[English] 日本語
Yorodumi
- PDB-6p5a: Drosophila P element transposase strand transfer complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6p5a
TitleDrosophila P element transposase strand transfer complex
Components
  • (Transposable element P ...) x 2
  • DNA (44-MER)
  • DNA (5'-D(P*AP*GP*GP*TP*GP*GP*TP*CP*CP*CP*GP*TP*CP*GP*G)-3')
  • DNA (5'-D(P*CP*GP*AP*AP*CP*TP*AP*TP*A)-3')
KeywordsTRANSFERASE/DNA / transposase / Strand Transfer Complex / TRANSFERASE-DNA complex
Function / homology
Function and homology information


P-element binding / transposase activity / DNA transposition / DNA integration / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / transferase activity / metal ion binding
Similarity search - Function
87kDa Transposase / : / : / : / 87kDa Transposase / TNP-like, RNase H N-terminal domain / TNP-like, GTP-binding insertion domain / TNP-like, RNase H C-terminal domain / THAP-type zinc finger superfamily / Zinc finger domain in CG10631, C. elegans LIN-15B and human P52rIPK. ...87kDa Transposase / : / : / : / 87kDa Transposase / TNP-like, RNase H N-terminal domain / TNP-like, GTP-binding insertion domain / TNP-like, RNase H C-terminal domain / THAP-type zinc finger superfamily / Zinc finger domain in CG10631, C. elegans LIN-15B and human P52rIPK. / THAP-type zinc finger / THAP domain / Zinc finger THAP-type profile
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / Transposable element P transposase
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsKellogg, E.H. / Nogales, E. / Ghanim, G. / Rio, D.C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)K99GM124463 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R35GM118121 United States
CitationJournal: Nat Struct Mol Biol / Year: 2019
Title: Structure of a P element transposase-DNA complex reveals unusual DNA structures and GTP-DNA contacts.
Authors: George E Ghanim / Elizabeth H Kellogg / Eva Nogales / Donald C Rio /
Abstract: P element transposase catalyzes the mobility of P element DNA transposons within the Drosophila genome. P element transposase exhibits several unique properties, including the requirement for a ...P element transposase catalyzes the mobility of P element DNA transposons within the Drosophila genome. P element transposase exhibits several unique properties, including the requirement for a guanosine triphosphate cofactor and the generation of long staggered DNA breaks during transposition. To gain insights into these features, we determined the atomic structure of the Drosophila P element transposase strand transfer complex using cryo-EM. The structure of this post-transposition nucleoprotein complex reveals that the terminal single-stranded transposon DNA adopts unusual A-form and distorted B-form helical geometries that are stabilized by extensive protein-DNA interactions. Additionally, we infer that the bound guanosine triphosphate cofactor interacts with the terminal base of the transposon DNA, apparently to position the P element DNA for catalysis. Our structure provides the first view of the P element transposase superfamily, offers new insights into P element transposition and implies a transposition pathway fundamentally distinct from other cut-and-paste DNA transposases.
History
DepositionMay 30, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 27, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-20254
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transposable element P transposase
B: Transposable element P transposase
C: DNA (5'-D(P*CP*GP*AP*AP*CP*TP*AP*TP*A)-3')
D: DNA (5'-D(P*AP*GP*GP*TP*GP*GP*TP*CP*CP*CP*GP*TP*CP*GP*G)-3')
E: DNA (44-MER)
G: Transposable element P transposase
H: Transposable element P transposase
I: DNA (5'-D(P*CP*GP*AP*AP*CP*TP*AP*TP*A)-3')
J: DNA (5'-D(P*AP*GP*GP*TP*GP*GP*TP*CP*CP*CP*GP*TP*CP*GP*G)-3')
K: DNA (44-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)246,23416
Polymers245,09010
Non-polymers1,1446
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area36480 Å2
ΔGint-178 kcal/mol
Surface area60190 Å2

-
Components

-
Transposable element P ... , 2 types, 4 molecules AGBH

#1: Protein Transposable element P transposase / P-element transposase / THAP domain-containing protein / DmTHAP


Mass: 65525.992 Da / Num. of mol.: 2 / Fragment: N-terminal domain (UNP residues 1-569)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q7M3K2, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Protein Transposable element P transposase / P-element transposase / THAP domain-containing protein / DmTHAP


Mass: 16086.797 Da / Num. of mol.: 2 / Fragment: C-terminal domain (UNP residues 613-747)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q7M3K2, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases

-
DNA chain , 3 types, 6 molecules CIDJEK

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


Mass: 4827.157 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Drosophila melanogaster (fruit fly)
#4: DNA chain DNA (5'-D(P*AP*GP*GP*TP*GP*GP*TP*CP*CP*CP*GP*TP*CP*GP*G)-3')


Mass: 11704.529 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Drosophila melanogaster (fruit fly)
#5: DNA chain DNA (44-MER)


Mass: 24400.576 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Drosophila melanogaster (fruit fly)

-
Non-polymers , 2 types, 6 molecules

#6: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#7: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Ternary complex of P element transposase in complex with strand transfer DNA
Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.6
Buffer component
IDConc.NameFormulaBuffer-ID
125 mMHEPESC8H18N2O4S1
2100 mMpotassium chlorideKCl1
310 mMmagnesium acetateMgC4H6O41
410 uMzinc sulfateZnSO41
50.5 mMTCEPC9H15O6P1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: UltrAuFoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K
Details: 4 microliters of concentrated STC complex was applied to a Quantifoil 1.2/1.3 UltraAuFoil grid. After a 30 second incubation, the sample was blotted using blot force of 8 pN and a blot time of 6 seconds.

-
Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI ARCTICA / Details: Dataset collected at 40 degree tilt.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 10 sec. / Electron dose: 60 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: 1857
Image scansWidth: 7420 / Height: 7676 / Movie frames/image: 39

-
Processing

EM software
IDNameVersionCategoryDetails
2SerialEMimage acquisition
4GctfCTF correction
7Cootmodel fitting
10RELION3final Euler assignmentbeta version
12RELION33D reconstructionbeta
13Rosettamodel refinement
14PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING ONLY
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 253209 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 100 / Protocol: AB INITIO MODEL / Space: REAL / Target criteria: correlation coefficient

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
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.
  • 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 Accession Codes are Changing Soon! / 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.
  • 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

-
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.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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