9LQQ | pdb_00009lqq

Structure of transposase-activated RAG target capture complex with X-form U-shaped target DNA (TCC-UDX)

PDB DOI: https://doi.org/10.2210/pdb9LQQ/pdb
EM Map EMD-63301: EMDB EMDataResource

Classification: DNA BINDING PROTEIN/DNA
Organism(s): synthetic construct, Mus musculus
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2025-01-28 Released: 2026-08-05
Deposition Author(s): Pang, J., Zhang, Y.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9LQQ

This is version 1.0 of the entry. See complete history.

Literature

Structural basis and dynamics of target capture and integration during cut-and-paste transposition

Pang, J., Martin, E.C., Zheng, X., Lu, Q., Schatz, D.G., Zhang, Y.

To be published.

Macromolecule Content

Total Structure Weight: 359.08 kDa
Atom Count: 16,144
Modeled Residue Count: 1,863
Deposited Residue Count: 2,690
Unique protein chains: 2
Unique nucleic acid chains: 6

Macromolecules

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
V(D)J recombination-activating protein 1	C [auth A], E [auth C]	750	Mus musculus	Mutation(s): 1 Gene Names: Rag1 EC: 3.1 (PDB Primary Data), 2.3.2.27 (PDB Primary Data)
UniProt
Find proteins for P15919 (Mus musculus) Explore P15919 Go to UniProtKB: P15919
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P15919
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Early growth response protein 1,V(D)J recombination-activating protein 2	D [auth B], F [auth D]	457	Mus musculus	Mutation(s): 0 Gene Names: Egr1, Egr-1, Krox-24, Rag2, Rag-2
UniProt & NIH Common Fund Data Resources
Find proteins for P08046 (Mus musculus) Explore P08046 Go to UniProtKB: P08046
IMPC: MGI:95295
Find proteins for P21784 (Mus musculus) Explore P21784 Go to UniProtKB: P21784
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	P08046 P21784
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism	Image
Entity ID: 1
Target DNA bottom strand	A [auth I]	59	synthetic construct
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism	Image
Entity ID: 2
Target DNA top strand	B [auth J]	59	synthetic construct
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism	Image
Entity ID: 5
12RSS top strand	G [auth L]	34	synthetic construct
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism	Image
Entity ID: 6
12RSS bottom strand	H [auth y]	34	synthetic construct
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism	Image
Entity ID: 7
23RSS top strand	I [auth M]	45	synthetic construct
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Reference Sequence

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Molecule	Chains	Length	Organism	Image
Entity ID: 8
23RSS bottom strand	J [auth x]	45	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain L [auth C] MOL2 format, chain K [auth A] MOL2 format, chain L [auth C] mmCIF format, chain K [auth A] mmCIF format, chain L [auth C]	K [auth A], L [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain L [auth C] Interactions & Density Focus chain K [auth A] Focus chain L [auth C]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain M [auth C] MOL2 format, chain M [auth C] mmCIF format, chain M [auth C]	M [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain M [auth C] Interactions & Density Focus chain M [auth C]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-08-05

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32171250

Revision History (Full details and data files)

Version 1.0: 2026-08-05
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.