[English] 日本語
Yorodumi
- EMDB-15805: RecBCD-DNA in complex with the phage protein Abc2 and host PpiB -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-15805
TitleRecBCD-DNA in complex with the phage protein Abc2 and host PpiB
Map dataFinal CryoEM map of the RecBCD-Abc2-DNA complex bound to the host PpiB protein
Sample
  • Complex: RecBCD-Abc2-PpiB-DNA complex
    • Complex: RecBCD enzyme subunits RecB, RecC and RecD
      • Protein or peptide: RecBCD enzyme subunit RecB
      • Protein or peptide: RecBCD enzyme subunit RecC
      • Protein or peptide: RecBCD enzyme subunit RecD
    • Complex: DNA (70-MER)
      • DNA: DNA (70-MER)
    • Complex: Anti-RecBCD protein 2
      • Protein or peptide: Anti-RecBCD protein 2
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
Function / homology
Function and homology information


exodeoxyribonuclease V / exodeoxyribonuclease V activity / exodeoxyribonuclease V complex / DNA 5'-3' helicase / clearance of foreign intracellular DNA / DNA 3'-5' helicase / recombinational repair / single-stranded DNA helicase activity / 3'-5' DNA helicase activity / DNA helicase activity ...exodeoxyribonuclease V / exodeoxyribonuclease V activity / exodeoxyribonuclease V complex / DNA 5'-3' helicase / clearance of foreign intracellular DNA / DNA 3'-5' helicase / recombinational repair / single-stranded DNA helicase activity / 3'-5' DNA helicase activity / DNA helicase activity / isomerase activity / helicase activity / double-strand break repair via homologous recombination / response to radiation / 5'-3' DNA helicase activity / DNA recombination / DNA damage response / magnesium ion binding / ATP hydrolysis activity / DNA binding / ATP binding / cytosol
Similarity search - Function
Anti-RecBCD protein 2, bacteriophage P22 / Bacteriophage P22, anti-RecBCD protein 2 / RecBCD enzyme subunit RecB / RecBCD enzyme subunit RecD / RecBCD enzyme subunit RecC / RecC, C-terminal / RecBCD enzyme subunit RecD, N-terminal domain / : / Exodeoxyribonuclease V, gamma subunit / RecC C-terminal domain ...Anti-RecBCD protein 2, bacteriophage P22 / Bacteriophage P22, anti-RecBCD protein 2 / RecBCD enzyme subunit RecB / RecBCD enzyme subunit RecD / RecBCD enzyme subunit RecC / RecC, C-terminal / RecBCD enzyme subunit RecD, N-terminal domain / : / Exodeoxyribonuclease V, gamma subunit / RecC C-terminal domain / RecBCD enzyme subunit RecD, N-terminal domain / PD-(D/E)XK endonuclease-like domain, AddAB-type / PD-(D/E)XK nuclease superfamily / DExx box DNA helicase domain superfamily / UvrD-like DNA helicase C-terminal domain profile. / UvrD-like DNA helicase, C-terminal / UvrD-like helicase C-terminal domain / AAA domain / UvrD-like helicase C-terminal domain / UvrD-like helicase C-terminal domain / UvrD/REP helicase N-terminal domain / UvrD-like helicase, ATP-binding domain / UvrD-like DNA helicase ATP-binding domain profile. / DNA helicase, UvrD/REP type / PD-(D/E)XK endonuclease-like domain superfamily / Restriction endonuclease type II-like / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
RecBCD enzyme subunit RecB / RecBCD enzyme subunit RecD / RecBCD enzyme subunit RecC / Anti-RecBCD protein 2
Similarity search - Component
Biological speciesEscherichia coli (E. coli) / synthetic construct (others) / Salmonella phage P22 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsWilkinson M / Wilkinson OJ / Feyerherm C / Fletcher EE / Wigley DB / Dillingham MS
Funding support United Kingdom, 3 items
OrganizationGrant numberCountry
Wellcome Trust100401/Z/12/Z United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/S007261/1 United Kingdom
Medical Research Council (MRC, United Kingdom) United Kingdom
CitationJournal: Elife / Year: 2022
Title: Structures of RecBCD in complex with phage-encoded inhibitor proteins reveal distinctive strategies for evasion of a bacterial immunity hub.
Authors: Martin Wilkinson / Oliver J Wilkinson / Connie Feyerherm / Emma E Fletcher / Dale B Wigley / Mark S Dillingham /
Abstract: Following infection of bacterial cells, bacteriophage modulate double-stranded DNA break repair pathways to protect themselves from host immunity systems and prioritise their own recombinases. Here, ...Following infection of bacterial cells, bacteriophage modulate double-stranded DNA break repair pathways to protect themselves from host immunity systems and prioritise their own recombinases. Here, we present biochemical and structural analysis of two phage proteins, gp5.9 and Abc2, which target the DNA break resection complex RecBCD. These exemplify two contrasting mechanisms for control of DNA break repair in which the RecBCD complex is either inhibited or co-opted for the benefit of the invading phage. Gp5.9 completely inhibits RecBCD by preventing it from binding to DNA. The RecBCD-gp5.9 structure shows that gp5.9 acts by substrate mimicry, binding predominantly to the RecB arm domain and competing sterically for the DNA binding site. Gp5.9 adopts a parallel coiled-coil architecture that is unprecedented for a natural DNA mimic protein. In contrast, binding of Abc2 does not substantially affect the biochemical activities of isolated RecBCD. The RecBCD-Abc2 structure shows that Abc2 binds to the Chi-recognition domains of the RecC subunit in a position that might enable it to mediate the loading of phage recombinases onto its single-stranded DNA products.
History
DepositionSep 12, 2022-
Header (metadata) releaseDec 28, 2022-
Map releaseDec 28, 2022-
UpdateDec 28, 2022-
Current statusDec 28, 2022Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_15805.png

