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- EMDB-63301: Structure of transposase-activated RAG target capture complex wit... -

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Entry
Database: EMDB / ID: EMD-63301
TitleStructure of transposase-activated RAG target capture complex with X-form U-shaped target DNA (TCC-UDX)
Map data
Sample
  • Complex: Transposase-activated RAG target capture complex with X-form U-shaped target DNA
    • DNA: Target DNA bottom strand
    • DNA: Target DNA top strand
    • Protein or peptide: V(D)J recombination-activating protein 1
    • Protein or peptide: Early growth response protein 1,V(D)J recombination-activating protein 2
    • DNA: 12RSS top strand
    • DNA: 12RSS bottom strand
    • DNA: 23RSS top strand
    • DNA: 23RSS bottom strand
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
KeywordsRAG / Transposase / TCC / evolution / DNA BINDING PROTEIN/DNA / 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
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsPang J / Zhang Y
Funding support China, 1 items
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 EC / Zheng X / Lu Q / Schatz DG / Zhang Y
History
DepositionJan 28, 2025-
Header (metadata) releaseAug 5, 2026-
Map releaseAug 5, 2026-
UpdateAug 5, 2026-
Current statusAug 5, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63301.png

Downloads & links

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Map

FileDownload / File: emd_63301.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 320 pix.
= 352. Å		1.1 Å/pix.
x 320 pix.
= 352. Å		1.1 Å/pix.
x 320 pix.
= 352. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.657
Minimum - Maximum-1.710068 - 3.3366258
Average (Standard dev.)-0.0007723838 (±0.08078824)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 352.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_63301_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_63301_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Transposase-activated RAG target capture complex with X-form U-sh...

EntireName: Transposase-activated RAG target capture complex with X-form U-shaped target DNA
Components
  • Complex: Transposase-activated RAG target capture complex with X-form U-shaped target DNA
    • DNA: Target DNA bottom strand
    • DNA: Target DNA top strand
    • Protein or peptide: V(D)J recombination-activating protein 1
    • Protein or peptide: Early growth response protein 1,V(D)J recombination-activating protein 2
    • DNA: 12RSS top strand
    • DNA: 12RSS bottom strand
    • DNA: 23RSS top strand
    • DNA: 23RSS bottom strand
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Transposase-activated RAG target capture complex with X-form U-sh...

SupramoleculeName: Transposase-activated RAG target capture complex with X-form U-shaped target DNA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Target DNA bottom strand

MacromoleculeName: Target DNA bottom strand / type: dna / ID: 1 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 18.06159 KDa
SequenceString: (DA)(DT)(DG)(DG)(DT)(DC)(DC)(DC)(DA)(DC) (DG)(DC)(DT)(DA)(DA)(DC)(DC)(DT)(DA)(DA) (DT)(DA)(DG)(DA)(DA)(DT)(DT)(DC)(DC) (DC)(DC)(DG)(DT)(DT)(DC)(DA)(DT)(DC)(DT) (DG) (DA)(DC)(DA)(DC)(DA)(DC) ...String:
(DA)(DT)(DG)(DG)(DT)(DC)(DC)(DC)(DA)(DC) (DG)(DC)(DT)(DA)(DA)(DC)(DC)(DT)(DA)(DA) (DT)(DA)(DG)(DA)(DA)(DT)(DT)(DC)(DC) (DC)(DC)(DG)(DT)(DT)(DC)(DA)(DT)(DC)(DT) (DG) (DA)(DC)(DA)(DC)(DA)(DC)(DA)(DG) (DC)(DG)(DT)(DG)(DG)(DG)(DA)(DC)(DC)(DA) (DG)

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Macromolecule #2: Target DNA top strand

