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- EMDB-20030: Cryo-EM structure of mouse RAG1/2 PRC complex (DNA0) -

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Basic information

Entry
Database: EMDB / ID: EMD-20030
TitleCryo-EM structure of mouse RAG1/2 PRC complex (DNA0)
Map datastructure of mouse RAG1/2 PRC complex
Sample
  • Complex: RAG1/2 pre-reaction complex
    • Protein or peptide: V(D)J recombination-activating protein 1
    • Protein or peptide: V(D)J recombination-activating protein 2
    • DNA: DNA (57-MER)
    • DNA: DNA (46-MER)
    • DNA: DNA (46-MER)
    • DNA: DNA (57-MER)
    • Protein or peptide: High mobility group protein B1
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
KeywordsV(D)J recombination / DNA Transposition / RAG / SCID / RECOMBINATION / RECOMBINATION-DNA complex
Function / homology
Function and homology information


endodeoxyribonuclease activator activity / regulation of tolerance induction / calcium-dependent protein kinase regulator activity / regulation of T cell mediated immune response to tumor cell / positive regulation of mismatch repair / negative regulation of apoptotic cell clearance / plasmacytoid dendritic cell activation / neutrophil clearance / negative regulation of RNA polymerase II transcription preinitiation complex assembly / T-helper 1 cell activation ...endodeoxyribonuclease activator activity / regulation of tolerance induction / calcium-dependent protein kinase regulator activity / regulation of T cell mediated immune response to tumor cell / positive regulation of mismatch repair / negative regulation of apoptotic cell clearance / plasmacytoid dendritic cell activation / neutrophil clearance / negative regulation of RNA polymerase II transcription preinitiation complex assembly / T-helper 1 cell activation / B cell homeostatic proliferation / myeloid dendritic cell activation / positive regulation of toll-like receptor 2 signaling pathway / mature B cell differentiation involved in immune response / positive regulation of dendritic cell differentiation / negative regulation of T cell differentiation in thymus / positive regulation of toll-like receptor 9 signaling pathway / C-X-C chemokine binding / negative regulation of CD4-positive, alpha-beta T cell differentiation / DNA recombinase complex / endodeoxyribonuclease complex / negative regulation of T cell apoptotic process / Scavenging by Class B Receptors / DNA geometric change / positive regulation of toll-like receptor 4 signaling pathway / positive regulation of organ growth / endothelial cell chemotaxis / pre-B cell allelic exclusion / RAGE receptor binding / positive regulation of interleukin-1 production / V(D)J recombination / Regulation of TLR by endogenous ligand / inflammatory response to antigenic stimulus / endothelial cell proliferation / bubble DNA binding / alphav-beta3 integrin-HMGB1 complex / Apoptosis induced DNA fragmentation / negative regulation of thymocyte apoptotic process / macrophage activation involved in immune response / positive regulation of monocyte chemotactic protein-1 production / phosphatidylinositol-3,4-bisphosphate binding / regulation of behavioral fear response / positive regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of monocyte chemotaxis / MyD88 deficiency (TLR2/4) / histone H3K4me3 reader activity / phosphatidylinositol-3,5-bisphosphate binding / positive regulation of vascular endothelial cell proliferation / positive regulation of activated T cell proliferation / apoptotic cell clearance / T cell lineage commitment / B cell lineage commitment / regulation of nucleotide-excision repair / positive regulation of DNA binding / DNA binding, bending / regulation of T cell differentiation / IRAK4 deficiency (TLR2/4) / T cell homeostasis / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / T-helper 1 cell differentiation / dendritic cell chemotaxis / positive regulation of T cell differentiation / supercoiled DNA binding / phosphatidylserine binding / positive regulation of wound healing / positive regulation of sprouting angiogenesis / chemoattractant activity / endoplasmic reticulum-Golgi intermediate compartment / negative regulation of type II interferon production / TRAF6 mediated NF-kB activation / DNA topological change / phosphatidylinositol-3,4,5-trisphosphate binding / positive regulation of interferon-alpha production / negative regulation of blood vessel endothelial cell migration / positive regulation of interleukin-10 production / T cell differentiation / Advanced glycosylation endproduct receptor signaling / Pyroptosis / positive regulation of blood vessel endothelial cell migration / protein kinase activator activity / thymus development / positive regulation of interleukin-12 production / protein autoubiquitination / transcription repressor complex / condensed chromosome / four-way junction DNA binding / B cell differentiation / DNA polymerase binding / phosphatidylinositol-4,5-bisphosphate binding / T cell differentiation in thymus / activation of innate immune response / positive regulation of interferon-beta production / phosphatidylinositol binding / positive regulation of autophagy / cytokine activity / positive regulation of interleukin-8 production / positive regulation of interleukin-1 beta production / lipopolysaccharide binding / visual learning / positive regulation of non-canonical NF-kappaB signal transduction
Similarity search - Function
HMG box A DNA-binding domain, conserved site / HMG box A DNA-binding domain signature. / 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 ...HMG box A DNA-binding domain, conserved site / HMG box A DNA-binding domain signature. / 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 / HMG-box domain / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily / 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
High mobility group protein B1 / V(D)J recombination-activating protein 1 / V(D)J recombination-activating protein 2
Similarity search - Component
Biological speciesMus musculus (house mouse) / Homo sapiens (human) / Escherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsChen X / Cui Y / Zhou ZH / Yang W / Gellert M
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK036167 United States
CitationJournal: Nat Struct Mol Biol / Year: 2020
Title: Cutting antiparallel DNA strands in a single active site.
Authors: Xuemin Chen / Yanxiang Cui / Robert B Best / Huaibin Wang / Z Hong Zhou / Wei Yang / Martin Gellert /
Abstract: A single enzyme active site that catalyzes multiple reactions is a well-established biochemical theme, but how one nuclease site cleaves both DNA strands of a double helix has not been well ...A single enzyme active site that catalyzes multiple reactions is a well-established biochemical theme, but how one nuclease site cleaves both DNA strands of a double helix has not been well understood. In analyzing site-specific DNA cleavage by the mammalian RAG1-RAG2 recombinase, which initiates V(D)J recombination, we find that the active site is reconfigured for the two consecutive reactions and the DNA double helix adopts drastically different structures. For initial nicking of the DNA, a locally unwound and unpaired DNA duplex forms a zipper via alternating interstrand base stacking, rather than melting as generally thought. The second strand cleavage and formation of a hairpin-DNA product requires a global scissor-like movement of protein and DNA, delivering the scissile phosphate into the rearranged active site.
History
DepositionMar 27, 2019-
Header (metadata) releaseJun 5, 2019-
Map releaseJan 29, 2020-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0217
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0217
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6oem
  • Surface level: 0.0217
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20030.png