Downloads & links

-
Map

FileDownload / File: emd_15805.map.gz / Format: CCP4 / Size: 47.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFinal CryoEM map of the RecBCD-Abc2-DNA complex bound to the host PpiB protein
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 232 pix.
= 245.92 Å		1.06 Å/pix.
x 232 pix.
= 245.92 Å		1.06 Å/pix.
x 232 pix.
= 245.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015
Minimum - Maximum-0.040271144 - 0.07460165
Average (Standard dev.)5.8282527e-05 (±0.0039121397)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions232232232
Spacing232232232
CellA=B=C: 245.91998 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: halfmap1

Fileemd_15805_half_map_1.map
Annotationhalfmap1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: halfmap2

Fileemd_15805_half_map_2.map
Annotationhalfmap2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : RecBCD-Abc2-PpiB-DNA complex

EntireName: RecBCD-Abc2-PpiB-DNA complex
Components
  • Complex: RecBCD-Abc2-PpiB-DNA complex
    • Complex: RecBCD enzyme subunits RecB, RecC and RecD
      • Protein or peptide: RecBCD enzyme subunit RecB
      • Protein or peptide: RecBCD enzyme subunit RecC
      • Protein or peptide: RecBCD enzyme subunit RecD
    • Complex: DNA (70-MER)
      • DNA: DNA (70-MER)
    • Complex: Anti-RecBCD protein 2
      • Protein or peptide: Anti-RecBCD protein 2
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION

+
Supramolecule #1: RecBCD-Abc2-PpiB-DNA complex

SupramoleculeName: RecBCD-Abc2-PpiB-DNA complex / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#5
Details: All proteins co-expressed and purified as one complex. DNA added prior to making grids in a 1.5x molar excess. Host PpiB interacts with complex and was pulled through purification.

