8W2G

Human liver phosphofructokinase-1 in the R-state conformation


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis for allosteric regulation of human phosphofructokinase-1.

Lynch, E.M.Hansen, H.Salay, L.Cooper, M.Timr, S.Kollman, J.M.Webb, B.A.

(2024) Nat Commun 15: 7323-7323

  • DOI: https://doi.org/10.1038/s41467-024-51808-6
  • Primary Citation of Related Structures:  
    8W2G, 8W2H, 8W2J

  • PubMed Abstract: 

    Phosphofructokinase-1 (PFK1) catalyzes the rate-limiting step of glycolysis, committing glucose to conversion into cellular energy. PFK1 is highly regulated to respond to the changing energy needs of the cell. In bacteria, the structural basis of PFK1 regulation is a textbook example of allostery; molecular signals of low and high cellular energy promote transition between an active R-state and inactive T-state conformation, respectively. Little is known, however, about the structural basis for regulation of eukaryotic PFK1. Here, we determine structures of the human liver isoform of PFK1 (PFKL) in the R- and T-state by cryoEM, providing insight into eukaryotic PFK1 allosteric regulatory mechanisms. The T-state structure reveals conformational differences between the bacterial and eukaryotic enzyme, the mechanisms of allosteric inhibition by ATP binding at multiple sites, and an autoinhibitory role of the C-terminus in stabilizing the T-state. We also determine structures of PFKL filaments that define the mechanism of higher-order assembly and demonstrate that these structures are necessary for higher-order assembly of PFKL in cells.


  • Organizational Affiliation

    Department of Biochemistry, University of Washington, Seattle, WA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-dependent 6-phosphofructokinase, liver typeA,
B [auth D],
C [auth B],
D [auth C]
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 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
K [auth D]
L [auth D]
F [auth A],
G [auth A],
H [auth A],
K [auth D],
L [auth D],
M [auth D],
P [auth B],
Q [auth B],
R [auth B],
U [auth C],
V [auth C],
W [auth C]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
FBP (Subject of Investigation/LOI)
Query on FBP

Download Ideal Coordinates CCD File 
I [auth A],
N [auth D],
S [auth B],
X [auth C]
1,6-di-O-phosphono-beta-D-fructofuranose
C6 H14 O12 P2
RNBGYGVWRKECFJ-ARQDHWQXSA-N
F6P (Subject of Investigation/LOI)
Query on F6P

Download Ideal Coordinates CCD File 
E [auth A],
J [auth D],
O [auth B],
T [auth C]
6-O-phosphono-beta-D-fructofuranose
C6 H13 O9 P
BGWGXPAPYGQALX-ARQDHWQXSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTISOLDE
MODEL REFINEMENTPHENIX

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 StatesR35 GM149542

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-11
    Type: Initial release
  • Version 1.1: 2024-09-18
    Changes: Data collection, Database references
  • Version 1.2: 2024-09-25
    Changes: Data collection, Database references