Downloads & links

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Map

FileDownload / File: emd_20030.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationstructure of mouse RAG1/2 PRC complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 256 pix.
= 273.92 Å		1.07 Å/pix.
x 256 pix.
= 273.92 Å		1.07 Å/pix.
x 256 pix.
= 273.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0217 / Movie #1: 0.0217
Minimum - Maximum-0.035329547 - 0.090047225
Average (Standard dev.)0.0006140652 (±0.0041229334)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 273.92 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z273.920273.920273.920
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0350.0900.001

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Supplemental data

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Sample components

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Entire : RAG1/2 pre-reaction complex

EntireName: RAG1/2 pre-reaction complex
Components
  • Complex: RAG1/2 pre-reaction complex
    • Protein or peptide: V(D)J recombination-activating protein 1
    • Protein or peptide: V(D)J recombination-activating protein 2
    • DNA: DNA (57-MER)
    • DNA: DNA (46-MER)
    • DNA: DNA (46-MER)
    • DNA: DNA (57-MER)
    • Protein or peptide: High mobility group protein B1
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION

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Supramolecule #1: RAG1/2 pre-reaction complex

SupramoleculeName: RAG1/2 pre-reaction complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
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: 119.388352 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAASLPSTLS FSSAPDEIQH PQIKFSEWKF KLFRVRSFEK APEEAQKEKD SSEGKPYLEQ SPVVPEKPGG QNSILTQRAL KLHPKFSKK FHADGKSSDK AVHQARLRHF CRICGNRFKS DGHSRRYPVH GPVDAKTQSL FRKKEKRVTS WPDLIARIFR I DVKADVDS ...String:
MAASLPSTLS FSSAPDEIQH PQIKFSEWKF KLFRVRSFEK APEEAQKEKD SSEGKPYLEQ SPVVPEKPGG QNSILTQRAL KLHPKFSKK FHADGKSSDK AVHQARLRHF CRICGNRFKS DGHSRRYPVH GPVDAKTQSL FRKKEKRVTS WPDLIARIFR I DVKADVDS IHPTEFCHDC WSIMHRKFSS SHSQVYFPRK VTVEWHPHTP SCDICFTAHR GLKRKRHQPN VQLSKKLKTV LN HARRDRR KRTQARVSSK EVLKKISNCS KIHLSTKLLA VDFPAHFVKS ISCQICEHIL ADPVETSCKH LFCRICILRC LKV MGSYCP SCRYPCFPTD LESPVKSFLN ILNSLMVKCP AQDCNEEVSL EKYNHHVSSH KESKETLVHI NKGGRPRQHL LSLT RRAQK HRLRELKIQV KEFADKEEGG DVKAVCLTLF LLALRARNEH RQADELEAIM QGRGSGLQPA VCLAIRVNTF LSCSQ YHKM YRTVKAITGR QIFQPLHALR NAEKVLLPGY HPFEWQPPLK NVSSRTDVGI IDGLSGLASS VDEYPVDTIA KRFRYD SAL VSALMDMEED ILEGMRSQDL DDYLNGPFTV VVKESCDGMG DVSEKHGSGP AVPEKAVRFS FTVMRITIEH GSQNVKV FE EPKPNSELCC KPLCLMLADE SDHETLTAIL SPLIAEREAM KSSELTLEMG GIPRTFKFIF RGTGYDEKLV REVEGLEA S GSVYICTLCD TTRLEASQNL VFHSITRSHA ENLQRYEVWR SNPYHESVEE LRDRVKGVSA KPFIETVPSI DALHCDIGN AAEFYKIFQL EIGEVYKHPN ASKEERKRWQ ATLDKHLRKR MNLKPIMRMN GNFARKLMTQ ETVDAVCELI PSEERHEALR ELMDLYLKM KPVWRSSCPA KECPESLCQY SFNSQRFAEL LSTKFKYRYE GKITNYFHKT LAHVPEIIER DGSIGAWASE G NQSGNKLF RRFRKMNARQ SKCYEMEDVL KHHWLYTSKY LQKFMNAHNA LKSSGFTMNS KETLGDPLGI EDSLESQDSM EF

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: 59.13841 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSLQMVTVGH NIALIQPGFS LMNFDGQVFF FGQKGWPKRS CPTGVFHFDI KQNHLKLKPA IFSKDSCYLP PLRYPATCSY KGSIDSDKH QYIIHGGKTP NNELSDKIYI MSVACKNNKK VTFRCTEKDL VGDVPEPRYG HSIDVVYSRG KSMGVLFGGR S YMPSTQRT ...String:
MSLQMVTVGH NIALIQPGFS LMNFDGQVFF FGQKGWPKRS CPTGVFHFDI KQNHLKLKPA IFSKDSCYLP PLRYPATCSY KGSIDSDKH QYIIHGGKTP NNELSDKIYI MSVACKNNKK VTFRCTEKDL VGDVPEPRYG HSIDVVYSRG KSMGVLFGGR S YMPSTQRT TEKWNSVADC LPHVFLIDFE FGCATSYILP ELQDGLSFHV SIARNDTVYI LGGHSLASNI RPANLYRIRV DL PLGTPAV NCTVLPGGIS VSSAILTQTN NDEFVIVGGY QLENQKRMVC SLVSLGDNTI EISEMETPDW TSDIKHSKIW FGS NMGNGT IFLGIPGDNK QAMSEAFYFY TLRCSEEDLS EDQKIVSNSQ TSTEDPGDST PFEDSEEFCF SAEATSFDGD DEFD TYNED DEDDESVTGY WITCCPTCDV DINTWVPFYS TELNKPAMIY CSHGDGHWVH AQCMDLEERT LIHLSEGSNK YYCNE HVQI ARALQTPKRN PPLQKPPMKS LHKKGSGKVL TPAKKSFLRR LFD

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

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Macromolecule #7: High mobility group protein B1

