[English] 日本語
Yorodumi
- EMDB-80336: Cryo-EM structure of the E. coli beta sliding clamp-Hda heterotrimer -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-80336
TitleCryo-EM structure of the E. coli beta sliding clamp-Hda heterotrimer
Map datasharpened map
Sample
  • Complex: Heterotrimeric complex of beta sliding clamp and Hda
    • Protein or peptide: Beta sliding clamp
    • Protein or peptide: DnaA regulatory inactivator Hda
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsReplication inactivator / Inhibitor / ATPase / TRANSFERASE
Function / homology
Function and homology information


replication inhibiting complex / Hda-beta clamp complex / DNA polymerase III complex / DNA strand elongation involved in DNA replication / DNA replication initiation / regulation of DNA-templated DNA replication initiation / 3'-5' exonuclease activity / negative regulation of DNA-templated DNA replication initiation / ADP binding / DNA replication ...replication inhibiting complex / Hda-beta clamp complex / DNA polymerase III complex / DNA strand elongation involved in DNA replication / DNA replication initiation / regulation of DNA-templated DNA replication initiation / 3'-5' exonuclease activity / negative regulation of DNA-templated DNA replication initiation / ADP binding / DNA replication / DNA-directed DNA polymerase activity / DNA binding / membrane / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
DnaA regulatory inactivator Hda, Enterobacteriaceae / : / DnaA regulatory inactivator Hda / Hda, lid domain / Chromosomal replication control, initiator DnaA-like / Chromosomal replication initiator protein DnaA / Bacterial DnaA ATPAse domain / DNA polymerase III, beta sliding clamp / DNA polymerase III, beta sliding clamp, N-terminal / DNA polymerase III, beta sliding clamp, C-terminal ...DnaA regulatory inactivator Hda, Enterobacteriaceae / : / DnaA regulatory inactivator Hda / Hda, lid domain / Chromosomal replication control, initiator DnaA-like / Chromosomal replication initiator protein DnaA / Bacterial DnaA ATPAse domain / DNA polymerase III, beta sliding clamp / DNA polymerase III, beta sliding clamp, N-terminal / DNA polymerase III, beta sliding clamp, C-terminal / DNA polymerase III, beta sliding clamp, central / DNA polymerase III beta subunit, N-terminal domain / DNA polymerase III beta subunit, central domain / DNA polymerase III beta subunit, C-terminal domain / DNA polymerase III beta subunit / : / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Beta sliding clamp / DnaA regulatory inactivator Hda
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.17 Å
AuthorsJiang X / Danev R / Kikkawa M
Funding support Japan, 4 items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJER2202 Japan
Japan Society for the Promotion of Science (JSPS)JP21H05247 Japan
Japan Society for the Promotion of Science (JSPS)JP24KF0141 Japan
Japan Society for the Promotion of Science (JSPS)JP24K18106 Japan
CitationJournal: Nucleic Acids Res. / Year: 2026
Title: Reversible autoinhibition of the bacterial replication-licensing Hda-beta clamp complex.
Authors: Jiang X / Danev R / Luan Y / Nakakido M / Tsumoto K / Kikkawa M
History
DepositionApr 16, 2026-
Header (metadata) releaseOct 7, 2026-
Map releaseOct 7, 2026-
UpdateOct 7, 2026-
Current statusOct 7, 2026Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_80336.png

Downloads & links

-
Map

FileDownload / File: emd_80336.map.gz / Format: CCP4 / Size: 11.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.14 Å/pix.
x 144 pix.
= 164.448 Å		1.14 Å/pix.
x 144 pix.
= 164.448 Å		1.14 Å/pix.
x 144 pix.
= 164.448 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.142 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.005771338 - 1.886114
Average (Standard dev.)0.0060291486 (±0.057684846)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions144144144
Spacing144144144
CellA=B=C: 164.448 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_80336_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: raw map

Fileemd_80336_additional_1.map
Annotationraw map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: halfmap2

Fileemd_80336_half_map_1.map
Annotationhalfmap2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: halfmap1

