[English] 日本語
Yorodumi
- EMDB-60896: Cryo-EM structure of the large serine recombinase Bxb1 in complex... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-60896
TitleCryo-EM structure of the large serine recombinase Bxb1 in complex with attP and attB (GT/TT CDN) in the pre-strand exchange state (attB-R)
Map data
Sample
  • Complex: The large serine recombinase Bxb1 in complex with attP and attB (GT/TT CDN) in the pre-strand exchange state (attB-R)
    • Complex: attB-R
      • DNA: attB-R
      • DNA: attB-R
    • Complex: large serine recombinase
      • Protein or peptide: Integrase
  • Ligand: ZINC ION
Keywordslarge serine recombinase / DNA BINDING PROTEIN
Function / homology
Function and homology information


DNA strand exchange activity / 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
Biological speciesMycolicibacterium smegmatis (bacteria) / Mycobacterium phage Bxb1 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.08 Å
AuthorsSoma T / Hiraizumi M / Yamashita K / Nishimasu H
Funding support Japan, 2 items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJAX232F Japan
Japan Science and TechnologyJPMJCR23B6 Japan
CitationJournal: To Be Published
Title: Cryo-EM structure of the large serine recombinase Bxb1 in complex with attP and attB (GT/TT CDN) in the pre-strand exchange state (attB-R)
Authors: Soma T
History
DepositionJul 20, 2024-
Header (metadata) releaseMar 4, 2026-
Map releaseMar 4, 2026-
UpdateMar 4, 2026-
Current statusMar 4, 2026Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_60896.png

Downloads & links

-
Map

FileDownload / File: emd_60896.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.18 Å/pix.
x 240 pix.
= 282.199 Å		1.18 Å/pix.
x 240 pix.
= 282.199 Å		1.18 Å/pix.
x 240 pix.
= 282.199 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.17583 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-2.7110777 - 4.1488523
Average (Standard dev.)-0.00010600713 (±0.046388596)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 282.1992 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_60896_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_60896_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_60896_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : The large serine recombinase Bxb1 in complex with attP and attB (...

EntireName: The large serine recombinase Bxb1 in complex with attP and attB (GT/TT CDN) in the pre-strand exchange state (attB-R)
Components
  • Complex: The large serine recombinase Bxb1 in complex with attP and attB (GT/TT CDN) in the pre-strand exchange state (attB-R)
    • Complex: attB-R
      • DNA: attB-R
      • DNA: attB-R
    • Complex: large serine recombinase
      • Protein or peptide: Integrase
  • Ligand: ZINC ION

-
Supramolecule #1: The large serine recombinase Bxb1 in complex with attP and attB (...

SupramoleculeName: The large serine recombinase Bxb1 in complex with attP and attB (GT/TT CDN) in the pre-strand exchange state (attB-R)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

-
Supramolecule #2: attB-R

SupramoleculeName: attB-R / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Mycolicibacterium smegmatis (bacteria)

-
Supramolecule #3: large serine recombinase

SupramoleculeName: large serine recombinase / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Mycobacterium phage Bxb1 (virus) / Synthetically produced: Yes

-
Macromolecule #1: attB-R

MacromoleculeName: attB-R / type: dna / ID: 1 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Mycolicibacterium smegmatis (bacteria)
Molecular weightTheoretical: 6.704316 KDa
SequenceString:
(DC)(DT)(DC)(DC)(DG)(DT)(DC)(DG)(DT)(DC) (DA)(DG)(DG)(DA)(DT)(DC)(DA)(DT)(DC)(DC) (DG)(DG)

GENBANK: GENBANK: LN831039.1

-
Macromolecule #2: attB-R

MacromoleculeName: attB-R / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Mycolicibacterium smegmatis (bacteria)
Molecular weightTheoretical: 7.410779 KDa
SequenceString:
(DC)(DC)(DG)(DG)(DA)(DT)(DG)(DA)(DT)(DC) (DC)(DT)(DG)(DA)(DC)(DG)(DA)(DC)(DG)(DG) (DA)(DG)(DT)(DT)

GENBANK: GENBANK: LN831039.1

-
Macromolecule #3: Integrase

MacromoleculeName: Integrase / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium phage Bxb1 (virus)
Molecular weightTheoretical: 56.439949 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MRALVVIRLS RVTDATTSPE RQLESCQQLC AQRGWDVVGV AEDLDVSGAV DPFDRKRRPN LARWLAFEEQ PFDVIVAYRV DRLTRSIRH LQQLVHWAED HKKLVVSATE AHFDTTTPFA AVVIALMGTV AQMELEAIKE RNRSAAHFNI RAGKYRGSLP P WGYLPTRV ...String:
MRALVVIRLS RVTDATTSPE RQLESCQQLC AQRGWDVVGV AEDLDVSGAV DPFDRKRRPN LARWLAFEEQ PFDVIVAYRV DRLTRSIRH LQQLVHWAED HKKLVVSATE AHFDTTTPFA AVVIALMGTV AQMELEAIKE RNRSAAHFNI RAGKYRGSLP P WGYLPTRV DGEWRLVPDP VQRERILEVY HRVVDNHEPL HLVAHDLNRR GVLSPKDYFA QLQGREPQGR EWSATALKRS MI SEAMLGY ATLNGKTVRD DDGAPLVRAE PILTREQLEA LRAELVKTSR AKPAVSTPSL LLRVLFCAVC GEPAYKFAGG GRK HPRYRC RSMGFPKHCG NGTVAMAEWD AFCEEQVLDL LGDAERLEKV WVAGSDSAVE LAEVNAELVD LTSLIGSPAY RAGS PQREA LDARIAALAA RQEELEGLEA RPSGWEWRET GQRFGDWWRE QDTAAKNTWL RSMNVRLTFD VRGGLTRTID FGDLQ EYEQ HLRLGSVVER LHTGMS

UniProtKB: Integrase

-
Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 51.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.08 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 266035
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

+
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