MacromoleculeName: High mobility group protein B1 / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.444963 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
SYAFFVQTCR EEHKKKHPDA SVNFSEFSKK CSERWKTMSA KEKGKFEDMA KADKARYERE MKTYIPPKGE TKKKFKDPNA PKRPPSAFF LFCSEYRPKI KGEHPGLSIG DVAKKLGEMW NNTAADDKQP YEKKAAKLKE KY

UniProtKB: High mobility group protein B1

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Macromolecule #3: DNA (57-MER)

MacromoleculeName: DNA (57-MER) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 18.809023 KDa
SequenceString: (DC)(DG)(DG)(DG)(DT)(DT)(DT)(DT)(DT)(DG) (DT)(DC)(DT)(DG)(DG)(DC)(DT)(DT)(DC)(DA) (DC)(DA)(DC)(DT)(DT)(DG)(DA)(DT)(DT) (DT)(DG)(DC)(DA)(DT)(DC)(DA)(DC)(DT)(DG) (DT) (DG)(DT)(DA)(DA)(DG)(DA) ...String:
(DC)(DG)(DG)(DG)(DT)(DT)(DT)(DT)(DT)(DG) (DT)(DC)(DT)(DG)(DG)(DC)(DT)(DT)(DC)(DA) (DC)(DA)(DC)(DT)(DT)(DG)(DA)(DT)(DT) (DT)(DG)(DC)(DA)(DT)(DC)(DA)(DC)(DT)(DG) (DT) (DG)(DT)(DA)(DA)(DG)(DA)(DC)(DA) (DG)(DG)(DC)(DC)(DA)(DG)(DA)(DT)(DC)(DC) (DA)(DG) (DG)

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Macromolecule #4: DNA (46-MER)

MacromoleculeName: DNA (46-MER) / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 15.275817 KDa
SequenceString:
(DC)(DC)(DT)(DG)(DG)(DA)(DT)(DC)(DT)(DG) (DG)(DC)(DC)(DT)(DG)(DT)(DC)(DT)(DT)(DA) (DC)(DA)(DC)(DA)(DG)(DT)(DG)(DA)(DT) (DA)(DC)(DA)(DG)(DC)(DC)(DC)(DT)(DT)(DA) (DA) (DC)(DA)(DA)(DA)(DA)(DA)(DC)(DC) (DC)(DG)

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Macromolecule #5: DNA (46-MER)

MacromoleculeName: DNA (46-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 15.528942 KDa
SequenceString:
(DC)(DG)(DG)(DG)(DT)(DT)(DT)(DT)(DT)(DG) (DT)(DT)(DA)(DA)(DG)(DG)(DG)(DC)(DT)(DG) (DT)(DA)(DT)(DC)(DA)(DC)(DT)(DG)(DT) (DG)(DT)(DA)(DA)(DG)(DA)(DC)(DA)(DG)(DG) (DC) (DC)(DA)(DG)(DA)(DT)(DC)(DC)(DA) (DG)(DG)

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Macromolecule #6: DNA (57-MER)

MacromoleculeName: DNA (57-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 18.792076 KDa
SequenceString: (DC)(DC)(DT)(DG)(DG)(DA)(DT)(DC)(DT)(DG) (DG)(DC)(DC)(DT)(DG)(DT)(DC)(DT)(DT)(DA) (DC)(DA)(DC)(DA)(DG)(DT)(DG)(DA)(DT) (DG)(DC)(DA)(DA)(DA)(DT)(DC)(DA)(DA)(DG) (DT) (DG)(DT)(DG)(DA)(DA)(DG) ...String:
(DC)(DC)(DT)(DG)(DG)(DA)(DT)(DC)(DT)(DG) (DG)(DC)(DC)(DT)(DG)(DT)(DC)(DT)(DT)(DA) (DC)(DA)(DC)(DA)(DG)(DT)(DG)(DA)(DT) (DG)(DC)(DA)(DA)(DA)(DT)(DC)(DA)(DA)(DG) (DT) (DG)(DT)(DG)(DA)(DA)(DG)(DC)(DC) (DA)(DG)(DA)(DC)(DA)(DA)(DA)(DA)(DA)(DC) (DC)(DC) (DG)

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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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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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
GridDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 57.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 109865
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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