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- EMDB-63299: Structure of RAG transposon end complex (TEC) -

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Basic information

Entry
Database: EMDB / ID: EMD-63299
TitleStructure of RAG transposon end complex (TEC)
Map data
Sample
  • Complex: RAG transposon end complex
    • Protein or peptide: V(D)J recombination-activating protein 1
    • Protein or peptide: V(D)J recombination-activating protein 2
    • DNA: 12RSS bottom strand
    • DNA: 12RSS top strand
    • DNA: 23RSS bottom strand
    • DNA: 23RSS top strand
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
KeywordsRAG / Transposase / TEC / evolution / DNA BINDING PROTEIN/DNA / 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
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: 3.0 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_63299.png

Downloads & links

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Map

FileDownload / File: emd_63299.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.53 Å/pix.
x 600 pix.
= 315. Å		0.53 Å/pix.
x 600 pix.
= 315. Å		0.53 Å/pix.
x 600 pix.
= 315. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.525 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.11
Minimum - Maximum-0.70980734 - 1.174554
Average (Standard dev.)0.0000027693561 (±0.018404284)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 315.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_63299_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_63299_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : RAG transposon end complex

EntireName: RAG transposon end complex
Components
  • Complex: RAG transposon end complex
    • Protein or peptide: V(D)J recombination-activating protein 1
    • Protein or peptide: V(D)J recombination-activating protein 2
    • DNA: 12RSS bottom strand
    • DNA: 12RSS top strand
    • DNA: 23RSS bottom strand
    • DNA: 23RSS top strand
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION

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Supramolecule #1: RAG transposon end complex

SupramoleculeName: RAG transposon end complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Mus musculus (house mouse)

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

MacromoleculeName: V(D)J recombination-activating protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: Hydrolases; Acting on ester bonds
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 85.690727 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 LADAS DHETLTAILS PLIAEREAMK SSELTLEMGG IPRTFKFIFR GTGYDEKLVR EVEGLEAAGA 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 NESGNKLFRR FRKMNARQ S KCYEMEDVLK HHWLYTSKYL QKFMNAHNA

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

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Macromolecule #2: V(D)J recombination-activating protein 2

MacromoleculeName: V(D)J recombination-activating protein 2 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 40.374816 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GPMSLQMVTV GHNIALIQPG FSLMNFDGQV FFFGQKGWPK RSCPTGVFHF DIKQNHLKLE PAIFSKDSCY LPPLRYPATC SYKGSIDSD KHQYIIHGGK TPNNELSDKI YIMSVACKNN KAVTFRCTEK DLVGDVPEPR YGHSIDVVYS RGKSMGVLFG G RSYMPSTQ ...String:
GPMSLQMVTV GHNIALIQPG FSLMNFDGQV FFFGQKGWPK RSCPTGVFHF DIKQNHLKLE PAIFSKDSCY LPPLRYPATC SYKGSIDSD KHQYIIHGGK TPNNELSDKI YIMSVACKNN KAVTFRCTEK DLVGDVPEPR YGHSIDVVYS RGKSMGVLFG G RSYMPSTQ RTTEKWNSVA DCLPHVFLID FEFGCATSYI LPELQDGLSF HVSIARNDTV YILGGHSLAS NIRPANLYRI RV DLPLGTP AVNCTVLPGG ISVSSAILTQ TNNDEFVIVG GYQLENQKRM VCSLVSLGDN TIEISEMETP DWTSDIKHSK IWF GSNMGN GTIFLGIPGD NKQAMSEAFY FYTLRCSEED LSEDQKI

UniProtKB: V(D)J recombination-activating protein 2

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Macromolecule #3: 12RSS bottom strand

MacromoleculeName: 12RSS bottom strand / type: dna / ID: 3 / 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 #4: 12RSS top strand

MacromoleculeName: 12RSS top strand / type: dna / ID: 4 / 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 #5: 23RSS bottom strand

MacromoleculeName: 23RSS bottom strand / type: dna / ID: 5 / 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 #6: 23RSS top strand

MacromoleculeName: 23RSS top strand / type: dna / ID: 6 / 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 #7: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 7 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #8: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 8 / Number of copies: 2 / 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 K2 QUANTUM (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 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: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 822335
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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