MacromoleculeName: Target DNA top strand / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 18.305699 KDa
SequenceString: (DC)(DT)(DG)(DG)(DT)(DC)(DC)(DC)(DA)(DC) (DG)(DC)(DT)(DG)(DT)(DG)(DT)(DG)(DT)(DC) (DA)(DG)(DA)(DT)(DG)(DA)(DA)(DC)(DG) (DG)(DG)(DG)(DA)(DA)(DT)(DT)(DC)(DT)(DA) (DT) (DT)(DA)(DG)(DG)(DT)(DT) ...String:
(DC)(DT)(DG)(DG)(DT)(DC)(DC)(DC)(DA)(DC) (DG)(DC)(DT)(DG)(DT)(DG)(DT)(DG)(DT)(DC) (DA)(DG)(DA)(DT)(DG)(DA)(DA)(DC)(DG) (DG)(DG)(DG)(DA)(DA)(DT)(DT)(DC)(DT)(DA) (DT) (DT)(DA)(DG)(DG)(DT)(DT)(DA)(DG) (DC)(DG)(DT)(DG)(DG)(DG)(DA)(DC)(DC)(DA) (DT)

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Macromolecule #5: 12RSS top strand

MacromoleculeName: 12RSS top strand / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 10.461758 KDa
SequenceString:
(DC)(DA)(DC)(DA)(DG)(DT)(DG)(DG)(DT)(DA) (DG)(DT)(DA)(DG)(DG)(DC)(DT)(DG)(DT)(DA) (DC)(DA)(DA)(DA)(DA)(DA)(DC)(DC)(DT) (DC)(DG)(DA)(DC)(DC)

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Macromolecule #6: 12RSS bottom strand

MacromoleculeName: 12RSS bottom strand / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 10.45671 KDa
SequenceString:
(DG)(DG)(DT)(DC)(DG)(DA)(DG)(DG)(DT)(DT) (DT)(DT)(DT)(DG)(DT)(DA)(DC)(DA)(DG)(DC) (DC)(DT)(DA)(DC)(DT)(DA)(DC)(DC)(DA) (DC)(DT)(DG)(DT)(DG)

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Macromolecule #7: 23RSS top strand

MacromoleculeName: 23RSS top strand / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 13.877906 KDa
SequenceString:
(DC)(DA)(DC)(DA)(DG)(DT)(DG)(DG)(DT)(DA) (DG)(DT)(DA)(DG)(DG)(DC)(DT)(DG)(DT)(DT) (DG)(DT)(DC)(DT)(DG)(DG)(DC)(DT)(DG) (DT)(DA)(DC)(DA)(DA)(DA)(DA)(DA)(DC)(DC) (DT) (DC)(DG)(DA)(DC)(DC)

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Macromolecule #8: 23RSS bottom strand

MacromoleculeName: 23RSS bottom strand / type: dna / ID: 8 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 13.837883 KDa
SequenceString:
(DG)(DG)(DT)(DC)(DG)(DA)(DG)(DG)(DT)(DT) (DT)(DT)(DT)(DG)(DT)(DA)(DC)(DA)(DG)(DC) (DC)(DA)(DG)(DA)(DC)(DA)(DA)(DC)(DA) (DG)(DC)(DC)(DT)(DA)(DC)(DT)(DA)(DC)(DC) (DA) (DC)(DT)(DG)(DT)(DG)

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Macromolecule #3: V(D)J recombination-activating protein 1

