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- PDB-9jts: CryoEM structure of mouse RAG SEC-1DNA (12RSS side) -

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Basic information

Entry
Database: PDB / ID: 9jts
TitleCryoEM structure of mouse RAG SEC-1DNA (12RSS side)
Components
  • (DNA (30-MER)) x 2
  • (DNA (39-MER)) x 2
  • (V(D)J recombination-activating protein ...) x 2
  • DNA (5'-D(*CP*AP*GP*GP*CP*CP*AP*GP*AP*TP*CP*CP*A)-3')
  • DNA (5'-D(P*TP*GP*GP*AP*TP*CP*TP*GP*GP*CP*CP*TP*G)-3')
KeywordsDNA BINDING PROTEIN/DNA / V(D)J recombination / RAG / PHD / Transposition / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


mature B cell differentiation involved in immune response / B cell homeostatic proliferation / negative regulation of T cell differentiation in thymus / DN2 thymocyte differentiation / pre-B cell allelic exclusion / positive regulation of organ growth / regulation of behavioral fear response / V(D)J recombination / negative regulation of T cell apoptotic process / phosphatidylinositol-3,4-bisphosphate binding ...mature B cell differentiation involved in immune response / B cell homeostatic proliferation / negative regulation of T cell differentiation in thymus / DN2 thymocyte differentiation / pre-B cell allelic exclusion / positive regulation of organ growth / regulation of behavioral fear response / V(D)J recombination / negative regulation of T cell apoptotic process / phosphatidylinositol-3,4-bisphosphate binding / histone H3K4me3 reader activity / negative regulation of thymocyte apoptotic process / phosphatidylinositol-3,5-bisphosphate binding / regulation of T cell differentiation / organ growth / positive regulation of T cell differentiation / T cell lineage commitment / B cell lineage commitment / phosphatidylinositol-3,4,5-trisphosphate binding / T cell homeostasis / T cell differentiation / protein autoubiquitination / phosphatidylinositol-4,5-bisphosphate binding / phosphatidylinositol binding / thymus development / B cell differentiation / RING-type E3 ubiquitin transferase / visual learning / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / T cell differentiation in thymus / chromatin organization / endonuclease activity / histone binding / DNA recombination / adaptive immune response / sequence-specific DNA binding / Hydrolases; Acting on ester bonds / defense response to bacterium / chromatin binding / protein homodimerization activity / DNA binding / zinc ion binding / nucleoplasm / 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 / RAG nonamer-binding domain / NBD domain profile. / Zinc finger RAG1-type profile. / V(D)J recombination-activating protein 1 / RAG1 importin-binding / RAG1 importin binding / Recombination-activation protein 1 (RAG1) nonamer-binding domain / Recombination activating protein 2 ...Recombination-activating protein 1 zinc-finger domain / V(D)J recombination-activating protein 1, Zinc finger / RAG nonamer-binding domain / NBD domain profile. / Zinc finger RAG1-type profile. / V(D)J recombination-activating protein 1 / RAG1 importin-binding / RAG1 importin binding / Recombination-activation protein 1 (RAG1) nonamer-binding domain / Recombination activating protein 2 / RAG2 PHD 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)
Escherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.36 Å
AuthorsChen, X. / Yao, L. / Yang, W. / Gellert, M.
Funding support United States, China, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK) United States
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: CryoEM structure of mouse RAG SEC-12DNA
Authors: Chen, X. / Yao, L. / Yang, W. / Gellert, M.
History
DepositionOct 7, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 23, 2025Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 23, 2025Data 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
I: DNA (5'-D(P*TP*GP*GP*AP*TP*CP*TP*GP*GP*CP*CP*TP*G)-3')
G: DNA (39-MER)
L: DNA (30-MER)
M: DNA (39-MER)
H: DNA (5'-D(*CP*AP*GP*GP*CP*CP*AP*GP*AP*TP*CP*CP*A)-3')
F: DNA (30-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)407,66214
Polymers407,45110
Non-polymers2114
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: 119389.352 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 V(D)J recombination-activating protein 2 / RAG-2


Mass: 59138.410 Da / Num. of mol.: 2
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 , 6 types, 6 molecules IGLMHF

#3: DNA chain DNA (5'-D(P*TP*GP*GP*AP*TP*CP*TP*GP*GP*CP*CP*TP*G)-3')


Mass: 3998.595 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#4: DNA chain DNA (39-MER)


Mass: 11968.660 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#5: DNA chain DNA (30-MER)


Mass: 9138.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#6: DNA chain DNA (39-MER)


Mass: 12036.805 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#7: DNA chain DNA (5'-D(*CP*AP*GP*GP*CP*CP*AP*GP*AP*TP*CP*CP*A)-3')


Mass: 3945.589 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#8: DNA chain DNA (30-MER)


Mass: 9306.969 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)

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Non-polymers , 2 types, 4 molecules

#9: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#10: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN
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: mouse RAG SEC / Type: COMPLEX / Entity ID: #1-#8 / Source: MULTIPLE SOURCES
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: 3000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 70 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionDetails: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.36 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 90752 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00319458
ELECTRON MICROSCOPYf_angle_d0.55726993
ELECTRON MICROSCOPYf_dihedral_angle_d21.1043732
ELECTRON MICROSCOPYf_chiral_restr0.042953
ELECTRON MICROSCOPYf_plane_restr0.0052914

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