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- EMDB-22272: Structure of RAG1 (R848M/E649V)-RAG2-DNA Strand Transfer Complex ... -

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Entry
Database: EMDB / ID: EMD-22272
TitleStructure of RAG1 (R848M/E649V)-RAG2-DNA Strand Transfer Complex (Dynamic-Form)
Map dataRAG1 (R848M/E649V)-RAG2-DNA Strand Transfer Complex (Dynamic-Form)
Sample
  • Complex: RAG recombinase strand transfer complex
    • Complex: V(D)J recombination-activating protein 1, V(D)J recombination-activating protein 2
      • Protein or peptide: V(D)J recombination-activating protein 1
      • Protein or peptide: V(D)J recombination-activating protein 2
    • Complex: DNA
      • DNA: 12RSS integration strand DNA (55-MER)
      • DNA: 23RSS integration strand DNA (66-MER)
      • DNA: Flanking DNA top strand DNA
      • DNA: 23RSS signal top strand DNA (45-MER)
      • DNA: 12RSS signal top strand DNA (34-MER)
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
KeywordsDNA Transposase / RECOMBINATION
Function / homology
Function and homology information


mature B cell differentiation involved in immune response / DNA recombinase complex / B cell homeostatic proliferation / negative regulation of T cell differentiation in thymus / DN2 thymocyte differentiation / 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 / negative regulation of T cell differentiation in thymus / DN2 thymocyte differentiation / 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 / positive regulation of T cell differentiation / regulation of T cell differentiation / organ growth / T cell lineage commitment / 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) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsZhang Y / Corbett E
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01 AI137079 United States
CitationJournal: EMBO J / Year: 2020
Title: Structural basis for the activation and suppression of transposition during evolution of the RAG recombinase.
Authors: Yuhang Zhang / Elizabeth Corbett / Shenping Wu / David G Schatz /
Abstract: Jawed vertebrate adaptive immunity relies on the RAG1/RAG2 (RAG) recombinase, a domesticated transposase, for assembly of antigen receptor genes. Using an integration-activated form of RAG1 with ...Jawed vertebrate adaptive immunity relies on the RAG1/RAG2 (RAG) recombinase, a domesticated transposase, for assembly of antigen receptor genes. Using an integration-activated form of RAG1 with methionine at residue 848 and cryo-electron microscopy, we determined structures that capture RAG engaged with transposon ends and U-shaped target DNA prior to integration (the target capture complex) and two forms of the RAG strand transfer complex that differ based on whether target site DNA is annealed or dynamic. Target site DNA base unstacking, flipping, and melting by RAG1 methionine 848 explain how this residue activates transposition, how RAG can stabilize sharp bends in target DNA, and why replacement of residue 848 by arginine during RAG domestication led to suppression of transposition activity. RAG2 extends a jawed vertebrate-specific loop to interact with target site DNA, and functional assays demonstrate that this loop represents another evolutionary adaptation acquired during RAG domestication to inhibit transposition. Our findings identify mechanistic principles of the final step in cut-and-paste transposition and the molecular and structural logic underlying the transformation of RAG from transposase to recombinase.
History
DepositionJul 5, 2020-
Header (metadata) releaseAug 26, 2020-
Map releaseAug 26, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.03
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  • Surface view with fitted model
  • Atomic models: PDB-6xnx
  • Surface level: 0.03
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22272.png

Downloads & links

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Map

FileDownload / File: emd_22272.map.gz / Format: CCP4 / Size: 55.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRAG1 (R848M/E649V)-RAG2-DNA Strand Transfer Complex (Dynamic-Form)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 244 pix.
= 256.2 Å		1.05 Å/pix.
x 244 pix.
= 256.2 Å		1.05 Å/pix.
x 244 pix.
= 256.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.091903694 - 0.19951604
Average (Standard dev.)0.00000961749 (±0.006341551)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions244244244
Spacing244244244
CellA=B=C: 256.19998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z244244244
origin x/y/z0.0000.0000.000
length x/y/z256.200256.200256.200
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ480480480
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS244244244
D min/max/mean-0.0920.2000.000

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Supplemental data

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Sample components

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Entire : RAG recombinase strand transfer complex

EntireName: RAG recombinase strand transfer complex
Components
  • Complex: RAG recombinase strand transfer complex
    • Complex: V(D)J recombination-activating protein 1, V(D)J recombination-activating protein 2
      • Protein or peptide: V(D)J recombination-activating protein 1
      • Protein or peptide: V(D)J recombination-activating protein 2
    • Complex: DNA
      • DNA: 12RSS integration strand DNA (55-MER)
      • DNA: 23RSS integration strand DNA (66-MER)
      • DNA: Flanking DNA top strand DNA
      • DNA: 23RSS signal top strand DNA (45-MER)
      • DNA: 12RSS signal top strand DNA (34-MER)
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION

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Supramolecule #1: RAG recombinase strand transfer complex

SupramoleculeName: RAG recombinase strand transfer complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7

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Supramolecule #2: V(D)J recombination-activating protein 1, V(D)J recombination-act...

