[English] 日本語
Yorodumi
- EMDB-47288: attPmm and attBmm bound serine integrase complex in the pre-rotat... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-47288
TitleattPmm and attBmm bound serine integrase complex in the pre-rotation state
Map datacomposite map
Sample
  • Complex: attLmm bound serine integrase and RDF complex in the pre-rotation state
    • Protein or peptide: Resolvase homolog YokA
    • DNA: DNA (34-MER)
    • DNA: DNA (33-MER)
    • DNA: DNA (25-MER)
  • DNA: DNA (24-MER)
  • Ligand: ZINC ION
KeywordsViral protein / Integrase / Recombinase / Complex / Recombination Directionality Factor / Integration / Excision / DNA BINDING PROTEIN
Function / homology
Function and homology information


DNA strand exchange activity / DNA integration / DNA recombination / DNA binding
Similarity search - Function
Recombinase / DNA-binding recombinase domain / DNA-binding recombinase domain superfamily / DNA-binding recombinase domain profile. / : / Resolvase/invertase-type recombinase catalytic domain profile. / Resolvase, N-terminal catalytic domain / Resolvase-like, N-terminal catalytic domain superfamily / Resolvase, N terminal domain / Resolvase, N terminal domain
Similarity search - Domain/homology
Resolvase homolog YokA
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.69 Å
AuthorsShin H / Rice PA / Olorunniji FJ
Funding support United States, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
CitationJournal: To Be Published
Title: Structural Basis of Directionality Control in Large Serine Integrases
Authors: Shin HS / Rice PA
History
DepositionOct 11, 2024-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_47288.png

Downloads & links

-
Map

FileDownload / File: emd_47288.map.gz / Format: CCP4 / Size: 290.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcomposite map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 387 pix.
= 412.155 Å		1.07 Å/pix.
x 453 pix.
= 482.445 Å		1.07 Å/pix.
x 435 pix.
= 463.275 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.065 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.000756608 - 1.641875
Average (Standard dev.)0.0006965972 (±0.018068139)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-83-80-68
Dimensions453435387
Spacing435453387
CellA: 463.27502 Å / B: 482.44504 Å / C: 412.15503 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : attLmm bound serine integrase and RDF complex in the pre-rotation...

EntireName: attLmm bound serine integrase and RDF complex in the pre-rotation state
Components
  • Complex: attLmm bound serine integrase and RDF complex in the pre-rotation state
    • Protein or peptide: Resolvase homolog YokA
    • DNA: DNA (34-MER)
    • DNA: DNA (33-MER)
    • DNA: DNA (25-MER)
  • DNA: DNA (24-MER)
  • Ligand: ZINC ION

-
Supramolecule #1: attLmm bound serine integrase and RDF complex in the pre-rotation...

SupramoleculeName: attLmm bound serine integrase and RDF complex in the pre-rotation state
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Bacillus subtilis (bacteria)

-
Macromolecule #1: Resolvase homolog YokA

MacromoleculeName: Resolvase homolog YokA / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 63.232066 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MELKNIVNSY NITNILGYLR RSRQDMEREK RTGEDTLTEQ KELMNKILTA IEIPYELKME IGSGESIDGR PVFKECLKDL EEGKYQAIA VKEITRLSRG SYSDAGQIVN LLQSKRLIII TPYKVYDPRN PVDMRQIRFE LFMAREEFEM TRERMTGAKY T YAAQGKWI ...String:
MELKNIVNSY NITNILGYLR RSRQDMEREK RTGEDTLTEQ KELMNKILTA IEIPYELKME IGSGESIDGR PVFKECLKDL EEGKYQAIA VKEITRLSRG SYSDAGQIVN LLQSKRLIII TPYKVYDPRN PVDMRQIRFE LFMAREEFEM TRERMTGAKY T YAAQGKWI SGLAPYGYQL NKKTSKLDPV EDEAKVVQLI FNIFLNGLNG KDYSYTAIAS HLTNLQIPTP SGKKRWNQYT IK AILQNEV YIGTVKYKVR EKTKDGKRTI RPEKEQIVVQ DAHAPIIDKE QFQQSQVKIA NKVPLLPNKD EFELSELAGV CTC SKCGEP LSKYESKRIR KNKDGTESVY HVKSLTCKKN KCTYVRYNDV ENAILDYLSS LNDLNDSTLT KHINSMLSKY EDDN SNMKT KKQMSEHLSQ KEKELKNKEN FIFDKYESGI YSDELFLKRK AALDEEFKEL QNAKNELNGL QDTQSEIDSN TVRNN INKI IDQYHIESSS EKKNELLRMV LKDVIVNMTQ KRKGPIPAQF EITPILRFNF IFDLTATNSF H

UniProtKB: Resolvase homolog YokA

-
Macromolecule #2: DNA (34-MER)

MacromoleculeName: DNA (34-MER) / type: dna / ID: 2 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 10.433742 KDa
SequenceString:
(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DG)(DT) (DA)(DG)(DT)(DA)(DA)(DG)(DT)(DA)(DT)(DC) (DT)(DT)(DA)(DA)(DT)(DA)(DT)(DA)(DC) (DA)(DG)(DC)(DT)(DT)

-
Macromolecule #3: DNA (33-MER)

MacromoleculeName: DNA (33-MER) / type: dna / ID: 3 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 10.161636 KDa
SequenceString:
(DA)(DG)(DC)(DT)(DG)(DT)(DA)(DT)(DA)(DT) (DT)(DA)(DA)(DG)(DA)(DT)(DA)(DC)(DT)(DT) (DA)(DC)(DT)(DA)(DC)(DA)(DA)(DA)(DA) (DA)(DA)(DA)(DA)

-
Macromolecule #4: DNA (25-MER)

MacromoleculeName: DNA (25-MER) / type: dna / ID: 4 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 7.655984 KDa
SequenceString:
(DC)(DA)(DT)(DG)(DT)(DC)(DA)(DT)(DT)(DA) (DA)(DT)(DA)(DT)(DC)(DA)(DG)(DT)(DA)(DC) (DA)(DG)(DA)(DT)(DT)

-
Macromolecule #5: DNA (24-MER)

MacromoleculeName: DNA (24-MER) / type: dna / ID: 5 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 7.382801 KDa
SequenceString:
(DA)(DT)(DC)(DT)(DG)(DT)(DA)(DC)(DT)(DG) (DA)(DT)(DA)(DT)(DT)(DA)(DA)(DT)(DG)(DA) (DC)(DA)(DT)(DG)

-
Macromolecule #6: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 6 / Number of copies: 4 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
Sugar embeddingMaterial: vitreous ice
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 291.15 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 65.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.69 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 44115
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

+
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