Fileemd_80336_half_map_2.map
Annotationhalfmap1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Heterotrimeric complex of beta sliding clamp and Hda

EntireName: Heterotrimeric complex of beta sliding clamp and Hda
Components
  • Complex: Heterotrimeric complex of beta sliding clamp and Hda
    • Protein or peptide: Beta sliding clamp
    • Protein or peptide: DnaA regulatory inactivator Hda
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION

-
Supramolecule #1: Heterotrimeric complex of beta sliding clamp and Hda

SupramoleculeName: Heterotrimeric complex of beta sliding clamp and Hda / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 132 KDa

-
Macromolecule #1: Beta sliding clamp

MacromoleculeName: Beta sliding clamp / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 42.801863 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MGSSHHHHHH SSGLVPRGSH MKFTVEREHL LKPLQQVSGP LGGRPTLPIL GNLLLQVADG TLSLTGTDLE MEMVARVALV QPHEPGATT VPARKFFDIC RGLPEGAEIA VQLEGERMLV RSGRSRFSLS TLPAADFPNL DDWQSEVEFT LPQATMKRLI E ATQFSMAH ...String:
MGSSHHHHHH SSGLVPRGSH MKFTVEREHL LKPLQQVSGP LGGRPTLPIL GNLLLQVADG TLSLTGTDLE MEMVARVALV QPHEPGATT VPARKFFDIC RGLPEGAEIA VQLEGERMLV RSGRSRFSLS TLPAADFPNL DDWQSEVEFT LPQATMKRLI E ATQFSMAH QDVRYYLNGM LFETEGEELR TVATDGHRLA VCSMPIGQSL PSHSVIVPRK GVIELMRMLD GGDNPLRVQI GS NNIRAHV GDFIFTSKLV DGRFPDYRRV LPKNPDKHLE AGCDLLKQAF ARAAILSNEK FRGVRLYVSE NQLKITANNP EQE EAEEIL DVTYSGAEME IGFNVSYVLD VLNALKCENV RMMLTDSVSS VQIEDAASQS AAYVVMPMRL

UniProtKB: Beta sliding clamp

-
Macromolecule #2: DnaA regulatory inactivator Hda

MacromoleculeName: DnaA regulatory inactivator Hda / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 26.663678 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MNTPAQLSLP LYLPDDETFA SFWPGDNSSL LAALQNVLRQ EHSGYIYLWA REGAGRSHLL HAACAELSQR GDAVGYVPLD KRTWFVPEV LDGMEHLSLV CIDNIECIAG DELWEMAIFD LYNRILESGK TRLLITGDRP PRQLNLGLPD LASRLDWGQI Y KLQPLSDE ...String:
MNTPAQLSLP LYLPDDETFA SFWPGDNSSL LAALQNVLRQ EHSGYIYLWA REGAGRSHLL HAACAELSQR GDAVGYVPLD KRTWFVPEV LDGMEHLSLV CIDNIECIAG DELWEMAIFD LYNRILESGK TRLLITGDRP PRQLNLGLPD LASRLDWGQI Y KLQPLSDE DKLQALQLRA RLRGFELPED VGRFLLKRLD REMRTLFMTL DQLDRASITA QRKLTIPFVK EILKL

UniProtKB: DnaA regulatory inactivator Hda

-
Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

-
Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration01.5 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 279 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeJEOL CRYO ARM 200
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 12396 / Average electron dose: 76.4 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 1.8 µm / Calibrated defocus min: 0.4 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 1.55 mm / Nominal defocus max: 1.3 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 80000
Sample stageCooling holder cryogen: NITROGEN

+
Image processing

Particle selectionNumber selected: 3682439
CTF correctionSoftware - Name: cryoSPARC (ver. 5.0.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab-Initio Reconstruction
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.17 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 5.0.0) / Number images used: 453440
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 5.0.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 5.0.0)
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC (ver. 5.0.0)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

5x06


Chain - Source name: PDB / Chain - Initial model type: experimental model / Details: Truncated model from 5X06
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-25sa:
Cryo-EM structure of the E. coli beta sliding clamp-Hda heterotrimer

+
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