6X67

Cryo-EM structure of piggyBac transposase strand transfer complex (STC)

PDB DOI: https://doi.org/10.2210/pdb6X67/pdb
NAKB: 6X67
EM Map EMD-22072: EMDB EMDataResource

Classification: DNA BINDING PROTEIN/DNA
Organism(s): Trichoplusia ni
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2020-05-27 Released: 2020-07-22
Deposition Author(s): Chen, Q., Hickman, A.B., Dyda, F.
Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.47 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structural basis of seamless excision and specific targeting by piggyBac transposase

Chen, Q., Luo, W., Veach, R.A., Hickman, A.B., Wilson, M.H., Dyda, F.

(2020) Nat Commun 11: 3446-3446

DOI: https://doi.org/10.1038/s41467-020-17128-1

Macromolecule Content

Total Structure Weight: 193.1 kDa
Atom Count: 10,984
Modelled Residue Count: 1,116
Deposited Residue Count: 1,372
Unique protein chains: 1
Unique nucleic acid chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transposase	A [auth C], B [auth D]	594	Trichoplusia ni	Mutation(s): 1
UniProt
Find proteins for Q283G1 (Trichoplusia ni) Explore Q283G1 Go to UniProtKB: Q283G1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q283G1
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (37-MER)	C [auth E], F [auth J]	37	Trichoplusia ni
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (47-MER)	D [auth F], G [auth K]	47	Trichoplusia ni
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (tDNA)	E [auth G], H [auth L]	8	Trichoplusia ni
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain I [auth C] SDF format, chain J [auth C] SDF format, chain M [auth D] SDF format, chain N [auth D] MOL2 format, chain I [auth C] MOL2 format, chain J [auth C] MOL2 format, chain M [auth D] MOL2 format, chain N [auth D] mmCIF format, chain I [auth C] mmCIF format, chain J [auth C] mmCIF format, chain M [auth D] mmCIF format, chain N [auth D]	I [auth C], J [auth C], M [auth D], N [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain I [auth C] Focus chain J [auth C] Focus chain M [auth D] Focus chain N [auth D] Interactions & Density Focus chain I [auth C] Focus chain J [auth C] Focus chain M [auth D] Focus chain N [auth D]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain K [auth C] SDF format, chain L [auth C] SDF format, chain O [auth D] SDF format, chain P [auth D] MOL2 format, chain K [auth C] MOL2 format, chain L [auth C] MOL2 format, chain O [auth D] MOL2 format, chain P [auth D] mmCIF format, chain K [auth C] mmCIF format, chain L [auth C] mmCIF format, chain O [auth D] mmCIF format, chain P [auth D]	K [auth C], L [auth C], O [auth D], P [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain K [auth C] Focus chain L [auth C] Focus chain O [auth D] Focus chain P [auth D] Interactions & Density Focus chain K [auth C] Focus chain L [auth C] Focus chain O [auth D] Focus chain P [auth D]