7LW1 | pdb_00007lw1

Human phosphofructokinase-1 liver type bound to activator NA-11


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 7LW1

This is version 1.1 of the entry. See complete history

Literature

Selective activation of PFKL suppresses the phagocytic oxidative burst.

Amara, N.Cooper, M.P.Voronkova, M.A.Webb, B.A.Lynch, E.M.Kollman, J.M.Ma, T.Yu, K.Lai, Z.Sangaraju, D.Kayagaki, N.Newton, K.Bogyo, M.Staben, S.T.Dixit, V.M.

(2021) Cell 184: 4480-4494.e15

  • DOI: https://doi.org/10.1016/j.cell.2021.07.004
  • Primary Citation Related Structures: 
    7LW1

  • PubMed Abstract: 

    In neutrophils, nicotinamide adenine dinucleotide phosphate (NADPH) generated via the pentose phosphate pathway fuels NADPH oxidase NOX2 to produce reactive oxygen species for killing invading pathogens. However, excessive NOX2 activity can exacerbate inflammation, as in acute respiratory distress syndrome (ARDS). Here, we use two unbiased chemical proteomic strategies to show that small-molecule LDC7559, or a more potent designed analog NA-11, inhibits the NOX2-dependent oxidative burst in neutrophils by activating the glycolytic enzyme phosphofructokinase-1 liver type (PFKL) and dampening flux through the pentose phosphate pathway. Accordingly, neutrophils treated with NA-11 had reduced NOX2-dependent outputs, including neutrophil cell death (NETosis) and tissue damage. A high-resolution structure of PFKL confirmed binding of NA-11 to the AMP/ADP allosteric activation site and explained why NA-11 failed to agonize phosphofructokinase-1 platelet type (PFKP) or muscle type (PFKM). Thus, NA-11 represents a tool for selective activation of PFKL, the main phosphofructokinase-1 isoform expressed in immune cells.


  • Organizational Affiliation
    • Physiological Chemistry Department, Genentech, South San Francisco, CA 94080, USA.

Macromolecule Content 

  • Total Structure Weight: 346.2 kDa 
  • Atom Count: 23,088 
  • Modeled Residue Count: 2,976 
  • Deposited Residue Count: 3,120 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP-dependent 6-phosphofructokinase, liver typeA,
B [auth D],
C [auth E],
D [auth F]
780Homo sapiensMutation(s): 0 
Gene Names: PFKL
EC: 2.7.1.11
UniProt & NIH Common Fund Data Resources
Find proteins for P17858 (Homo sapiens)
Explore P17858 
Go to UniProtKB:  P17858
PHAROS:  P17858
GTEx:  ENSG00000141959 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17858
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP

Query on ADP



Download:Ideal Coordinates CCD File
H [auth A],
L [auth D],
P [auth E],
T [auth F]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
YG1
(Subject of Investigation/LOI)

Query on YG1



Download:Ideal Coordinates CCD File
E [auth A],
I [auth D],
M [auth E],
Q [auth F]
N-{(11S)-2-[2-(5-hydroxypent-1-yn-1-yl)phenyl]-4H,10H-pyrazolo[5,1-c][1,4]benzoxazepin-7-yl}acetamide
C24 H23 N3 O3
VVMOXIHBNMUNFJ-UHFFFAOYSA-N
FBP

Query on FBP



Download:Ideal Coordinates CCD File
F [auth A],
J [auth D],
N [auth E],
R [auth F]
1,6-di-O-phosphono-beta-D-fructofuranose
C6 H14 O12 P2
RNBGYGVWRKECFJ-ARQDHWQXSA-N
F6P

Query on F6P



Download:Ideal Coordinates CCD File
G [auth A],
K [auth D],
O [auth E],
S [auth F]
6-O-phosphono-beta-D-fructofuranose
C6 H13 O9 P
BGWGXPAPYGQALX-ARQDHWQXSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1
MODEL REFINEMENTISOLDE1

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM118396

Revision History  (Full details and data files)

  • Version 1.0: 2022-01-26
    Type: Initial release
  • Version 1.1: 2024-05-29
    Changes: Data collection