7S6D | pdb_00007s6d

CryoEM structure of modular PKS holo-Lsd14 bound to antibody fragment 1B2, composite structure


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7S6D

This is version 1.2 of the entry. See complete history

Literature

Modular polyketide synthase contains two reaction chambers that operate asynchronously.

Bagde, S.R.Mathews, I.I.Fromme, J.C.Kim, C.Y.

(2021) Science 374: 723-729

  • DOI: https://doi.org/10.1126/science.abi8532
  • Primary Citation Related Structures: 
    7S6B, 7S6C, 7S6D

  • PubMed Abstract: 

    Type I modular polyketide synthases are homodimeric multidomain assembly line enzymes that synthesize a variety of polyketide natural products by performing polyketide chain extension and β-keto group modification reactions. We determined the 2.4-angstrom-resolution x-ray crystal structure and the 3.1-angstrom-resolution cryo–electron microscopy structure of the Lsd14 polyketide synthase, stalled at the transacylation and condensation steps, respectively. These structures revealed how the constituent domains are positioned relative to each other, how they rearrange depending on the step in the reaction cycle, and the specific interactions formed between the domains. Like the evolutionarily related mammalian fatty acid synthase, Lsd14 contains two reaction chambers, but only one chamber in Lsd14 has the full complement of catalytic domains, indicating that only one chamber produces the polyketide product at any given time.


  • Organizational Affiliation
    • Department of Chemistry and Biochemistry, The University of Texas at El Paso, El Paso, TX 79968, USA.

Macromolecule Content 

  • Total Structure Weight: 627.09 kDa 
  • Atom Count: 23,347 
  • Modeled Residue Count: 3,112 
  • Deposited Residue Count: 5,917 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
6-deoxyerythronolide-B synthase EryA2, modules 3 and 4, Lsd14 Polyketide synthase fusionA [auth C],
B [auth A],
C [auth B]
1,649Saccharopolyspora erythraeaStreptomyces lasalocidi
This entity is chimeric
Mutation(s): 0 
Gene Names: eryAlsd14
EC: 2.3.1.94
UniProt
Find proteins for B6ZK67 (Streptomyces lasalocidi)
Explore B6ZK67 
Go to UniProtKB:  B6ZK67
Find proteins for Q03132 (Saccharopolyspora erythraea)
Explore Q03132 
Go to UniProtKB:  Q03132
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsB6ZK67Q03132
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Fab 1B2 heavy chainD [auth E],
F [auth D]
249Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Fab 1B2 light chainE [auth G],
G [auth F]
236Homo sapiensMutation(s): 0 

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATR

Query on ATR



Download:Ideal Coordinates CCD File
H [auth C]2'-MONOPHOSPHOADENOSINE-5'-DIPHOSPHATE
C10 H16 N5 O13 P3
YPTPYQSAVGGMFN-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONPHENIX

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 StatesR35GM136258
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1R01GM138990
National Science Foundation (NSF, United States)United StatesDMR-1719875

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-03
    Type: Initial release
  • Version 1.1: 2021-11-17
    Changes: Database references
  • Version 1.2: 2024-11-20
    Changes: Data collection, Refinement description, Structure summary