8V32 | pdb_00008v32

TnsD-TnsC-DNA complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.01 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8V32

This is version 1.3 of the entry. See complete history

Literature

Structure of TnsABCD transpososome reveals mechanisms of targeted DNA transposition.

Wang, S.Siddique, R.Hall, M.C.Rice, P.A.Chang, L.

(2024) Cell 187: 6865-6881.e16

  • DOI: https://doi.org/10.1016/j.cell.2024.09.023
  • Primary Citation Related Structures: 
    8V32, 9BW1

  • PubMed Abstract: 

    Tn7-like transposons are characterized by their ability to insert specifically into host chromosomes. Recognition of the attachment (att) site by TnsD recruits the TnsABC proteins to form the transpososome and facilitate transposition. Although this pathway is well established, atomic-level structural insights of this process remain largely elusive. Here, we present the cryo-electron microscopy (cryo-EM) structures of the TnsC-TnsD-att DNA complex and the TnsABCD transpososome from the Tn7-like transposon in Peltigera membranacea cyanobiont 210A, a type I-B CRISPR-associated transposon. Our structures reveal a striking bending of the att DNA, featured by the intercalation of an arginine side chain of TnsD into a CC/GG dinucleotide step. The TnsABCD transpososome structure reveals TnsA-TnsB interactions and demonstrates that TnsC not only recruits TnsAB but also directly participates in the transpososome assembly. These findings provide mechanistic insights into targeted DNA insertion by Tn7-like transposons, with implications for improving the precision and efficiency of their genome-editing applications.


  • Organizational Affiliation
    • Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA.

Macromolecule Content 

  • Total Structure Weight: 410.66 kDa 
  • Atom Count: 24,592 
  • Modeled Residue Count: 2,904 
  • Deposited Residue Count: 3,303 
  • Unique protein chains: 2
  • Unique nucleic acid chains: 2

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
TnsC383Peltigera membranaceaMutation(s): 0 
Gene Names: CDG76_08990
UniProt
Find proteins for A0ACD6BA40 (Nostoc sp. 'Peltigera membranacea cyanobiont' 210A)
Explore A0ACD6BA40 
Go to UniProtKB:  A0ACD6BA40
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0ACD6BA40
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
TnsD462Peltigera membranaceaMutation(s): 0 
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (41-MER)80Peltigera membranacea
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  (by identity cutoff) 
Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (41-MER)80Peltigera membranacea
Sequence Annotations
Expand
Reference Sequence

Small Molecules

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

Query on ATP



Download:Ideal Coordinates CCD File
K [auth Q]
M [auth R]
O [auth S]
Q [auth T]
S [auth U]
K [auth Q],
M [auth R],
O [auth S],
Q [auth T],
S [auth U],
U [auth V],
W
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ZN
(Subject of Investigation/LOI)

Query on ZN



Download:Ideal Coordinates CCD File
Y [auth J],
Z [auth J]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
(Subject of Investigation/LOI)

Query on MG



Download:Ideal Coordinates CCD File
L [auth Q]
N [auth R]
P [auth S]
R [auth T]
T [auth U]
L [auth Q],
N [auth R],
P [auth S],
R [auth T],
T [auth U],
V,
X [auth W]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.01 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
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 States--

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-16
    Type: Initial release
  • Version 1.1: 2024-10-23
    Changes: Data collection, Database references
  • Version 1.2: 2024-12-11
    Changes: Data collection, Database references
  • Version 1.3: 2025-05-14
    Changes: Data collection