[English] 日本語
Yorodumi
- PDB-8phu: Asymmetric structure of the portal-containing cap of the Borrelia... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8phu
TitleAsymmetric structure of the portal-containing cap of the Borrelia bacteriophage BB1 procapsid
Components
  • (Decorator protein ...) x 3
  • Major capsid protein
  • Portal protein
  • Scaffold protein
KeywordsVIRAL PROTEIN / Portal / capsid / procapsid / scaffold
Function / homologyUncharacterised conserved protein UCP020357 / Protein of unknown function DUF1073 / Anti-CBASS protein Acb1-like / Protein of unknown function DUF1357 / Protein of unknown function (DUF1357) / Uncharacterized protein / Phage portal protein
Function and homology information
Biological speciesBorreliella burgdorferi B31 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.41 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 20, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 19, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 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 1.2Nov 15, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AB: Major capsid protein
AC: Major capsid protein
AD: Decorator protein P03
AF: Decorator protein P05
AH: Scaffold protein
AI: Scaffold protein
AJ: Major capsid protein
AK: Major capsid protein
AL: Major capsid protein
AM: Decorator protein P04
AN: Decorator protein P05
AO: Decorator protein P03
AP: Scaffold protein
AQ: Scaffold protein
AR: Scaffold protein
AS: Major capsid protein
AT: Major capsid protein
AU: Major capsid protein
AV: Decorator protein P05
AW: Decorator protein P03
AX: Decorator protein P03
AY: Scaffold protein
AZ: Scaffold protein
BA: Scaffold protein
BB: Major capsid protein
BC: Major capsid protein
BD: Major capsid protein
BE: Decorator protein P05
BF: Decorator protein P03
BG: Decorator protein P03
BH: Scaffold protein
BI: Scaffold protein
BJ: Scaffold protein
BK: Major capsid protein
BL: Major capsid protein
BM: Major capsid protein
BN: Decorator protein P03
BO: Decorator protein P03
BP: Decorator protein P05
BQ: Scaffold protein
BR: Scaffold protein
BS: Scaffold protein
BT: Major capsid protein
BU: Major capsid protein
BV: Major capsid protein
BW: Decorator protein P03
BX: Decorator protein P03
BY: Decorator protein P05
BZ: Scaffold protein
CA: Scaffold protein
CB: Scaffold protein
CC: Major capsid protein
CD: Major capsid protein
CE: Major capsid protein
CF: Decorator protein P03
CG: Decorator protein P03
CH: Decorator protein P03
CI: Scaffold protein
CJ: Scaffold protein
CK: Scaffold protein
CL: Major capsid protein
CM: Major capsid protein
CN: Major capsid protein
CO: Decorator protein P05
CP: Decorator protein P03
CQ: Decorator protein P03
CR: Scaffold protein
CS: Scaffold protein
CT: Scaffold protein
CU: Major capsid protein
CV: Major capsid protein
CW: Major capsid protein
CX: Scaffold protein
CY: Scaffold protein
CZ: Scaffold protein
DB: Major capsid protein
DC: Major capsid protein
DD: Decorator protein P03
DF: Decorator protein P05
DH: Scaffold protein
DI: Scaffold protein
DJ: Major capsid protein
DK: Major capsid protein
DL: Major capsid protein
DM: Decorator protein P04
DN: Decorator protein P05
DO: Decorator protein P03
DP: Scaffold protein
DQ: Scaffold protein
DR: Scaffold protein
DS: Major capsid protein
DT: Major capsid protein
DU: Major capsid protein
DV: Decorator protein P05
DW: Decorator protein P03
DX: Decorator protein P03
DY: Scaffold protein
DZ: Scaffold protein
EA: Scaffold protein
EB: Major capsid protein
EC: Major capsid protein
ED: Major capsid protein
EE: Decorator protein P05
EF: Decorator protein P03
EG: Decorator protein P03
EH: Scaffold protein
EI: Scaffold protein
EJ: Scaffold protein
EK: Major capsid protein
EL: Major capsid protein
EM: Major capsid protein
EN: Decorator protein P03
EO: Decorator protein P03
EP: Decorator protein P05
EQ: Scaffold protein
ER: Scaffold protein
ES: Scaffold protein
ET: Major capsid protein
EU: Major capsid protein
EV: Major capsid protein
EW: Decorator protein P03
EX: Decorator protein P03
EY: Decorator protein P05
EZ: Scaffold protein
FA: Scaffold protein
FB: Scaffold protein
FC: Major capsid protein
FD: Major capsid protein
FE: Major capsid protein
FF: Decorator protein P03
FG: Decorator protein P03
FH: Decorator protein P03
FI: Scaffold protein
FJ: Scaffold protein
FK: Scaffold protein
FL: Major capsid protein
FM: Major capsid protein
FN: Major capsid protein
FO: Decorator protein P05
FP: Decorator protein P03
FQ: Decorator protein P03
FR: Scaffold protein
FS: Scaffold protein
FT: Scaffold protein
FU: Major capsid protein
FV: Major capsid protein
FW: Major capsid protein
FX: Scaffold protein
FY: Scaffold protein
FZ: Scaffold protein
GB: Major capsid protein
GC: Major capsid protein
GD: Decorator protein P03
GF: Decorator protein P05
