[English] 日本語
Yorodumi
- PDB-8pkh: Borrelia bacteriophage BB1 procapsid, fivefold-symmetrized outer shell -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8pkh
TitleBorrelia bacteriophage BB1 procapsid, fivefold-symmetrized outer shell
Components
  • Decorator protein P03
  • Decorator protein P04
  • Decorator protein P05
  • Major capsid protein
  • Scaffold protein
KeywordsVIRAL PROTEIN / Bacteriophage / capsid / procapsid
Function / homologyProtein of unknown function DUF1357 / Protein of unknown function (DUF1357) / Uncharacterized protein
Function and homology information
Biological speciesBorreliella burgdorferi B31 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.35 Å
AuthorsRumnieks, J. / Fuzik, T. / Tars, K.
Funding supportEuropean Union, 3items
OrganizationGrant numberCountry
European Regional Development Fund1.1.1.2/VIAA/4/20/704European Union
iNEXT-Discovery18826European Union
iNEXT-Discovery24421European Union
CitationJournal: J Mol Biol / Year: 2023
Title: Structure of the Borrelia Bacteriophage φBB1 Procapsid.
Authors: Jānis Rūmnieks / Tibor Füzik / Kaspars Tārs /
Abstract: Bacteriophages of Borrelia burgdorferi are a biologically important but under-investigated feature of the Lyme disease-causing spirochete. No virulent borrelial viruses have been identified, but all ...Bacteriophages of Borrelia burgdorferi are a biologically important but under-investigated feature of the Lyme disease-causing spirochete. No virulent borrelial viruses have been identified, but all B. burgdorferi isolates carry a prophage φBB1 as resident circular plasmids. Like its host, the φBB1 phage is quite distinctive and shares little sequence similarity with other known bacteriophages. We expressed φBB1 head morphogenesis proteins in Escherichia coli which resulted in assembly of homogeneous prolate procapsid structures and used cryo-electron microscopy to determine the three-dimensional structure of these particles. The φBB1 procapsids consist of 415 copies of the major capsid protein and an equal combined number of three homologous capsid decoration proteins that form trimeric knobs on the outside of the particle. One of the end vertices of the particle is occupied by a portal assembled from twelve copies of the portal protein. The φBB1 scaffolding protein is entirely α-helical and has an elongated shape with a small globular domain in the middle. Within the tubular section of the procapsid, the internal scaffold is built of stacked rings, each composed of 32 scaffolding protein molecules, which run in opposite directions from both caps with a heterogeneous part in the middle. Inside the portal-containing cap, the scaffold is organized asymmetrically with ten scaffolding protein molecules bound to the portal. The φBB1 procapsid structure provides better insight into the vast structural diversity of bacteriophages and presents clues of how elongated bacteriophage particles might be assembled.
History
DepositionJun 26, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2023Group: Database references / Category: struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _struct_ref.db_code / _struct_ref.db_name ..._struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession
Revision 1.2Nov 1, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Nov 15, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AA: Major capsid protein
AB: Major capsid protein
AC: Major capsid protein
AD: Major capsid protein
AE: Major capsid protein
AF: Major capsid protein
AG: Major capsid protein
AH: Major capsid protein
AI: Major capsid protein
AJ: Major capsid protein
AK: Major capsid protein
AL: Major capsid protein
AM: Major capsid protein
AN: Major capsid protein
AO: Major capsid protein
AP: Major capsid protein
AQ: Major capsid protein
AR: Major capsid protein
AS: Major capsid protein
AT: Major capsid protein
AU: Major capsid protein
AV: Major capsid protein
AW: Major capsid protein
AX: Major capsid protein
AY: Major capsid protein
AZ: Major capsid protein
BA: Major capsid protein
BB: Major capsid protein
BC: Major capsid protein
BD: Major capsid protein
BE: Major capsid protein
BF: Major capsid protein
BG: Major capsid protein
BH: Major capsid protein
BI: Major capsid protein
BJ: Major capsid protein
BK: Major capsid protein
BL: Major capsid protein
BM: Major capsid protein
BN: Major capsid protein
BO: Major capsid protein
BP: Major capsid protein
BQ: Major capsid protein
BR: Major capsid protein
BS: Major capsid protein
BT: Major capsid protein
BU: Major capsid protein
BV: Major capsid protein
BW: Major capsid protein
BX: Major capsid protein
BY: Major capsid protein
BZ: Major capsid protein
