[English] 日本語
Yorodumi
- PDB-6b40: BbRAGL-3'TIR synaptic complex with nicked DNA refined with C2 symmetry -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 6b40
TitleBbRAGL-3'TIR synaptic complex with nicked DNA refined with C2 symmetry
Components
  • (31TIR pre-nicked strand of ...) x 2
  • 31TIR intact strand
  • RAG1L,RAG1L
  • RAG2L
KeywordsRECOMBINATION / DNA transposase / DNA cut and paste transposition / DDE family RNase H fold DNA transposase
Function / homologyZinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Kelch-type beta propeller / Zinc finger, RING-type, conserved site / V(D)J recombination-activating protein 1 / RAG1 importin-binding / RAG1 importin binding / Recombination-activation protein 1 (RAG1), recombinase / Zinc finger RING-type signature. / Zinc finger RING-type profile. ...Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Kelch-type beta propeller / Zinc finger, RING-type, conserved site / V(D)J recombination-activating protein 1 / RAG1 importin-binding / RAG1 importin binding / Recombination-activation protein 1 (RAG1), recombinase / Zinc finger RING-type signature. / Zinc finger RING-type profile. / V(D)J recombination / ubiquitin protein ligase activity / endonuclease activity / sequence-specific DNA binding / RAG1L / RAG2L
Function and homology information
Specimen sourceBranchiostoma belcheri (Belcher's lancelet)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsZhang, Y. / Cheng, T.C. / Xiong, Y. / Schatz, D.G.
Funding supportUnited States , Romania , 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesNIH R37AI32524United States
UEFISCDIPN-III-ID-PCE-2016-0650Romania
CitationJournal: Nature / Year: 2019
Title: Transposon molecular domestication and the evolution of the RAG recombinase.
Authors: Yuhang Zhang / Tat Cheung Cheng / Guangrui Huang / Qingyi Lu / Marius D Surleac / Jeffrey D Mandell / Pierre Pontarotti / Andrei J Petrescu / Anlong Xu / Yong Xiong / David G Schatz /
Abstract: Domestication of a transposon (a DNA sequence that can change its position in a genome) to give rise to the RAG1-RAG2 recombinase (RAG) and V(D)J recombination, which produces the diverse repertoire ...Domestication of a transposon (a DNA sequence that can change its position in a genome) to give rise to the RAG1-RAG2 recombinase (RAG) and V(D)J recombination, which produces the diverse repertoire of antibodies and T cell receptors, was a pivotal event in the evolution of the adaptive immune system of jawed vertebrates. The evolutionary adaptations that transformed the ancestral RAG transposase into a RAG recombinase with appropriately regulated DNA cleavage and transposition activities are not understood. Here, beginning with cryo-electron microscopy structures of the amphioxus ProtoRAG transposase (an evolutionary relative of RAG), we identify amino acid residues and domains the acquisition or loss of which underpins the propensity of RAG for coupled cleavage, its preference for asymmetric DNA substrates and its inability to perform transposition in cells. In particular, we identify two adaptations specific to jawed-vertebrates-arginine 848 in RAG1 and an acidic region in RAG2-that together suppress RAG-mediated transposition more than 1,000-fold. Our findings reveal a two-tiered mechanism for the suppression of RAG-mediated transposition, illuminate the evolution of V(D)J recombination and provide insight into the principles that govern the molecular domestication of transposons.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Sep 25, 2017 / Release: Mar 20, 2019
RevisionDateData content typeGroupCategoryItemProviderType
1.0Mar 20, 2019Structure modelrepositoryInitial release
1.1Apr 10, 2019Structure modelAuthor supporting evidence / Data collectionpdbx_audit_support_pdbx_audit_support.funding_organization

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-7046
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RAG1L,RAG1L
B: 31TIR intact strand
C: 31TIR pre-nicked strand of signal DNA
D: 31TIR pre-nicked strand of flanking DNA
M: RAG2L
E: RAG1L,RAG1L
F: 31TIR intact strand
G: 31TIR pre-nicked strand of signal DNA
H: 31TIR pre-nicked strand of flanking DNA
N: RAG2L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)304,46514
Polyers304,25410
Non-polymers2114
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)26360
ΔGint (kcal/M)-162
Surface area (Å2)95760

-
Components

-
Protein/peptide , 2 types, 4 molecules AEMN

#1: Protein/peptide RAG1L,RAG1L


Mass: 74440.133 Da / Num. of mol.: 2
Source: (gene. exp.) Branchiostoma belcheri (Belcher's lancelet)
Gene: RAG1L / Production host: Homo sapiens (human) / References: UniProt: A0A185KID9
#5: Protein/peptide RAG2L


Mass: 39509.254 Da / Num. of mol.: 2
Source: (gene. exp.) Branchiostoma belcheri (Belcher's lancelet)
Gene: RAG2L / Production host: Homo sapiens (human) / References: UniProt: A0A185KIE0

-
DNA chain , 1 types, 2 molecules BF

#2: DNA chain 31TIR intact strand / 31TIR intact strand


Mass: 19218.312 Da / Num. of mol.: 2
Source: (synth.) Branchiostoma belcheri (Belcher's lancelet)

-
31TIR pre-nicked strand of ... , 2 types, 4 molecules CGDH

#3: DNA chain 31TIR pre-nicked strand of signal DNA / 31TIR pre-nicked strand of signal DNA


Mass: 14357.206 Da / Num. of mol.: 2
Source: (synth.) Branchiostoma belcheri (Belcher's lancelet)
#4: DNA chain 31TIR pre-nicked strand of flanking DNA / 31TIR pre-nicked strand of flanking DNA


Mass: 4601.971 Da / Num. of mol.: 2
Source: (synth.) Branchiostoma belcheri (Belcher's lancelet)

-
Non-polymers , 2 types, 4 molecules

#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Formula: Ca / Calcium
#7: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Formula: Zn / Zinc

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: BbRAGL-31TIR synaptic complex with nicked DNA / Type: COMPLEX / Entity ID: 1, 2, 3, 4, 5 / Source: RECOMBINANT
Molecular weightValue: 0.35 MDa / Experimental value: NO
Source (natural)Organism: Branchiostoma belcheri (Belcher's lancelet)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.6
SpecimenConc.: 0.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 / Grid type: C-flat-1.2/1.3 4C
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283 kelvins

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 81000 / Nominal defocus max: 2500 nm / Nominal defocus min: 1200 nm / Cs: 0.01 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 10 sec. / Electron dose: 54 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4429
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter upper: 20 eV / Energyfilter lower: 0 eV
Image scansSampling size: 5 microns / Width: 7676 / Height: 7420 / Movie frames/image: 40 / Used frames/image: 3-40

-
Processing

EM software
IDNameVersionCategory
1RELION2.1particle selection
2SerialEM3.6image acquisition
4Gctf1.08CTF correction
7MDFFmodel fitting
8Rosettamodel fitting
9Cootmodel fitting
11RELION2.1initial Euler assignment
12RELION2.1final Euler assignment
13RELION2.1classification
14RELION2.13D reconstruction
15PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 496221
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 350143 / Algorithm: BACK PROJECTION / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL

+
About Yorodumi

-
News

-
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.: Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator

External links: EMDB at PDBe / Contact to PDBj

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more