8Q4D

IstA-IstB(E167Q) Strand Transfer Complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.62 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Molecular basis for transposase activation by a dedicated AAA+ ATPase.

de la Gandara, A.Spinola-Amilibia, M.Araujo-Bazan, L.Nunez-Ramirez, R.Berger, J.M.Arias-Palomo, E.

(2024) Nature 630: 1003-1011

  • DOI: https://doi.org/10.1038/s41586-024-07550-6
  • Primary Citation of Related Structures:  
    8Q3W, 8Q4D

  • PubMed Abstract: 

    Transposases drive chromosomal rearrangements and the dissemination of drug-resistance genes and toxins 1-3 . Although some transposases act alone, many rely on dedicated AAA+ ATPase subunits that regulate site selectivity and catalytic function through poorly understood mechanisms. Using IS21 as a model transposase system, we show how an ATPase regulator uses nucleotide-controlled assembly and DNA deformation to enable structure-based site selectivity, transposase recruitment, and activation and integration. Solution and cryogenic electron microscopy studies show that the IstB ATPase self-assembles into an autoinhibited pentamer of dimers that tightly curves target DNA into a half-coil. Two of these decamers dimerize, which stabilizes the target nucleic acid into a kinked S-shaped configuration that engages the IstA transposase at the interface between the two IstB oligomers to form an approximately 1 MDa transpososome complex. Specific interactions stimulate regulator ATPase activity and trigger a large conformational change on the transposase that positions the catalytic site to perform DNA strand transfer. These studies help explain how AAA+ ATPase regulators-which are used by classical transposition systems such as Tn7, Mu and CRISPR-associated elements-can remodel their substrate DNA and cognate transposases to promote function.


  • Organizational Affiliation

    Centro de Investigaciones Biológicas Margarita Salas, CSIC, Madrid, Spain.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative transposase for insertion sequence element IS5376
A, B, C, D
373Geobacillus stearothermophilusMutation(s): 0 
UniProt
Find proteins for Q45618 (Geobacillus stearothermophilus)
Explore Q45618 
Go to UniProtKB:  Q45618
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ45618
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Insertion sequence IS5376 putative ATP-binding protein
E, F, G, H, I
E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X
247Geobacillus stearothermophilusMutation(s): 1 
UniProt
Find proteins for Q45619 (Geobacillus stearothermophilus)
Explore Q45619 
Go to UniProtKB:  Q45619
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ45619
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (118-MER) / TIR-transferred strandBA [auth d],
Y [auth a]
118Geobacillus stearothermophilus
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains LengthOrganismImage
DNA (58-MER) / TIR non-transferred strandCA [auth e],
Z [auth b]
58Geobacillus stearothermophilus
Sequence Annotations
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  • Reference Sequence
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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA (58-MER) / target-reverse complementAA [auth c],
DA [auth f]
58Geobacillus stearothermophilus
Sequence Annotations
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  • 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 
BB [auth P]
DB [auth Q]
FB [auth R]
HB [auth S]
IA [auth F]
BB [auth P],
DB [auth Q],
FB [auth R],
HB [auth S],
IA [auth F],
JB [auth T],
KA [auth G],
LB [auth U],
MA [auth H],
NB [auth V],
OA [auth I],
PB [auth W],
QA [auth J],
RB [auth X],
SA [auth K],
UA [auth L],
WA [auth M],
YA [auth N]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
GA [auth E],
ZA [auth O]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
AB [auth P]
CB [auth Q]
EA [auth A]
EB [auth R]
FA [auth B]
AB [auth P],
CB [auth Q],
EA [auth A],
EB [auth R],
FA [auth B],
GB [auth S],
HA [auth F],
IB [auth T],
JA [auth G],
KB [auth U],
LA [auth H],
MB [auth V],
NA [auth I],
OB [auth W],
PA [auth J],
QB [auth X],
RA [auth K],
TA [auth L],
VA [auth M],
XA [auth N]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.62 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19
RECONSTRUCTIONRELION4.0

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Spanish Ministry of Science, Innovation, and UniversitiesSpainPID2020-120275GB-I00
Spanish Ministry of Science, Innovation, and UniversitiesSpainPRE2018-086026

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-10
    Type: Initial release