+
Supramolecule #2: RecBCD enzyme subunits RecB, RecC and RecD

SupramoleculeName: RecBCD enzyme subunits RecB, RecC and RecD / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#3
Source (natural)Organism: Escherichia coli (E. coli)

+
Supramolecule #3: DNA (70-MER)

SupramoleculeName: DNA (70-MER) / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4
Source (natural)Organism: synthetic construct (others)

+
Supramolecule #4: Anti-RecBCD protein 2

SupramoleculeName: Anti-RecBCD protein 2 / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #5
Source (natural)Organism: Salmonella phage P22 (virus)

+
Macromolecule #1: RecBCD enzyme subunit RecB

MacromoleculeName: RecBCD enzyme subunit RecB / type: protein_or_peptide / ID: 1 / Details: Nuclease-dead mutant D1080A / Number of copies: 1 / Enantiomer: LEVO / EC number: exodeoxyribonuclease V
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 134.066625 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MSDVAETLDP LRLPLQGERL IEASAGTGKT FTIAALYLRL LLGLGGSAAF PRPLTVEELL VVTFTEAATA ELRGRIRSNI HELRIACLR ETTDNPLYER LLEEIDDKAQ AAQWLLLAER QMDEAAVFTI HGFCQRMLNL NAFESGMLFE QQLIEDESLL R YQACADFW ...String:
MSDVAETLDP LRLPLQGERL IEASAGTGKT FTIAALYLRL LLGLGGSAAF PRPLTVEELL VVTFTEAATA ELRGRIRSNI HELRIACLR ETTDNPLYER LLEEIDDKAQ AAQWLLLAER QMDEAAVFTI HGFCQRMLNL NAFESGMLFE QQLIEDESLL R YQACADFW RRHCYPLPRE IAQVVFETWK GPQALLRDIN RYLQGEAPVI KAPPPDDETL ASRHAQIVAR IDTVKQQWRD AV GELDALI ESSGIDRRKF NRSNQAKWID KISAWAEEET NSYQLPESLE KFSQRFLEDR TKAGGETPRH PLFEAIDQLL AEP LSIRDL VITRALAEIR ETVAREKRRR GELGFDDMLS RLDSALRSES GEVLAAAIRT RFPVAMIDEF QDTDPQQYRI FRRI WHHQP ETALLLIGDP KQAIYAFRGA DIFTYMKARS EVHAHYTLDT NWRSAPGMVN SVNKLFSQTD DAFMFREIPF IPVKS AGKN QALRFVFKGE TQPAMKMWLM EGESCGVGDY QSTMAQVCAA QIRDWLQAGQ RGEALLMNGD DARPVRASDI SVLVRS RQE AAQVRDALTL LEIPSVYLSN RDSVFETLEA QEMLWLLQAV MTPERENTLR SALATSMMGL NALDIETLNN DEHAWDV VV EEFDGYRQIW RKRGVMPMLR ALMSARNIAE NLLATAGGER RLTDILHISE LLQEAGTQLE SEHALVRWLS QHILEPDS N ASSQQMRLES DKHLVQIVTI HKSKGLEYPL VWLPFITNFR VQEQAFYHDR HSFEAVLDLN AAPESVDLAE AERLAEDLR LLYVALTRSV WHCSLGVAPL VRRRGDKKGD TDVHQSALGR LLQKGEPQDA AGLRTCIEAL CDDDIAWQTA QTGDNQPWQV NDVSTAELN AKTLQRLPGD NWRVTSYSGL QQRGHGIAQD LMPRLDVDAA GVASVVEEPT LTPHQFPRGA SPGTFLHSLF E DLDFTQPV DPNWVREKLE LGGFESQWEP VLTEWITAVL QAPLNETGVS LSQLSARNKQ VEMEFYLPIS EPLIASQLDT LI RQFDPLS AGCPPLEFMQ VRGMLKGFID LVFRHEGRYY LLAYKSNWLG EDSSAYTQQA MAAAMQAHRY DLQYQLYTLA LHR YLRHRI ADYDYEHHFG GVIYLFLRGV DKEHPQQGIY TTRPNAGLIA LMDEMFAGMT LEEA

