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- PDB-9lqo: Structure of RAG transposon end complex (TEC) -

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Basic information

Entry
Database: PDB / ID: 9lqo
TitleStructure of RAG transposon end complex (TEC)
Components
  • (V(D)J recombination-activating protein ...) x 2
  • 12RSS bottom strand
  • 12RSS top strand
  • 23RSS bottom strand
  • 23RSS top strand
KeywordsDNA BINDING PROTEIN/DNA / RAG / Transposase / TEC / evolution / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


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 organ growth / pre-B cell allelic exclusion / V(D)J recombination / negative regulation of thymocyte apoptotic process ...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 organ growth / pre-B cell allelic exclusion / V(D)J recombination / 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 / regulation of T cell differentiation / T cell homeostasis / positive regulation of T cell differentiation / phosphatidylinositol-3,4,5-trisphosphate binding / T cell differentiation / thymus development / protein autoubiquitination / B cell differentiation / phosphatidylinositol-4,5-bisphosphate binding / T cell differentiation in thymus / phosphatidylinositol binding / visual learning / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / endonuclease activity / DNA recombination / histone binding / chromatin organization / sequence-specific DNA binding / Hydrolases; Acting on ester bonds / adaptive immune response / defense response to bacterium / hydrolase activity / chromatin binding / protein homodimerization activity / nucleoplasm / zinc ion binding / metal ion binding / identical protein binding / nucleus
Similarity search - Function
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 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, RING-type, conserved site / Zinc finger RING-type signature. / Zinc finger C2H2 superfamily / Ring finger / 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) / 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 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: V(D)J recombination-activating protein 2
C: V(D)J recombination-activating protein 1
D: V(D)J recombination-activating protein 2
F: 12RSS bottom strand
L: 12RSS top strand
G: 23RSS bottom strand
M: 23RSS top strand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)300,94512
Polymers300,7658
Non-polymers1794
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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V(D)J recombination-activating protein ... , 2 types, 4 molecules ACBD

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


Mass: 85690.727 Da / Num. of mol.: 2 / Mutation: E662A, S721A, S723A, and R848M
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 V(D)J recombination-activating protein 2 / RAG-2


Mass: 40374.816 Da / Num. of mol.: 2 / Mutation: K58E and K119A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rag2, Rag-2 / Production host: Homo sapiens (human) / References: UniProt: P21784

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DNA chain , 4 types, 4 molecules FLGM

#3: DNA chain 12RSS bottom strand


Mass: 10456.710 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain 12RSS top strand


Mass: 10461.758 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: DNA chain 23RSS bottom strand


Mass: 13837.883 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)

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Non-polymers , 2 types, 4 molecules

#7: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / 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: RAG transposon end complex / Type: COMPLEX / Entity ID: #1-#6 / 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: GATAN K2 QUANTUM (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 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 822335 / Symmetry type: POINT
RefinementHighest resolution: 3 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00315708
ELECTRON MICROSCOPYf_angle_d0.51121480
ELECTRON MICROSCOPYf_dihedral_angle_d16.9622561
ELECTRON MICROSCOPYf_chiral_restr0.0412344
ELECTRON MICROSCOPYf_plane_restr0.0042557

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