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- PDB-9lqv: Structure of transposase-activated RAG strand transfer complex in... -

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Basic information

Entry
Database: PDB / ID: 9lqv
TitleStructure of transposase-activated RAG strand transfer complex in state 1 (STC-1)
Components
  • (Flanking DNA in target DNA ...) x 2
  • 12RSS integration strand
  • 12RSS top strand
  • 23RSS integration strand
  • 23RSS top strand
  • Early growth response protein 1,V(D)J recombination-activating protein 2
  • V(D)J recombination-activating protein 1
KeywordsDNA BINDING PROTEIN/DNA / RAG / Transposase / STC / evolution / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


regulation of protein sumoylation / glomerular mesangial cell proliferation / positive regulation of glomerular metanephric mesangial cell proliferation / cellular response to interleukin-8 / positive regulation of post-translational protein modification / regulation of progesterone biosynthetic process / cellular response to heparin / cellular response to mycophenolic acid / circadian temperature homeostasis / B cell homeostatic proliferation ...regulation of protein sumoylation / glomerular mesangial cell proliferation / positive regulation of glomerular metanephric mesangial cell proliferation / cellular response to interleukin-8 / positive regulation of post-translational protein modification / regulation of progesterone biosynthetic process / cellular response to heparin / cellular response to mycophenolic acid / circadian temperature homeostasis / B cell homeostatic proliferation / mature B cell differentiation involved in immune response / negative regulation of T cell differentiation in thymus / DNA recombinase complex / endodeoxyribonuclease complex / negative regulation of T cell apoptotic process / positive regulation of hormone biosynthetic process / double-stranded methylated DNA binding / positive regulation of organ growth / pre-B cell allelic exclusion / hemi-methylated DNA-binding / V(D)J recombination / positive regulation of gene expression via chromosomal CpG island demethylation / negative regulation of thymocyte apoptotic process / phosphatidylinositol-3,4-bisphosphate binding / regulation of behavioral fear response / histone H3K4me3 reader activity / phosphatidylinositol-3,5-bisphosphate binding / T cell lineage commitment / B cell lineage commitment / positive regulation of smooth muscle cell migration / interleukin-1-mediated signaling pathway / regulation of T cell differentiation / T cell homeostasis / positive regulation of T cell differentiation / histone acetyltransferase binding / locomotor rhythm / skeletal muscle cell differentiation / phosphatidylinositol-3,4,5-trisphosphate binding / T cell differentiation / BMP signaling pathway / response to glucose / thymus development / estrous cycle / RNA polymerase II core promoter sequence-specific DNA binding / long-term memory / protein autoubiquitination / positive regulation of chemokine production / B cell differentiation / phosphatidylinositol-4,5-bisphosphate binding / T cell differentiation in thymus / positive regulation of smooth muscle cell proliferation / response to ischemia / regulation of neuron apoptotic process / phosphatidylinositol binding / positive regulation of interleukin-1 beta production / RNA polymerase II transcription regulatory region sequence-specific DNA binding / circadian regulation of gene expression / regulation of long-term neuronal synaptic plasticity / negative regulation of canonical Wnt signaling pathway / promoter-specific chromatin binding / visual learning / response to insulin / cellular response to gamma radiation / RING-type E3 ubiquitin transferase / positive regulation of miRNA transcription / sequence-specific double-stranded DNA binding / ubiquitin-protein transferase activity / positive regulation of neuron apoptotic process / ubiquitin protein ligase activity / endonuclease activity / double-stranded DNA binding / DNA recombination / DNA-binding transcription activator activity, RNA polymerase II-specific / histone binding / chromatin organization / regulation of apoptotic process / sequence-specific DNA binding / Hydrolases; Acting on ester bonds / adaptive immune response / response to hypoxia / DNA-binding transcription factor activity, RNA polymerase II-specific / learning or memory / defense response to bacterium / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / hydrolase activity / positive regulation of gene expression / chromatin binding / regulation of transcription by RNA polymerase II / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / enzyme binding / positive regulation of transcription by RNA polymerase II / protein homodimerization activity / DNA binding / nucleoplasm / zinc ion binding
Similarity search - Function
Early growth response protein 1, C-terminal / Early growth response, N-terminal / Domain of unknown function (DUF3432) / Early growth response N-terminal domain / Recombination-activating protein 1 zinc-finger domain / V(D)J recombination-activating protein 1, Zinc finger / : / NBD domain profile. / Zinc finger RAG1-type profile. / RAG nonamer-binding domain ...Early growth response protein 1, C-terminal / Early growth response, N-terminal / Domain of unknown function (DUF3432) / Early growth response N-terminal domain / Recombination-activating protein 1 zinc-finger domain / V(D)J recombination-activating protein 1, Zinc finger / : / NBD domain profile. / Zinc finger RAG1-type profile. / RAG nonamer-binding domain / V(D)J recombination-activating protein 1 / RAG1 importin-binding / : / : / : / : / : / : / Recombination activating protein 2 / RAG1 importin binding / Recombination-activation protein 1 (RAG1) nonamer-binding domain / RAG2 PHD domain / Recombination-activation protein 1 (RAG1) DNA-binding domain / Recombination-activation protein 1 (RAG1) pre-RNase H domain / Recombination-activation protein 1 (RAG1) RNase H domain / Recombination-activation protein 1 (RAG1) ZnC2 domain / Recombination-activation protein 1 (RAG1) ZnH2 domain / Recombination-activation protein 1 (RAG1) C-terminal domain / V-D-J recombination activating protein 2 / Recombination activating protein 2, PHD domain / Galactose oxidase/kelch, beta-propeller / Kelch-type beta propeller / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Zinc finger, C2H2 type / zinc finger / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Ring finger / Zinc finger C2H2-type / Zinc finger, FYVE/PHD-type / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
DNA / DNA (> 10) / Early growth response protein 1 / V(D)J recombination-activating protein 1 / V(D)J recombination-activating protein 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsPang, J. / Zhang, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171250 China
CitationJournal: To Be Published
Title: Structural basis and dynamics of target capture and integration during cut-and-paste transposition
Authors: Pang, J. / Martin, E.C. / Zheng, X. / Lu, Q. / Schatz, D.G. / Zhang, Y.
History
DepositionJan 28, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 5, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: V(D)J recombination-activating protein 1
B: Early growth response protein 1,V(D)J recombination-activating protein 2
C: V(D)J recombination-activating protein 1
D: Early growth response protein 1,V(D)J recombination-activating protein 2
I: Flanking DNA in target DNA bottom strand
J: Flanking DNA in target DNA top strand
x: 23RSS integration strand
M: 23RSS top strand
y: 12RSS integration strand
L: 12RSS top strand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)378,97215
Polymers378,76810
Non-polymers2045
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein V(D)J recombination-activating protein 1 / RAG-1