CA: Major capsid protein
CB: Major capsid protein
CC: Major capsid protein
CD: Major capsid protein
CE: Major capsid protein
CF: Major capsid protein
CG: Major capsid protein
CH: Major capsid protein
CI: Major capsid protein
CJ: Major capsid protein
CK: Major capsid protein
CL: Major capsid protein
CM: Major capsid protein
CN: Major capsid protein
CO: Major capsid protein
CP: Major capsid protein
CQ: Major capsid protein
CR: Major capsid protein
CS: Major capsid protein
CT: Major capsid protein
CU: Major capsid protein
CV: Major capsid protein
CW: Major capsid protein
CX: Major capsid protein
CY: Major capsid protein
CZ: Major capsid protein
DA: Major capsid protein
DB: Major capsid protein
DC: Major capsid protein
DD: Major capsid protein
DE: Major capsid protein
DF: Decorator protein P03
DG: Decorator protein P03
DH: Decorator protein P03
DI: Decorator protein P03
DJ: Decorator protein P03
DK: Decorator protein P03
DL: Decorator protein P03
DM: Decorator protein P03
DN: Decorator protein P03
DO: Decorator protein P03
DP: Decorator protein P03
DQ: Decorator protein P03
DR: Decorator protein P03
DS: Decorator protein P03
DT: Decorator protein P03
DU: Decorator protein P03
DV: Decorator protein P03
DW: Decorator protein P03
DX: Decorator protein P03
DY: Decorator protein P03
DZ: Decorator protein P03
EA: Decorator protein P03
EB: Decorator protein P03
EC: Decorator protein P03
ED: Decorator protein P03
EE: Decorator protein P03
EF: Decorator protein P03
EG: Decorator protein P03
EH: Decorator protein P03
EI: Decorator protein P03
EJ: Decorator protein P03
EK: Decorator protein P03
EL: Decorator protein P03
EM: Decorator protein P03
EN: Decorator protein P03
EO: Decorator protein P03
EP: Decorator protein P03
EQ: Decorator protein P03
ER: Decorator protein P03
ES: Decorator protein P03
ET: Decorator protein P03
EU: Decorator protein P03
EV: Decorator protein P03
EW: Decorator protein P03
EX: Decorator protein P03
EY: Decorator protein P03
EZ: Decorator protein P03
FA: Decorator protein P03
FB: Decorator protein P03
FC: Decorator protein P03
FD: Decorator protein P03
FE: Decorator protein P03
FF: Decorator protein P03
FG: Decorator protein P03
FH: Decorator protein P03
FI: Decorator protein P03
FJ: Decorator protein P04
FK: Decorator protein P05
FL: Decorator protein P05
FM: Decorator protein P05
FN: Decorator protein P05
FO: Decorator protein P05
FP: Decorator protein P05
FQ: Decorator protein P05
FR: Decorator protein P05
FS: Decorator protein P05
FT: Decorator protein P05
FU: Decorator protein P05
FV: Decorator protein P05
FW: Decorator protein P05
FX: Decorator protein P05
FY: Decorator protein P05
FZ: Decorator protein P05
GA: Decorator protein P05
GB: Decorator protein P05
GC: Decorator protein P05
GD: Decorator protein P05
GE: Decorator protein P05
GF: Decorator protein P05
GG: Decorator protein P05
GH: Decorator protein P05
GI: Decorator protein P05
GJ: Decorator protein P05
GK: Scaffold protein
GL: Scaffold protein
GM: Scaffold protein
GN: Scaffold protein
GO: Scaffold protein
GP: Scaffold protein
GQ: Scaffold protein
GR: Scaffold protein
GS: Scaffold protein
GT: Scaffold protein
GU: Scaffold protein
GV: Scaffold protein
GW: Scaffold protein
GX: Scaffold protein
GY: Scaffold protein
GZ: Scaffold protein
HA: Scaffold protein
HB: Scaffold protein
HC: Scaffold protein
HD: Scaffold protein
HE: Scaffold protein
HF: Scaffold protein
HG: Scaffold protein
HH: Scaffold protein
HI: Scaffold protein
HJ: Scaffold protein
HK: Scaffold protein
HL: Scaffold protein
HM: Scaffold protein
HN: Scaffold protein
HO: Scaffold protein
HP: Scaffold protein
HQ: Scaffold protein
HR: Scaffold protein
HS: Scaffold protein
HT: Scaffold protein
HU: Scaffold protein
HV: Scaffold protein
HW: Scaffold protein
HX: Scaffold protein
HY: Scaffold protein
HZ: Scaffold protein
IA: Scaffold protein
IB: Scaffold protein
IC: Scaffold protein
ID: Scaffold protein
IE: Scaffold protein
IF: Scaffold protein
IG: Scaffold protein
IH: Scaffold protein
II: Scaffold protein
IJ: Scaffold protein
IK: Scaffold protein
IL: Scaffold protein
IM: Scaffold protein
IN: Scaffold protein
IO: Scaffold protein
IP: Scaffold protein
IQ: Scaffold protein
IR: Scaffold protein
IS: Scaffold protein
IT: Scaffold protein
IU: Scaffold protein
IV: Scaffold protein
IW: Scaffold protein
IX: Scaffold protein
IY: Scaffold protein
IZ: Scaffold protein
JA: Scaffold protein
JB: Scaffold protein
JC: Scaffold protein
JD: Scaffold protein
JE: Scaffold protein
JF: Scaffold protein
JG: Scaffold protein
JH: Scaffold protein
JI: Scaffold protein
JJ: Scaffold protein
JK: Scaffold protein
JL: Scaffold protein
JM: Scaffold protein
JN: Scaffold protein
JO: Scaffold protein


