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- PDB-9jpu: CryoEM structure of mouse RAG SEC-PHD -

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Basic information

Entry
Database: PDB / ID: 9jpu
TitleCryoEM structure of mouse RAG SEC-PHD
Components
  • (V(D)J recombination-activating protein ...) x 2
  • DNA (5'-D(*CP*AP*CP*AP*GP*TP*GP*AP*TP*AP*CP*AP*GP*CP*C)-3')
  • DNA (5'-D(*CP*AP*CP*AP*GP*TP*GP*AP*TP*GP*CP*AP*AP*A)-3')
  • DNA (5'-D(P*GP*GP*CP*TP*GP*TP*AP*TP*CP*AP*CP*TP*GP*TP*G)-3')
  • DNA (5'-D(P*TP*TP*TP*GP*CP*AP*TP*CP*AP*CP*TP*GP*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 / DNA recombinase complex / B cell homeostatic proliferation / endodeoxyribonuclease complex / negative regulation of T cell differentiation in thymus / pre-B cell allelic exclusion / positive regulation of organ growth / V(D)J recombination / negative regulation of T cell apoptotic process / regulation of behavioral fear response ...mature B cell differentiation involved in immune response / DNA recombinase complex / B cell homeostatic proliferation / endodeoxyribonuclease complex / negative regulation of T cell differentiation in thymus / pre-B cell allelic exclusion / positive regulation of organ growth / V(D)J recombination / negative regulation of T cell apoptotic process / regulation of behavioral fear response / phosphatidylinositol-3,4-bisphosphate binding / negative regulation of thymocyte apoptotic process / phosphatidylinositol-3,5-bisphosphate binding / histone H3K4me3 reader activity / regulation of T cell differentiation / 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 / B cell differentiation / thymus development / RING-type E3 ubiquitin transferase / visual learning / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / T cell differentiation in thymus / chromatin organization / endonuclease activity / DNA recombination / histone binding / sequence-specific DNA binding / Hydrolases; Acting on ester bonds / adaptive immune response / defense response to bacterium / hydrolase activity / chromatin binding / protein homodimerization activity / 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 / : / 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 / : / : / : / : / : / : / RAG1 importin binding / Recombination-activation protein 1 (RAG1) nonamer-binding 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 / 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: 3.25 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: Proc Natl Acad Sci U S A / Year: 2025
Title: How RAG1/2 evolved from ancestral transposases to initiate V(D)J recombination without transposition.
Authors: Xuemin Chen / Liangrui Yao / Wenwen Li / Shanshan Ma / Xingyun Yuan / Yang Yang / Yuan Yuan / Yumei Liu / Lan Liu / Huaibin Wang / Martin Gellert / Wei Yang /
Abstract: The recombination activating genes 1 and 2 (RAG1/2) recombinase, which initiates V(D)J recombination in jawed vertebrates, evolved from RNaseH-like transposases such as Transib and ProtoRAG. However, ...The recombination activating genes 1 and 2 (RAG1/2) recombinase, which initiates V(D)J recombination in jawed vertebrates, evolved from RNaseH-like transposases such as Transib and ProtoRAG. However, its postcleavage transposase activity is strictly suppressed. Previous structural studies have focused only on the conserved core domains of RAG1/2, leaving the regulatory mechanisms of the noncore regions unclear. To investigate how RAG1/2 suppresses transposition and regulates DNA cleavage, we determined cryo-electron microscopy (cryo-EM) structures of nearly full-length RAG1/2 complexed with cleaved recombination signal sequences (RSS) in a signal-end complex (SEC) at resolutions up to 2.95 Å. Two key structures, SEC-0 and SEC-Plant Homeodomain (PHD), reveal distinct regulatory roles of RAG2, which is absent in Transib transposase. SEC-0 displays a closed conformation, revealing that the core RAG2 facilitates sequential DNA cleavage by stabilizing the RSS-cleaved states in a "spring-loaded" mechanism. SEC-PHD reveals how RAG2's noncore PHD and Acidic Hinge (AH), which are absent in ProtoRAG, inhibit target DNA binding in transposition. Histone H3K4me3, which recruits RAG1/2 to RSS sites, does not influence RAG1/2 binding to V, D, or J gene segments bordered by RSS. In contrast, the suppressed transposition can be activated by H3K4me3 peptides that dislodge the inhibitory PHD. To achieve this derepression in vivo, however, would require an unlikely close placement of two nucleosomes flanking a target DNA bent by nearly 180°. Our structural and biochemical results elucidate how RAG1 has acquired RAG2 and utilizes its core and noncore domains to enhance V(D)J recombination and suppress transposition.
History
DepositionSep 26, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 23, 2025Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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: DNA (5'-D(P*GP*GP*CP*TP*GP*TP*AP*TP*CP*AP*CP*TP*GP*TP*G)-3')
G: DNA (5'-D(P*TP*TP*TP*GP*CP*AP*TP*CP*AP*CP*TP*GP*TP*G)-3')
L: DNA (5'-D(*CP*AP*CP*AP*GP*TP*GP*AP*TP*AP*CP*AP*GP*CP*C)-3')
M: DNA (5'-D(*CP*AP*CP*AP*GP*TP*GP*AP*TP*GP*CP*AP*AP*A)-3')
E: V(D)J recombination-activating protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)434,27415
Polymers433,9339
Non-polymers3426
Water362
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, 5 molecules ACBDE

#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.: 3
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 FGLM

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


Mass: 4615.995 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#4: DNA chain DNA (5'-D(P*TP*TP*TP*GP*CP*AP*TP*CP*AP*CP*TP*GP*TP*G)-3')


Mass: 4261.775 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#5: DNA chain DNA (5'-D(*CP*AP*CP*AP*GP*TP*GP*AP*TP*AP*CP*AP*GP*CP*C)-3')


Mass: 4562.988 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#6: DNA chain DNA (5'-D(*CP*AP*CP*AP*GP*TP*GP*AP*TP*GP*CP*AP*AP*A)-3')


Mass: 4297.832 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)

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Non-polymers , 3 types, 8 molecules

#7: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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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-#6 / 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: 3.25 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 57418 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00216451
ELECTRON MICROSCOPYf_angle_d0.44922496
ELECTRON MICROSCOPYf_dihedral_angle_d13.2096202
ELECTRON MICROSCOPYf_chiral_restr0.042445
ELECTRON MICROSCOPYf_plane_restr0.0042703

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