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- EMDB-20036: Cryo-EM structure of mouse RAG1/2 STC complex (without NBD domain) -

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Basic information

Entry
Database: EMDB / ID: EMD-20036
TitleCryo-EM structure of mouse RAG1/2 STC complex (without NBD domain)
Map dataStructure of mouse RAG1/2 STC complex (without NBD domain)
Sample
  • Complex: RAG1/2 strand transfer complex
    • Protein or peptide: V(D)J recombination-activating protein 1
    • Protein or peptide: V(D)J recombination-activating protein 2
    • DNA: DNA (35-MER)
    • DNA: DNA (5'-D(*CP*CP*TP*GP*GP*AP*TP*CP*TP*GP*GP*CP*CP*TP*G)-3')
    • DNA: DNA (34-MER)
    • DNA: DNA (5'-D(P*CP*AP*CP*AP*GP*TP*GP*AP*TP*AP*CP*AP*GP*CP*C)-3')
    • DNA: DNA (5'-D(P*CP*AP*CP*AP*GP*TP*GP*AP*TP*GP*CP*AP*AP*A)-3')
  • Ligand: CALCIUM ION
  • Ligand: ZINC ION
  • Ligand: water
KeywordsV(D)J recombination / DNA Transposition / RAG / SCID / RECOMBINATION / RECOMBINATION-DNA complex
Function / homology
Function and homology information


mature B cell differentiation involved in immune response / DNA recombinase complex / B cell homeostatic proliferation / DN2 thymocyte differentiation / negative regulation of T cell differentiation in thymus / endodeoxyribonuclease complex / pre-B cell allelic exclusion / positive regulation of organ growth / regulation of behavioral fear response / V(D)J recombination ...mature B cell differentiation involved in immune response / DNA recombinase complex / B cell homeostatic proliferation / DN2 thymocyte differentiation / negative regulation of T cell differentiation in thymus / endodeoxyribonuclease complex / 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 / negative regulation of thymocyte apoptotic process / phosphatidylinositol-3,5-bisphosphate binding / T cell lineage commitment / organ growth / positive regulation of T cell differentiation / regulation of T cell differentiation / B cell lineage commitment / T cell homeostasis / phosphatidylinositol-3,4,5-trisphosphate binding / T cell differentiation / protein autoubiquitination / phosphatidylinositol-4,5-bisphosphate binding / methylated histone binding / B cell differentiation / phosphatidylinositol binding / thymus development / RING-type E3 ubiquitin transferase / visual learning / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / chromatin organization / histone binding / T cell differentiation in thymus / endonuclease activity / DNA recombination / sequence-specific DNA binding / adaptive immune response / Hydrolases; Acting on ester bonds / defense response to bacterium / chromatin binding / protein homodimerization activity / zinc ion binding / nucleoplasm / identical protein binding / nucleus / metal ion binding
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), recombinase / 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), recombinase / 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 / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Kelch-type beta propeller / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Zinc finger C2H2 superfamily / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, FYVE/PHD-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) / Mus musculus (house mouse) / Escherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.06 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: How mouse RAG recombinase avoids DNA transposition.
Authors: Xuemin Chen / Yanxiang Cui / Huaibin Wang / Z Hong Zhou / Martin Gellert / Wei Yang /
Abstract: The RAG1-RAG2 recombinase (RAG) cleaves DNA to initiate V(D)J recombination, but RAG also belongs to the RNH-type transposase family. To learn how RAG-catalyzed transposition is inhibited in ...The RAG1-RAG2 recombinase (RAG) cleaves DNA to initiate V(D)J recombination, but RAG also belongs to the RNH-type transposase family. To learn how RAG-catalyzed transposition is inhibited in developing lymphocytes, we determined the structure of a DNA-strand transfer complex of mouse RAG at 3.1-Å resolution. The target DNA is a T form (T for transpositional target), which contains two >80° kinks towards the minor groove, only 3 bp apart. RAG2, a late evolutionary addition in V(D)J recombination, appears to enforce the sharp kinks and additional inter-segment twisting in target DNA and thus attenuates unwanted transposition. In contrast to strand transfer complexes of genuine transposases, where severe kinks occur at the integration sites of target DNA and thus prevent the reverse reaction, the sharp kink with RAG is 1 bp away from the integration site. As a result, RAG efficiently catalyzes the disintegration reaction that restores the RSS (donor) and target DNA.
History
DepositionMar 27, 2019-
Header (metadata) releaseMay 15, 2019-
Map releaseJan 22, 2020-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0493
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0493
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6oes
  • Surface level: 0.0493
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20036.png