Theoretical massNumber of molelcules
Total (without water)6,928,869249
Polymers6,928,869249
Non-polymers00
Water0
1
AA: Major capsid protein
AB: Major capsid protein
AC: Major capsid protein
AD: Major capsid protein
AE: Major capsid protein
AF: Major capsid protein
AG: Major capsid protein
AH: Major capsid protein
AI: Major capsid protein
AJ: Major capsid protein
AK: Major capsid protein
AL: Major capsid protein
AM: Major capsid protein
AN: Major capsid protein
AO: Major capsid protein
AP: Major capsid protein
AQ: Major capsid protein
AR: Major capsid protein
AS: Major capsid protein
AT: Major capsid protein
AU: Major capsid protein
AV: Major capsid protein
AW: Major capsid protein
AX: Major capsid protein
AY: Major capsid protein
AZ: Major capsid protein
BA: Major capsid protein
BB: Major capsid protein
BC: Major capsid protein
BD: Major capsid protein
BE: Major capsid protein
BF: Major capsid protein
BG: Major capsid protein
BH: Major capsid protein
BI: Major capsid protein
BJ: Major capsid protein
BK: Major capsid protein
BL: Major capsid protein
BM: Major capsid protein
BN: Major capsid protein
BO: Major capsid protein
BP: Major capsid protein
BQ: Major capsid protein
BR: Major capsid protein
BS: Major capsid protein
BT: Major capsid protein
BU: Major capsid protein
BV: Major capsid protein
BW: Major capsid protein
BX: Major capsid protein
BY: Major capsid protein
BZ: Major capsid protein
CA: Major capsid protein
CB: Major capsid protein
CC: Major capsid protein
CD: Major capsid protein
CE: Major capsid protein
CF: Major capsid protein
CG: Major capsid protein
CH: Major capsid protein
CI: Major capsid protein
CJ: Major capsid protein
CK: Major capsid protein
CL: Major capsid protein
CM: Major capsid protein
CN: Major capsid protein
CO: Major capsid protein
CP: Major capsid protein
CQ: Major capsid protein
CR: Major capsid protein
CS: Major capsid protein
CT: Major capsid protein
CU: Major capsid protein
CV: Major capsid protein
CW: Major capsid protein
CX: Major capsid protein
CY: Major capsid protein
CZ: Major capsid protein
DA: Major capsid protein
DB: Major capsid protein
DC: Major capsid protein
DD: Major capsid protein
DE: Major capsid protein
DF: Decorator protein P03
DG: Decorator protein P03
DH: Decorator protein P03
DI: Decorator protein P03
DJ: Decorator protein P03
DK: Decorator protein P03
DL: Decorator protein P03
DM: Decorator protein P03
DN: Decorator protein P03
DO: Decorator protein P03
DP: Decorator protein P03
DQ: Decorator protein P03
DR: Decorator protein P03
DS: Decorator protein P03
DT: Decorator protein P03
DU: Decorator protein P03
DV: Decorator protein P03
DW: Decorator protein P03
DX: Decorator protein P03
DY: Decorator protein P03
DZ: Decorator protein P03
EA: Decorator protein P03
EB: Decorator protein P03
EC: Decorator protein P03
ED: Decorator protein P03
EE: Decorator protein P03
EF: Decorator protein P03
EG: Decorator protein P03
EH: Decorator protein P03
EI: Decorator protein P03
EJ: Decorator protein P03
EK: Decorator protein P03
EL: Decorator protein P03