Mass: 85780.766 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rag1 / Production host: Homo sapiens (human)
References: UniProt: P15919, Hydrolases; Acting on ester bonds, RING-type E3 ubiquitin transferase
#2: Protein Early growth response protein 1,V(D)J recombination-activating protein 2 / EGR-1 / Nerve growth factor-induced protein A / NGFI-A / Transcription factor Zif268 / Zinc finger ...EGR-1 / Nerve growth factor-induced protein A / NGFI-A / Transcription factor Zif268 / Zinc finger protein Krox-24 / RAG-2


Mass: 51195.125 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Zinc finger domain fused to the N-terminal of transposase-activated RAG2 (with deletion of residues 336-341) via a flexible linker.
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Egr1, Egr-1, Krox-24, Rag2, Rag-2 / Production host: Homo sapiens (human) / References: UniProt: P08046, UniProt: P21784

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Flanking DNA in target DNA ... , 2 types, 2 molecules IJ

#3: DNA chain Flanking DNA in target DNA bottom strand


Mass: 18061.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain Flanking DNA in target DNA top strand


Mass: 18305.699 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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DNA chain , 4 types, 4 molecules xMyL

#5: DNA chain 23RSS integration strand


Mass: 23655.125 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#6: DNA chain 23RSS top strand


Mass: 13877.906 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#7: DNA chain 12RSS integration strand


Mass: 20454.061 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#8: DNA chain 12RSS top strand


Mass: 10461.758 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 2 types, 5 molecules

#9: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Transposase-activated RAG strand transfer complex in state 1
Type: COMPLEX / Entity ID: #1-#8 / Source: RECOMBINANT
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMPotassium chlorideKCl1
22 mMMagnesium chlorideMgCl21
320 mM4-(2-Hydroxyethyl)Piperazine-1-Ethan sulfonic AcidHEPES1
40.5 mMTris(2-carboxyethyl)phosphineTCEP1
SpecimenConc.: 0.15 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 303 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
12cryoSPARC3D reconstruction
13PHENIX1.21.2_5419model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 81808 / Symmetry type: POINT
RefinementHighest resolution: 3.1 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00417049
ELECTRON MICROSCOPYf_angle_d0.58723525
ELECTRON MICROSCOPYf_dihedral_angle_d21.8213172
ELECTRON MICROSCOPYf_chiral_restr0.0422569
ELECTRON MICROSCOPYf_plane_restr0.0052632

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