8ZD3 | pdb_00008zd3

Crystal structure of ALPK1-N+K in complex with CDP-heptose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.269 (Depositor), 0.269 (DCC) 
  • R-Value Work: 
    0.240 (Depositor), 0.239 (DCC) 
  • R-Value Observed: 
    0.241 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8ZD3

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

The beta-d-manno-heptoses are immune agonists across kingdoms.

Tang, Y.Tian, X.Wang, M.Cui, Y.She, Y.Shi, Z.Liu, J.Mao, H.Liu, L.Li, C.Zhang, Y.Li, P.Ma, Y.Sun, J.Du, Q.Li, J.Wang, J.Li, D.F.Wu, B.Shao, F.Chen, Y.

(2024) Science 385: 678-684

  • DOI: https://doi.org/10.1126/science.adk7314
  • Primary Citation Related Structures: 
    8ZD3

  • PubMed Abstract: 

    Bacterial small molecule metabolites such as adenosine-diphosphate-d- glycero -β-d- manno -heptose (ADP-heptose) and their derivatives act as effective innate immune agonists in mammals. We show that functional nucleotide-diphosphate-heptose biosynthetic enzymes (HBEs) are distributed widely in bacteria, archaea, eukaryotes, and viruses. We identified a conserved STT R5 motif as a hallmark of heptose nucleotidyltransferases that can synthesize not only ADP-heptose but also cytidine-diphosphate (CDP)- and uridine-diphosphate (UDP)-heptose. Both CDP- and UDP-heptoses are agonists that trigger stronger alpha-protein kinase 1 (ALPK1)-dependent immune responses than ADP-heptose in human and mouse cells and mice. We also produced ADP-heptose in archaea and verified its innate immune agonist functions. Hence, the β-d- manno -heptoses are cross-kingdom, small-molecule, pathogen-associated molecular patterns that activate the ALPK1-dependent innate immune signaling cascade.


  • Organizational Affiliation
    • State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.

Macromolecule Content 

  • Total Structure Weight: 169.84 kDa 
  • Atom Count: 11,342 
  • Modeled Residue Count: 1,378 
  • Deposited Residue Count: 1,484 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Alpha-protein kinase 1
A, C
456Homo sapiensMutation(s): 0 
Gene Names: ALPK1KIAA1527LAK
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q96QP1 (Homo sapiens)
Explore Q96QP1 
Go to UniProtKB:  Q96QP1
PHAROS:  Q96QP1
GTEx:  ENSG00000073331 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96QP1
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Alpha-protein kinase 1
B, D
286Homo sapiensMutation(s): 0 
Gene Names: ALPK1KIAA1527LAK
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q96QP1 (Homo sapiens)
Explore Q96QP1 
Go to UniProtKB:  Q96QP1
PHAROS:  Q96QP1
GTEx:  ENSG00000073331 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96QP1
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDP
(Subject of Investigation/LOI)

Query on CDP



Download:Ideal Coordinates CCD File
E [auth A],
H [auth C]
CYTIDINE-5'-DIPHOSPHATE
C9 H15 N3 O11 P2
ZWIADYZPOWUWEW-XVFCMESISA-N
A1L1P
(Subject of Investigation/LOI)

Query on A1L1P



Download:Ideal Coordinates CCD File
F [auth A],
I [auth C]
(2R,3S,4S,5S,6R)-6-[(1S)-1,2-bis(oxidanyl)ethyl]oxane-2,3,4,5-tetrol
C7 H14 O7
BGWQRWREUZVRGI-KLJZZCKASA-N
ZN
(Subject of Investigation/LOI)

Query on ZN



Download:Ideal Coordinates CCD File
G [auth B],
J [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.269 (Depositor), 0.269 (DCC) 
  • R-Value Work:  0.240 (Depositor), 0.239 (DCC) 
  • R-Value Observed: 0.241 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.787α = 89.619
b = 65.944β = 107.771
c = 108.679γ = 111.122
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-07
    Type: Initial release
  • Version 1.1: 2025-11-19
    Changes: Database references