EM: Decorator protein P03
EN: Decorator protein P03
EO: Decorator protein P03
EP: Decorator protein P03
EQ: Decorator protein P03
ER: Decorator protein P03
ES: Decorator protein P03
ET: Decorator protein P03
EU: Decorator protein P03
EV: Decorator protein P03
EW: Decorator protein P03
EX: Decorator protein P03
EY: Decorator protein P03
EZ: Decorator protein P03
FA: Decorator protein P03
FB: Decorator protein P03
FC: Decorator protein P03
FD: Decorator protein P03
FE: Decorator protein P03
FF: Decorator protein P03
FG: Decorator protein P03
FH: Decorator protein P03
FI: Decorator protein P03
FJ: Decorator protein P04
FK: Decorator protein P05
FL: Decorator protein P05
FM: Decorator protein P05
FN: Decorator protein P05
FO: Decorator protein P05
FP: Decorator protein P05
FQ: Decorator protein P05
FR: Decorator protein P05
FS: Decorator protein P05
FT: Decorator protein P05
FU: Decorator protein P05
FV: Decorator protein P05
FW: Decorator protein P05
FX: Decorator protein P05
FY: Decorator protein P05
FZ: Decorator protein P05
GA: Decorator protein P05
GB: Decorator protein P05
GC: Decorator protein P05
GD: Decorator protein P05
GE: Decorator protein P05
GF: Decorator protein P05
GG: Decorator protein P05
GH: Decorator protein P05
GI: Decorator protein P05
GJ: Decorator protein P05
GK: Scaffold protein
GL: Scaffold protein
GM: Scaffold protein
GN: Scaffold protein
GO: Scaffold protein
GP: Scaffold protein
GQ: Scaffold protein
GR: Scaffold protein
GS: Scaffold protein
GT: Scaffold protein
GU: Scaffold protein
GV: Scaffold protein
GW: Scaffold protein
GX: Scaffold protein
GY: Scaffold protein
GZ: Scaffold protein
HA: Scaffold protein
HB: Scaffold protein
HC: Scaffold protein
HD: Scaffold protein
HE: Scaffold protein
HF: Scaffold protein
HG: Scaffold protein
HH: Scaffold protein
HI: Scaffold protein
HJ: Scaffold protein
HK: Scaffold protein
HL: Scaffold protein
HM: Scaffold protein
HN: Scaffold protein
HO: Scaffold protein
HP: Scaffold protein
HQ: Scaffold protein
HR: Scaffold protein
HS: Scaffold protein
HT: Scaffold protein
HU: Scaffold protein
HV: Scaffold protein
HW: Scaffold protein
HX: Scaffold protein
HY: Scaffold protein
HZ: Scaffold protein
IA: Scaffold protein
IB: Scaffold protein
IC: Scaffold protein
ID: Scaffold protein
IE: Scaffold protein
IF: Scaffold protein
IG: Scaffold protein
IH: Scaffold protein
II: Scaffold protein
IJ: Scaffold protein
IK: Scaffold protein
IL: Scaffold protein
IM: Scaffold protein
IN: Scaffold protein
IO: Scaffold protein
IP: Scaffold protein
IQ: Scaffold protein
IR: Scaffold protein
IS: Scaffold protein
IT: Scaffold protein
IU: Scaffold protein
IV: Scaffold protein
IW: Scaffold protein
IX: Scaffold protein
IY: Scaffold protein
IZ: Scaffold protein
JA: Scaffold protein
JB: Scaffold protein
JC: Scaffold protein
JD: Scaffold protein
JE: Scaffold protein
JF: Scaffold protein
JG: Scaffold protein
JH: Scaffold protein
JI: Scaffold protein
JJ: Scaffold protein
JK: Scaffold protein
JL: Scaffold protein
JM: Scaffold protein
JN: Scaffold protein
JO: Scaffold protein
x 5