MacromoleculeName: V(D)J recombination-activating protein 1 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO / EC number: Hydrolases; Acting on ester bonds
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 85.76575 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GPKKISNCSK IHLSTKLLAV DFPAHFVKSI SCQICEHILA DPVETSCKHL FCRICILRCL KVMGSYCPSC RYPCFPTDLE SPVKSFLNI LNSLMVKCPA QDCNEEVSLE KYNHHVSSHK ESKETLVHIN KGGRPRQHLL SLTRRAQKHR LRELKIQVKE F ADKEEGGD ...String:
GPKKISNCSK IHLSTKLLAV DFPAHFVKSI SCQICEHILA DPVETSCKHL FCRICILRCL KVMGSYCPSC RYPCFPTDLE SPVKSFLNI LNSLMVKCPA QDCNEEVSLE KYNHHVSSHK ESKETLVHIN KGGRPRQHLL SLTRRAQKHR LRELKIQVKE F ADKEEGGD VKAVCLTLFL LALRARNEHR QADELEAIMQ GRGSGLQPAV CLAIRVNTFL SCSQYHKMYR TVKAITGRQI FQ PLHALRN AEKVLLPGYH PFEWQPPLKN VSSRTDVGII DGLSGLASSV DEYPVDTIAK RFRYDSALVS ALMDMEEDIL EGM RSQDLD DYLNGPFTVV VKESCDGMGD VSEKHGSGPA VPEKAVRFSF TVMRITIEHG SQNVKVFEEP KPNSELCCKP LCLM LADES DHETLTAILS PLIAEREAMK SSELTLEMGG IPRTFKFIFR GTGYDEKLVR EVEGLEASGS VYICTLCDTT RLEAS QNLV FHSITRSHAE NLQRYEVWRS NPYHESVEEL RDRVKGVSAK PFIETVPSID ALHCDIGNAA EFYKIFQLEI GEVYKH PNA SKEERKRWQA TLDKHLRKRM NLKPIMMMNG NFARKLMTQE TVDAVCELIP SEERHEALRE LMDLYLKMKP VWRSSCP AK ECPESLCQYS FNSQRFAELL STKFKYRYEG KITNYFHKTL AHVPEIIERD GSIGAWASEG NNSGNKLFRR FRKMNARQ S KCYEMEDVLK HHWLYTSKYL QKFMNAHNA

UniProtKB: V(D)J recombination-activating protein 1

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Macromolecule #4: Early growth response protein 1,V(D)J recombination-activating pr...

MacromoleculeName: Early growth response protein 1,V(D)J recombination-activating protein 2
type: protein_or_peptide / ID: 4
Details: Zinc finger domain fused to the N-terminal of transposase-activated RAG2 (with deletion of residues 336-341) via a flexible linker.
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 51.195125 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GPMERPYACP VESCDRRFSD SSNLTRHIRI HTGQKPFQCR ICMRNFSRSD HLTTHIRTHT GEKPFACDIC GRKFARSDER KRHTKIHLR QKDGGGNGSG GSGMSLQMVT VGHNIALIQP GFSLMNFDGQ VFFFGQKGWP KRSCPTGVFH FDIKQNHLKL K PAIFSKDS ...String:
GPMERPYACP VESCDRRFSD SSNLTRHIRI HTGQKPFQCR ICMRNFSRSD HLTTHIRTHT GEKPFACDIC GRKFARSDER KRHTKIHLR QKDGGGNGSG GSGMSLQMVT VGHNIALIQP GFSLMNFDGQ VFFFGQKGWP KRSCPTGVFH FDIKQNHLKL K PAIFSKDS CYLPPLRYPA TCSYKGSIDS DKHQYIIHGG KTPNNELSDK IYIMSVACKN NKKVTFRCTE KDLVGDVPEP RY GHSIDVV YSRGKSMGVL FGGRSYMPST QRTTEKWNSV ADCLPHVFLI DFEFGCATSY ILPELQDGLS FHVSIARNDT VYI LGGHSL ASNIRPANLY RIRVDLPLGT PAVNCTVLPG GISVSSAILT QTNNDEFVIV GGYQLENQKR MVCSLVSLGD NTIE ISEME TPDWTSDIKH SKIWFGSNMG NGTIFLGIPG DNAFYFYTLR CSEEDLSEDQ KI

UniProtKB: Early growth response protein 1, V(D)J recombination-activating protein 2, V(D)J recombination-activating protein 2

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Macromolecule #9: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 9 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #10: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 10 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.15 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
150.0 mMKClPotassium chloride
2.0 mMMgCl2Magnesium chloride
20.0 mMHEPES4-(2-Hydroxyethyl)Piperazine-1-Ethan sulfonic Acid
0.5 mMTCEPTris(2-carboxyethyl)phosphine
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 303 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 72.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 123668
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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