+
Macromolecule #2: RecBCD enzyme subunit RecC

MacromoleculeName: RecBCD enzyme subunit RecC / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: exodeoxyribonuclease V
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 128.974102 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MLRVYHSNRL DVLEALMEFI VERERLDDPF EPEMILVQST GMAQWLQMTL SQKFGIAANI DFPLPASFIW DMFVRVLPEI PKESAFNKQ SMSWKLMTLL PQLLEREDFT LLRHYLTDDS DKRKLFQLSS KAADLFDQYL VYRPDWLAQW ETGHLVEGLG E AQAWQAPL ...String:
MLRVYHSNRL DVLEALMEFI VERERLDDPF EPEMILVQST GMAQWLQMTL SQKFGIAANI DFPLPASFIW DMFVRVLPEI PKESAFNKQ SMSWKLMTLL PQLLEREDFT LLRHYLTDDS DKRKLFQLSS KAADLFDQYL VYRPDWLAQW ETGHLVEGLG E AQAWQAPL WKALVEYTHQ LGQPRWHRAN LYQRFIETLE SATTCPPGLP SRVFICGISA LPPVYLQALQ ALGKHIEIHL LF TNPCRYY WGDIKDPAYL AKLLTRQRRH SFEDRELPLF RDSENAGQLF NSDGEQDVGN PLLASWGKLG RDYIYLLSDL ESS QELDAF VDVTPDNLLH NIQSDILELE NRAVAGVNIE EFSRSDNKRP LDPLDSSITF HVCHSPQREV EVLHDRLLAM LEED PTLTP RDIIVMVADI DSYSPFIQAV FGSAPADRYL PYAISDRRAR QSHPVLEAFI SLLSLPDSRF VSEDVLALLD VPVLA ARFD ITEEGLRYLR QWVNESGIRW GIDDDNVREL ELPATGQHTW RFGLTRMLLG YAMESAQGEW QSVLPYDESS GLIAEL VGH LASLLMQLNI WRRGLAQERP LEEWLPVCRD MLNAFFLPDA ETEAAMTLIE QQWQAIIAEG LGAQYGDAVP LSLLRDE LA QRLDQERISQ RFLAGPVNIC TLMPMRSIPF KVVCLLGMND GVYPRQLAPL GFDLMSQKPK RGDRSRRDDD RYLFLEAL I SAQQKLYISY IGRSIQDNSE RFPSVLVQEL IDYIGQSHYL PGDEALNCDE SEARVKAHLT CLHTRMPFDP QNYQPGERQ SYAREWLPAA SQAGKAHSEF VQPLPFTLPE TVPLETLQRF WAHPVRAFFQ MRLQVNFRTE DSEIPDTEPF ILEGLSRYQI NQQLLNALV EQDDAERLFR RFRAAGDLPY GAFGEIFWET QCQEMQQLAD RVIACRQPGQ SMEIDLACNG VQITGWLPQV Q PDGLLRWR PSLLSVAQGM QLWLEHLVYC ASGGNGESRL FLRKDGEWRF PPLAAEQALH YLSQLIEGYR EGMSAPLLVL PE SGGAWLK TCYDAQNDAM LDDDSTLQKA RTKFLQAYEG NMMVRGEGDD IWYQRLWRQL TPETMEAIVE QSQRFLLPLF RFN QS

+
Macromolecule #3: RecBCD enzyme subunit RecD

MacromoleculeName: RecBCD enzyme subunit RecD / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: exodeoxyribonuclease V
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 66.990367 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MKLQKQLLEA VEHKQLRPLD VQFALTVAGD EHPAVTLAAA LLSHDAGEGH VCLPLSRLEN NEASHPLLAT CVSEIGELQN WEECLLASQ AVSRGDEPTP MILCGDRLYL NRMWCNERTV ARFFNEVNHA IEVDEALLAQ TLDKLFPVSD EINWQKVAAA V ALTRRISV ...String:
MKLQKQLLEA VEHKQLRPLD VQFALTVAGD EHPAVTLAAA LLSHDAGEGH VCLPLSRLEN NEASHPLLAT CVSEIGELQN WEECLLASQ AVSRGDEPTP MILCGDRLYL NRMWCNERTV ARFFNEVNHA IEVDEALLAQ TLDKLFPVSD EINWQKVAAA V ALTRRISV ISGGPGTGKT TTVAKLLAAL IQMADGERCR IRLAAPTGKA AARLTESLGK ALRQLPLTDE QKKRIPEDAS TL HRLLGAQ PGSQRLRHHA GNPLHLDVLV VDEASMIDLP MMSRLIDALP DHARVIFLGD RDQLASVEAG AVLGDICAYA NAG FTAERA RQLSRLTGTH VPAGTGTEAA SLRDSLCLLQ KSYRFGSDSG IGQLAAAINR GDKTAVKTVF QQDFTDIEKR LLQS GEDYI AMLEEALAGY GRYLDLLQAR AEPDLIIQAF NEYQLLCALR EGPFGVAGLN ERIEQFMQQK RKIHRHPHSR WYEGR PVMI ARNDSALGLF NGDIGIALDR GQGTRVWFAM PDGNIKSVQP SRLPEHETTW AMTVHKSQGS EFDHAALILP SQRTPV VTR ELVYTAVTRA RRRLSLYADE RILSAAIATR TERRSGLAAL FSSRE