  • defined by author&software
  • Evidence: electron microscopy, not applicable
  • 34.6 MDa, 1245 polymers
Theoretical massNumber of molelcules
Total (without water)34,644,3471245
Polymers34,644,3471245
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4

-
Components

#1: Protein ...
Major capsid protein


Mass: 36255.551 Da / Num. of mol.: 83
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borreliella burgdorferi B31 (bacteria) / Gene: BB_L06 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): AI
#2: Protein ...
Decorator protein P03


Mass: 20026.479 Da / Num. of mol.: 56
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borreliella burgdorferi B31 (bacteria) / Gene: BB_L03 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): AI
#3: Protein Decorator protein P04


Mass: 28067.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borreliella burgdorferi B31 (bacteria) / Gene: BB_L04 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): AI
#4: Protein ...
Decorator protein P05


Mass: 21274.934 Da / Num. of mol.: 26
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borreliella burgdorferi B31 (bacteria) / Gene: BbuZS7_P05 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): AI
#5: Protein ...
Scaffold protein /


Mass: 26710.363 Da / Num. of mol.: 83
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borreliella burgdorferi B31 (bacteria) / Gene: BB_L02 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): AI / References: UniProt: Q9R2Q2

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Procapsid of Borrelia bacteriophage BB1 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Borreliella burgdorferi B31 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21-AI
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTris-HClTris1
2100 mMsodium chlorideNaClSodium chloride1
310 mMmagnesium sulfateMgSO41
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 16500 X / Nominal defocus max: 1800 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 44 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum

-
Processing

EM software
IDNameVersionCategory
1RELION3.1.3particle selection
4Gctf1.18CTF correction
7Coot0.9.8.4model fitting
9PHENIX1.20.1-4487model refinement
10RELION3.1.3initial Euler assignment
11RELION3.1.3final Euler assignment
13RELION3.1.33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C5 (5 fold cyclic)
3D reconstructionResolution: 3.35 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 25958 / Symmetry type: POINT
Atomic model buildingDetails: previous reconstruction / Source name: Other / Type: experimental model

+
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