000138356 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ06278
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD (Subject of Investigation/LOI)
Query on FAD

Download Ideal Coordinates CCD File 
G [auth B],
L [auth A]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
MTE
Query on MTE

Download Ideal Coordinates CCD File 
E [auth B],
J [auth A]
PHOSPHONIC ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER
C10 H14 N5 O6 P S2
HPEUEJRPDGMIMY-IFQPEPLCSA-N
FES
Query on FES

Download Ideal Coordinates CCD File 
C [auth B],
D [auth B],
H [auth A],
I [auth A]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
MOS
Query on MOS

Download Ideal Coordinates CCD File 
F [auth B],
K [auth A]
DIOXOTHIOMOLYBDENUM(VI) ION
H Mo O2 S
BDSRWPHSAKXXRG-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.92 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-10
    Type: Initial release
  • Version 1.1: 2023-11-15
    Changes: Data collection, Database references