SupramoleculeName: V(D)J recombination-activating protein 1, V(D)J recombination-activating protein 2
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Mus musculus (house mouse)

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Supramolecule #3: DNA

SupramoleculeName: DNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#7
Source (natural)Organism: Homo sapiens (human)

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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: 85.750781 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GPKKISNCSK IHLSTKLLAV DFPAHFVKSI SCQICEHILA DPVETSCKHL FCRICILRCL KVMGSYCPSC RYPCFPTDLE SPVKSFLNI LNSLMVKCPA QDCNEEVSLE KYNHHVSSHK ESKETLVHIN KGGRPRQHLL SLTRRAQKHR LRELKIQVKE F ADKEEGGD ...String:
GPKKISNCSK IHLSTKLLAV DFPAHFVKSI SCQICEHILA DPVETSCKHL FCRICILRCL KVMGSYCPSC RYPCFPTDLE SPVKSFLNI LNSLMVKCPA QDCNEEVSLE KYNHHVSSHK ESKETLVHIN KGGRPRQHLL SLTRRAQKHR LRELKIQVKE F ADKEEGGD VKAVCLTLFL LALRARNEHR QADELEAIMQ GRGSGLQPAV CLAIRVNTFL SCSQYHKMYR TVKAITGRQI FQ PLHALRN AEKVLLPGYH PFEWQPPLKN VSSRTDVGII DGLSGLASSV DEYPVDTIAK RFRYDSALVS ALMDMEEDIL EGM RSQDLD DYLNGPFTVV VKESCDGMGD VSEKHGSGPA VPEKAVRFSF TVMRITIEHG SQNVKVFEEP KPNSVLCCKP LCLM LADES DHETLTAILS PLIAEREAMK SSELTLEMGG IPRTFKFIFR GTGYDEKLVR EVEGLEASGS VYICTLCDTT RLEAS QNLV FHSITRSHAE NLQRYEVWRS NPYHESVEEL RDRVKGVSAK PFIETVPSID ALHCDIGNAA EFYKIFQLEI GEVYKH PNA SKEERKRWQA TLDKHLRKRM NLKPIMMMNG NFARKLMTQE TVDAVCELIP SEERHEALRE LMDLYLKMKP VWRSSCP AK ECPESLCQYS FNSQRFAELL STKFKYRYEG KITNYFHKTL AHVPEIIERD GSIGAWASEG NESGNKLFRR FRKMNARQ S KCYEMEDVLK HHWLYTSKYL QKFMNAHNA

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: 40.416984 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GPMALQMVTV GHNIALIQPG FSLMNFDGQV FFFGQKGWPK RSCPTGVFHF DIKQNHLKLK PAIFSKDSCY LPPLRYPATC SYKGSIDSD KHQYIIHGGK TPNNELSDKI YIMSVACKNN KKVTFRCTEK DLVGDVPEPR YGHSIDVVYS RGKSMGVLFG G RSYMPSTQ ...String:
GPMALQMVTV GHNIALIQPG FSLMNFDGQV FFFGQKGWPK RSCPTGVFHF DIKQNHLKLK PAIFSKDSCY LPPLRYPATC SYKGSIDSD KHQYIIHGGK TPNNELSDKI YIMSVACKNN KKVTFRCTEK DLVGDVPEPR YGHSIDVVYS RGKSMGVLFG G RSYMPSTQ RTTEKWNSVA DCLPHVFLID FEFGCATSYI LPELQDGLSF HVSIARNDTV YILGGHSLAS NIRPANLYRI RV DLPLGTP AVNCTVLPGG ISVSSAILTQ TNNDEFVIVG GYQLENQKRM VCSLVSLGDN TIEISEMETP DWTSDIKHSK IWF GSNMGN GTIFLGIPGD NKQAMSEAFY FYTLRCSEED LSEDQKI

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

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Macromolecule #3: 12RSS integration strand DNA (55-MER)