Downloads & links

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Map

FileDownload / File: emd_20036.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of mouse RAG1/2 STC complex (without NBD domain)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 280 pix.
= 299.6 Å		1.07 Å/pix.
x 280 pix.
= 299.6 Å		1.07 Å/pix.
x 280 pix.
= 299.6 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: 0.0493 / Movie #1: 0.0493
Minimum - Maximum-0.18483075 - 0.35905084
Average (Standard dev.)0.0004129147 (±0.0077902083)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 299.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z299.600299.600299.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS280280280
D min/max/mean-0.1850.3590.000

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Supplemental data

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Sample components

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Entire : RAG1/2 strand transfer complex

EntireName: RAG1/2 strand transfer complex
Components
  • Complex: RAG1/2 strand transfer complex
    • Protein or peptide: V(D)J recombination-activating protein 1
    • Protein or peptide: V(D)J recombination-activating protein 2
    • DNA: DNA (35-MER)
    • DNA: DNA (5'-D(*CP*CP*TP*GP*GP*AP*TP*CP*TP*GP*GP*CP*CP*TP*G)-3')
    • DNA: DNA (34-MER)
    • DNA: DNA (5'-D(P*CP*AP*CP*AP*GP*TP*GP*AP*TP*AP*CP*AP*GP*CP*C)-3')
    • DNA: DNA (5'-D(P*CP*AP*CP*AP*GP*TP*GP*AP*TP*GP*CP*AP*AP*A)-3')
  • Ligand: CALCIUM ION
  • Ligand: ZINC ION
  • Ligand: water

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Supramolecule #1: RAG1/2 strand transfer complex

SupramoleculeName: RAG1/2 strand transfer 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 #3: DNA (35-MER)

MacromoleculeName: DNA (35-MER) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 15.521905 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)(DC)(DG)(DG)(DC)(DG)(DC)(DA)(DG)(DG) (DC) (DC)(DA)(DG)(DA)(DT)(DC)(DC)(DA) (DG)(DG)

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Macromolecule #4: DNA (5'-D(*CP*CP*TP*GP*GP*AP*TP*CP*TP*GP*GP*CP*CP*TP*G)-3')

MacromoleculeName: DNA (5'-D(*CP*CP*TP*GP*GP*AP*TP*CP*TP*GP*GP*CP*CP*TP*G)-3')
type: dna / ID: 4 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 4.576958 KDa
SequenceString:
(DC)(DC)(DT)(DG)(DG)(DA)(DT)(DC)(DT)(DG) (DG)(DC)(DC)(DT)(DG)

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Macromolecule #5: DNA (34-MER)

MacromoleculeName: DNA (34-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 18.761963 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)(DC)(DG)(DC)(DC)(DG) ...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)(DC)(DG)(DC)(DC)(DG)(DC)(DA) (DG)(DG)(DC)(DC)(DA)(DG)(DA)(DT)(DC)(DC) (DA)(DG) (DG)

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Macromolecule #6: DNA (5'-D(P*CP*AP*CP*AP*GP*TP*GP*AP*TP*AP*CP*AP*GP*CP*C)-3')

MacromoleculeName: DNA (5'-D(P*CP*AP*CP*AP*GP*TP*GP*AP*TP*AP*CP*AP*GP*CP*C)-3')
type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Escherichia coli K-12 (bacteria)
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 #7: DNA (5'-D(P*CP*AP*CP*AP*GP*TP*GP*AP*TP*GP*CP*AP*AP*A)-3')

MacromoleculeName: DNA (5'-D(P*CP*AP*CP*AP*GP*TP*GP*AP*TP*GP*CP*AP*AP*A)-3')
type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Escherichia coli K-12 (bacteria)
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 #8: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 8 / Number of copies: 2 / Formula: CA
Molecular weightTheoretical: 40.078 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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Macromolecule #10: water

MacromoleculeName: water / type: ligand / ID: 10 / Number of copies: 2 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 45.0 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

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 283634
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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