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- EMDB-7480: Cryo-EM structure of mouse RAG1/2 HFC complex containing partial ... -

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Basic information

Entry
Database: EMDB / ID: EMD-7480
TitleCryo-EM structure of mouse RAG1/2 HFC complex containing partial HMGB1 linker(3.9 A)
Map dataCryo-EM structure of mouse RAG1/2 HFC complex
Sample
  • Complex: RAG1/2 in complex with nicked DNAs
    • Protein or peptide: x 3 types
    • DNA: x 6 types
  • Ligand: x 2 types
KeywordsV(D)J recombination / RAG1/2 / RSS / Immunity / RECOMBINATION / RECOMBINATION-DNA complex
Function / homology
Function and homology information


: / regulation of tolerance induction / calcium-dependent protein kinase regulator activity / positive regulation of myeloid progenitor cell differentiation / 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 / negative regulation of RNA polymerase II transcription preinitiation complex assembly / myeloid dendritic cell activation ...: / regulation of tolerance induction / calcium-dependent protein kinase regulator activity / positive regulation of myeloid progenitor cell differentiation / 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 / negative regulation of RNA polymerase II transcription preinitiation complex assembly / myeloid dendritic cell activation / T-helper 1 cell activation / mature B cell differentiation involved in immune response / T-helper 1 cell differentiation / positive regulation of myeloid cell differentiation / positive regulation of toll-like receptor 2 signaling pathway / positive regulation of dendritic cell differentiation / C-X-C chemokine binding / negative regulation of CD4-positive, alpha-beta T cell differentiation / positive regulation of toll-like receptor 9 signaling pathway / B cell homeostatic proliferation / neutrophil clearance / negative regulation of T cell differentiation in thymus / positive regulation of glycogen catabolic process / DN2 thymocyte differentiation / pre-B cell allelic exclusion / DNA geometric change / positive regulation of toll-like receptor 4 signaling pathway / endothelial cell chemotaxis / RAGE receptor binding / positive regulation of organ growth / eye development / positive regulation of interleukin-1 production / Regulation of TLR by endogenous ligand / bubble DNA binding / regulation of behavioral fear response / V(D)J recombination / negative regulation of T cell apoptotic process / myeloid cell differentiation / alphav-beta3 integrin-HMGB1 complex / Apoptosis induced DNA fragmentation / myeloid progenitor cell differentiation / inflammatory response to antigenic stimulus / phosphatidylinositol-3,4-bisphosphate binding / macrophage activation involved in immune response / negative regulation of thymocyte apoptotic process / histone H3K4me3 reader activity / positive regulation of monocyte chemotaxis / MyD88 deficiency (TLR2/4) / regulation of nucleotide-excision repair / positive regulation of monocyte chemotactic protein-1 production / cellular response to interleukin-7 / endothelial cell proliferation / phosphatidylinositol-3,5-bisphosphate binding / positive regulation of chemokine (C-X-C motif) ligand 2 production / glycogen catabolic process / apoptotic cell clearance / supercoiled DNA binding / positive regulation of vascular endothelial cell proliferation / DNA binding, bending / IRAK4 deficiency (TLR2/4) / dendritic cell chemotaxis / regulation of T cell differentiation / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / positive regulation of DNA binding / organ growth / positive regulation of T cell differentiation / T cell lineage commitment / positive regulation of wound healing / phosphatidylserine binding / B cell lineage commitment / positive regulation of sprouting angiogenesis / chemoattractant activity / endoplasmic reticulum-Golgi intermediate compartment / positive regulation of activated T cell proliferation / phosphatidylinositol-3,4,5-trisphosphate binding / TRAF6 mediated NF-kB activation / T cell homeostasis / negative regulation of type II interferon production / DNA topological change / positive regulation of interferon-alpha production / Advanced glycosylation endproduct receptor signaling / positive regulation of interleukin-10 production / negative regulation of blood vessel endothelial cell migration / T cell differentiation / protein kinase activator activity / positive regulation of blood vessel endothelial cell migration / Pyroptosis / protein autoubiquitination / four-way junction DNA binding / condensed chromosome / DNA polymerase binding / phosphatidylinositol-4,5-bisphosphate binding / transcription repressor complex / positive regulation of interleukin-12 production / positive regulation of autophagy / phosphatidylinositol binding / activation of innate immune response / lung development / positive regulation of interferon-beta production / response to glucocorticoid
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 / RAG nonamer-binding domain / NBD domain profile. / Zinc finger RAG1-type profile. / V(D)J recombination-activating protein 1 / RAG1 importin-binding ...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 / 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 / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsChen X / Kim M
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)1ZIADK036167-11 United States
CitationJournal: Mol Cell / Year: 2018
Title: Cracking the DNA Code for V(D)J Recombination.
Authors: Min-Sung Kim / Watchalee Chuenchor / Xuemin Chen / Yanxiang Cui / Xing Zhang / Z Hong Zhou / Martin Gellert / Wei Yang /
Abstract: To initiate V(D)J recombination for generating the adaptive immune response of vertebrates, RAG1/2 recombinase cleaves DNA at a pair of recombination signal sequences, the 12- and 23-RSS. We have ...To initiate V(D)J recombination for generating the adaptive immune response of vertebrates, RAG1/2 recombinase cleaves DNA at a pair of recombination signal sequences, the 12- and 23-RSS. We have determined crystal and cryo-EM structures of RAG1/2 with DNA in the pre-reaction and hairpin-forming complexes up to 2.75 Å resolution. Both protein and DNA exhibit structural plasticity and undergo dramatic conformational changes. Coding-flank DNAs extensively rotate, shift, and deform for nicking and hairpin formation. Two intertwined RAG1 subunits crisscross four times between the asymmetric pair of severely bent 12/23-RSS DNAs. Location-sensitive bending of 60° and 150° in 12- and 23-RSS spacers, respectively, must occur for RAG1/2 to capture the nonamers and pair the heptamers for symmetric double-strand breakage. DNA pairing is thus sequence-context dependent and structure specific, which partly explains the "beyond 12/23" restriction. Finally, catalysis in crystallo reveals the process of DNA hairpin formation and its stabilization by interleaved base stacking.
History
DepositionFeb 24, 2018-
Header (metadata) releaseMar 21, 2018-
Map releaseApr 25, 2018-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6cij
  • Surface level: 0.02
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7480.png