MacromoleculeName: 12RSS integration strand DNA (55-MER) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.901791 KDa
SequenceString: (DG)(DG)(DT)(DC)(DG)(DA)(DG)(DG)(DT)(DT) (DT)(DT)(DT)(DG)(DT)(DA)(DC)(DA)(DG)(DC) (DC)(DT)(DA)(DC)(DT)(DA)(DC)(DC)(DA) (DC)(DT)(DG)(DT)(DG)(DC)(DG)(DC)(DC)(DG) (DG) (DT)(DA)(DG)(DC)(DC)(DC) ...String:
(DG)(DG)(DT)(DC)(DG)(DA)(DG)(DG)(DT)(DT) (DT)(DT)(DT)(DG)(DT)(DA)(DC)(DA)(DG)(DC) (DC)(DT)(DA)(DC)(DT)(DA)(DC)(DC)(DA) (DC)(DT)(DG)(DT)(DG)(DC)(DG)(DC)(DC)(DG) (DG) (DT)(DA)(DG)(DC)(DC)(DC)(DT)(DA) (DT)(DC)(DC)(DT)(DG)(DA)(DG)

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Macromolecule #4: 23RSS integration strand DNA (66-MER)

MacromoleculeName: 23RSS integration strand DNA (66-MER) / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.322986 KDa
SequenceString: (DG)(DG)(DT)(DC)(DG)(DA)(DG)(DG)(DT)(DT) (DT)(DT)(DT)(DG)(DT)(DA)(DC)(DA)(DG)(DC) (DC)(DA)(DG)(DA)(DC)(DA)(DA)(DC)(DA) (DG)(DC)(DC)(DT)(DA)(DC)(DT)(DA)(DC)(DC) (DA) (DC)(DT)(DG)(DT)(DG)(DC) ...String:
(DG)(DG)(DT)(DC)(DG)(DA)(DG)(DG)(DT)(DT) (DT)(DT)(DT)(DG)(DT)(DA)(DC)(DA)(DG)(DC) (DC)(DA)(DG)(DA)(DC)(DA)(DA)(DC)(DA) (DG)(DC)(DC)(DT)(DA)(DC)(DT)(DA)(DC)(DC) (DA) (DC)(DT)(DG)(DT)(DG)(DC)(DG)(DG) (DC)(DG)(DG)(DT)(DA)(DG)(DC)(DC)(DC)(DT) (DA)(DT) (DC)(DC)(DT)(DG)(DA)(DG)

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Macromolecule #5: Flanking DNA top strand DNA

MacromoleculeName: Flanking DNA top strand DNA / type: dna / ID: 5 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 4.923204 KDa
SequenceString:
(DC)(DT)(DC)(DA)(DG)(DG)(DA)(DT)(DA)(DG) (DG)(DG)(DC)(DT)(DA)(DC)

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Macromolecule #6: 23RSS signal top strand DNA (45-MER)

MacromoleculeName: 23RSS signal top strand DNA (45-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.877906 KDa
SequenceString:
(DC)(DA)(DC)(DA)(DG)(DT)(DG)(DG)(DT)(DA) (DG)(DT)(DA)(DG)(DG)(DC)(DT)(DG)(DT)(DT) (DG)(DT)(DC)(DT)(DG)(DG)(DC)(DT)(DG) (DT)(DA)(DC)(DA)(DA)(DA)(DA)(DA)(DC)(DC) (DT) (DC)(DG)(DA)(DC)(DC)

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Macromolecule #7: 12RSS signal top strand DNA (34-MER)

MacromoleculeName: 12RSS signal top strand DNA (34-MER) / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.461758 KDa
SequenceString:
(DC)(DA)(DC)(DA)(DG)(DT)(DG)(DG)(DT)(DA) (DG)(DT)(DA)(DG)(DG)(DC)(DT)(DG)(DT)(DA) (DC)(DA)(DA)(DA)(DA)(DA)(DC)(DC)(DT) (DC)(DG)(DA)(DC)(DC)

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Macromolecule #8: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 8 / Number of copies: 4 / 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

Concentration0.4 mg/mL
BufferpH: 7.6
Details: 20 mM HEPES pH7.6, 0.5 mM TCEP, 5 mM MgCl2 and 150 mM KCl
GridModel: C-flat-2/1 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number real images: 3527 / Average exposure time: 11.0 sec. / Average electron dose: 72.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 636773
Startup modelType of model: INSILICO MODEL
In silico model: the initial model generated by RELION with a small group selected particles.
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 106374
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final 3D classificationSoftware - Name: RELION (ver. 3.0)

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Atomic model buiding 1

Initial modelPDB ID:

5zdz


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-6xnx:
Structure of RAG1 (R848M/E649V)-RAG2-DNA Strand Transfer Complex (Dynamic-Form)

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