+
Macromolecule #5: Anti-RecBCD protein 2

MacromoleculeName: Anti-RecBCD protein 2 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Salmonella phage P22 (virus)
Molecular weightTheoretical: 11.64021 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
MPAPLYGADD PRRCSGNSVS EVLDKFRKNY DLIMSLPQET KEEKEFRHCI WLAEKEERER IYQTAIRPFR KATYTKFIEI DPRLRDYRS RYAGISNN

+
Macromolecule #4: DNA (70-MER)

MacromoleculeName: DNA (70-MER) / type: dna / ID: 4
Details: Synthesised hairpin substrate with unpaired ssDNA tails
Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 21.440707 KDa
SequenceString: (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DC)(DT)(DA)(DA)(DT)(DG)(DC) (DG)(DA)(DG)(DC)(DA)(DC)(DT)(DG)(DC) (DT)(DA)(DC)(DA)(DG)(DC)(DA)(DT)(DT)(DT) (DC) (DC)(DC)(DA)(DT)(DG)(DC) ...String:
(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DC)(DT)(DA)(DA)(DT)(DG)(DC) (DG)(DA)(DG)(DC)(DA)(DC)(DT)(DG)(DC) (DT)(DA)(DC)(DA)(DG)(DC)(DA)(DT)(DT)(DT) (DC) (DC)(DC)(DA)(DT)(DG)(DC)(DT)(DG) (DT)(DA)(DG)(DC)(DA)(DG)(DT)(DG)(DC)(DT) (DC)(DG) (DC)(DA)(DT)(DT)(DA)(DG)(DA) (DT)(DT)(DT)

+
Macromolecule #6: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 6 / Number of copies: 1 / Formula: ANP
Molecular weightTheoretical: 506.196 Da
Chemical component information

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

+
Macromolecule #7: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 7 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.1 mg/mL
BufferpH: 7.5
Component:
ConcentrationNameFormula
25.0 mMTris-HCl
100.0 mMSodium chlorideNaCl
0.5 mMTCEP
5.0 mMMagnesium chlorideMgCl2
2.0 mMADPNP
GridModel: C-flat-2/1 / Material: COPPER / Mesh: 400 / Support film - Material: GRAPHENE OXIDE
Details: Mixture of graphene oxide with 0.3 mM DDM detergent applied directly to grids twice before application of sample
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Instrument: FEI VITROBOT MARK IV / Details: 1.5s blot time.
DetailsRecBCD-Abc2 mixed with 1.5x molar excess of synthesised DNA substrate, 2 mM ADPNP and 5 mM MgCl2 prior to making grids

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 2500 / Average exposure time: 12.0 sec. / Average electron dose: 56.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 467613
Startup modelType of model: EMDB MAP
EMDB ID:

4038


Details: 30 Angstrom lowpass-filtered template
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 37072
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)

-
Atomic model buiding 1

Initial modelPDB ID:

8b1t

RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 68 / Target criteria: Correlation coefficient
Output model

PDB-8b1u:
RecBCD-DNA in complex with the phage protein Abc2 and host PpiB

+
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://pdbjlvh1.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