Downloads & links

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Map

FileDownload / File: emd_7480.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of mouse RAG1/2 HFC complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 288 pix.
= 308.16 Å		1.07 Å/pix.
x 288 pix.
= 308.16 Å		1.07 Å/pix.
x 288 pix.
= 308.16 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 EMDB: 0.014 / Movie #1: 0.02
Minimum - Maximum-0.043013204 - 0.117319636
Average (Standard dev.)0.0003944063 (±0.0041077877)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 308.16 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z288288288
origin x/y/z0.0000.0000.000
length x/y/z308.160308.160308.160
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS288288288
D min/max/mean-0.0430.1170.000

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Supplemental data

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Sample components

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Entire : RAG1/2 in complex with nicked DNAs

EntireName: RAG1/2 in complex with nicked DNAs
Components
  • Complex: RAG1/2 in complex with nicked DNAs
    • Protein or peptide: V(D)J recombination-activating protein 1
    • DNA: DNA (46-MER)
    • DNA: DNA (5'-D(*GP*AP*TP*CP*TP*GP*GP*CP*CP*TP*GP*TP*CP*TP*TP*A)-3')
    • DNA: DNA (5'-D(P*CP*TP*GP*GP*AP*TP*CP*TP*GP*GP*CP*CP*TP*GP*TP*CP*TP*TP*A)-3')
    • DNA: DNA (60-MER)
    • Protein or peptide: High mobility group protein B1
    • DNA: DNA (30-MER)
    • Protein or peptide: V(D)J recombination-activating protein 2
    • DNA: DNA (41-MER)
  • Ligand: ZINC ION
  • Ligand: CALCIUM ION

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Supramolecule #1: RAG1/2 in complex with nicked DNAs

SupramoleculeName: RAG1/2 in complex with nicked DNAs / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9
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: 88.670805 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: NCSKIHLSTK LLAVDFPAHF VKSISCQICE HILADPVETS CKHLFCRICI LRCLKVMGSY CPSCRYPCFP TDLESPVKSF LNILNSLMV KCPAQDCNEE VSLEKYNHHV SSHKESKETL VHINKGGRPR QHLLSLTRRA QKHRLRELKI QVKEFADKEE G GDVKAVCL ...String:
NCSKIHLSTK LLAVDFPAHF VKSISCQICE HILADPVETS CKHLFCRICI LRCLKVMGSY CPSCRYPCFP TDLESPVKSF LNILNSLMV KCPAQDCNEE VSLEKYNHHV SSHKESKETL VHINKGGRPR QHLLSLTRRA QKHRLRELKI QVKEFADKEE G GDVKAVCL TLFLLALRAR NEHRQADELE AIMQGRGSGL QPAVCLAIRV NTFLSCSQYH KMYRTVKAIT GRQIFQPLHA LR NAEKVLL PGYHPFEWQP PLKNVSSRTD VGIIDGLSGL ASSVDEYPVD TIAKRFRYDS ALVSALMDME EDILEGMRSQ DLD DYLNGP FTVVVKESCD GMGDVSEKHG SGPAVPEKAV RFSFTVMRIT IEHGSQNVKV FEEPKPNSEL CCKPLCLMLA DESD HETLT AILSPLIAER EAMKSSELTL EMGGIPRTFK FIFRGTGYDE KLVREVEGLE ASGSVYICTL CDTTRLEASQ NLVFH SITR SHAENLQRYE VWRSNPYHES VEELRDRVKG VSAKPFIETV PSIDALHCDI GNAAEFYKIF QLEIGEVYKH PNASKE ERK RWQATLDKHL RKRMNLKPIM RMNGNFARKL MTQETVDAVC ELIPSEERHE ALRELMDLYL KMKPVWRSSC PAKECPE SL CQYSFNSQRF AELLSTKFKY RYEGKITNYF HKTLAHVPEI IERDGSIGAW ASEGNQSGNK LFRRFRKMNA RQSKCYEM E DVLKHHWLYT SKYLQKFMNA HNALKSSGFT MNSKETLGDP LGIEDSLESQ DSMEF

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

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Macromolecule #6: High mobility group protein B1

MacromoleculeName: High mobility group protein B1 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 18.897885 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString:
MGKGDPKKPR GKMSSYAFFV QTCREEHKKK HPDASVNFSE FSKKCSERWK TMSAKEKGKF EDMAKADKAR YEREMKTYIP PKGETKKKF KDPNAPKRPP SAFFLFCSEY RPKIKGEHPG LSIGDVAKKL GEMWNNTAAD DKQPYEKKAA KLKEKYEKDI A AYR

UniProtKB: High mobility group protein B1

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Macromolecule #8: V(D)J recombination-activating protein 2

MacromoleculeName: V(D)J recombination-activating protein 2 / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 58.158254 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 ARALQAPKRN PPLQKPPMKS LHKKGSGKVL TPAKKS

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

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Macromolecule #2: DNA (46-MER)

MacromoleculeName: DNA (46-MER) / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.268144 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)

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Macromolecule #3: DNA (5'-D(*GP*AP*TP*CP*TP*GP*GP*CP*CP*TP*GP*TP*CP*TP*TP*A)-3')

MacromoleculeName: DNA (5'-D(*GP*AP*TP*CP*TP*GP*GP*CP*CP*TP*GP*TP*CP*TP*TP*A)-3')
type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 4.880164 KDa
SequenceString:
(DG)(DA)(DT)(DC)(DT)(DG)(DG)(DC)(DC)(DT) (DG)(DT)(DC)(DT)(DT)(DA)

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Macromolecule #4: DNA (5'-D(P*CP*TP*GP*GP*AP*TP*CP*TP*GP*GP*CP*CP*TP*GP*TP*CP*TP*TP...

MacromoleculeName: DNA (5'-D(P*CP*TP*GP*GP*AP*TP*CP*TP*GP*GP*CP*CP*TP*GP*TP*CP*TP*TP*A)-3')
type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 6.091926 KDa
SequenceString:
(DC)(DC)(DT)(DG)(DG)(DA)(DT)(DC)(DT)(DG) (DG)(DC)(DC)(DT)(DG)(DT)(DC)(DT)(DT)(DA)

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Macromolecule #5: DNA (60-MER)

MacromoleculeName: DNA (60-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
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 #7: DNA (30-MER)

MacromoleculeName: DNA (30-MER) / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 9.138938 KDa
SequenceString:
(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 #9: DNA (41-MER)

MacromoleculeName: DNA (41-MER) / type: dna / ID: 9 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.655191 KDa
SequenceString:
(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 #10: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 10 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #11: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 11 / Number of copies: 2 / Formula: CA
Molecular weightTheoretical: 40.078 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

Concentration0.3 mg/mL
BufferpH: 7.4
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: 57.6 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: PDB ENTRY
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 49624
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: COMMON LINE

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT / Target criteria: Correlation Coefficient
Output model

PDB-6cij:
Cryo-EM structure of mouse RAG1/2 HFC complex containing partial HMGB1 linker(3.9 A)

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