GH: Scaffold protein
GI: Scaffold protein
GJ: Major capsid protein
GK: Major capsid protein
GL: Major capsid protein
GM: Decorator protein P04
GN: Decorator protein P05
GO: Decorator protein P03
GP: Scaffold protein
GQ: Scaffold protein
GR: Scaffold protein
GS: Major capsid protein
GT: Major capsid protein
GU: Major capsid protein
GV: Decorator protein P05
GW: Decorator protein P03
GX: Decorator protein P03
GY: Scaffold protein
GZ: Scaffold protein
HA: Scaffold protein
HB: Major capsid protein
HC: Major capsid protein
HD: Major capsid protein
HE: Decorator protein P05
HF: Decorator protein P03
HG: Decorator protein P03
HH: Scaffold protein
HI: Scaffold protein
HJ: Scaffold protein
HK: Major capsid protein
HL: Major capsid protein
HM: Major capsid protein
HN: Decorator protein P03
HO: Decorator protein P03
HP: Decorator protein P05
HQ: Scaffold protein
HR: Scaffold protein
HS: Scaffold protein
HT: Major capsid protein
HU: Major capsid protein
HV: Major capsid protein
HW: Decorator protein P03
HX: Decorator protein P03
HY: Decorator protein P05
HZ: Scaffold protein
IA: Scaffold protein
IB: Scaffold protein
IC: Major capsid protein
ID: Major capsid protein
IE: Major capsid protein
IF: Decorator protein P03
IG: Decorator protein P03
IH: Decorator protein P03
II: Scaffold protein
IJ: Scaffold protein
IK: Scaffold protein
IL: Major capsid protein
IM: Major capsid protein
IN: Major capsid protein
IO: Decorator protein P05
IP: Decorator protein P03
IQ: Decorator protein P03
IR: Scaffold protein
IS: Scaffold protein
IT: Scaffold protein
IU: Major capsid protein
IV: Major capsid protein
IW: Major capsid protein
IX: Scaffold protein
IY: Scaffold protein
IZ: Scaffold protein
JB: Major capsid protein
JC: Major capsid protein
JD: Decorator protein P03
JF: Decorator protein P05
JH: Scaffold protein
JI: Scaffold protein
JJ: Major capsid protein
JK: Major capsid protein
JL: Major capsid protein
JM: Decorator protein P04
JN: Decorator protein P05
JO: Decorator protein P03
JP: Scaffold protein
JQ: Scaffold protein
JR: Scaffold protein
JS: Major capsid protein
JT: Major capsid protein
JU: Major capsid protein
JV: Decorator protein P05
JW: Decorator protein P03
JX: Decorator protein P03
JY: Scaffold protein
JZ: Scaffold protein
KA: Scaffold protein
KB: Major capsid protein
KC: Major capsid protein
KD: Major capsid protein
KE: Decorator protein P05
KF: Decorator protein P03
KG: Decorator protein P03
KH: Scaffold protein
KI: Scaffold protein
KJ: Scaffold protein
KK: Major capsid protein
KL: Major capsid protein
KM: Major capsid protein
KN: Decorator protein P03
KO: Decorator protein P03
KP: Decorator protein P05
KQ: Scaffold protein
KR: Scaffold protein
KS: Scaffold protein
KT: Major capsid protein
KU: Major capsid protein
KV: Major capsid protein
KW: Decorator protein P03
KX: Decorator protein P03
KY: Decorator protein P05
KZ: Scaffold protein
LA: Scaffold protein
LB: Scaffold protein
LC: Major capsid protein
LD: Major capsid protein
LE: Major capsid protein
LF: Decorator protein P03
LG: Decorator protein P03
LH: Decorator protein P03
LI: Scaffold protein
LJ: Scaffold protein
LK: Scaffold protein
LL: Major capsid protein
LM: Major capsid protein
LN: Major capsid protein
LO: Decorator protein P05
LP: Decorator protein P03
LQ: Decorator protein P03
LR: Scaffold protein
LS: Scaffold protein
LT: Scaffold protein
LU: Major capsid protein
LV: Major capsid protein
LW: Major capsid protein
LX: Scaffold protein
LY: Scaffold protein
LZ: Scaffold protein
MB: Major capsid protein
MC: Major capsid protein
MD: Decorator protein P03
MF: Decorator protein P05
MH: Scaffold protein
MI: Scaffold protein
MJ: Major capsid protein
MK: Major capsid protein
ML: Major capsid protein
MM: Decorator protein P04
MN: Decorator protein P05
MO: Decorator protein P03
MP: Scaffold protein
MQ: Scaffold protein
MR: Scaffold protein
MS: Major capsid protein
MT: Major capsid protein
MU: Major capsid protein
MV: Decorator protein P05
MW: Decorator protein P03
MX: Decorator protein P03
MY: Scaffold protein
MZ: Scaffold protein
NA: Scaffold protein
NB: Major capsid protein
NC: Major capsid protein
ND: Major capsid protein
NE: Decorator protein P05
NF: Decorator protein P03
NG: Decorator protein P03
NH: Scaffold protein
NI: Scaffold protein
NJ: Scaffold protein
NK: Major capsid protein
NL: Major capsid protein
NM: Major capsid protein
NN: Decorator protein P03
NO: Decorator protein P03
NP: Decorator protein P05
NQ: Scaffold protein
NR: Scaffold protein
NS: Scaffold protein
NT: Major capsid protein
NU: Major capsid protein
NV: Major capsid protein
NW: Decorator protein P03
NX: Decorator protein P03
NY: Decorator protein P05
NZ: Scaffold protein
OA: Scaffold protein
OB: Scaffold protein
OC: Major capsid protein
OD: Major capsid protein
OE: Major capsid protein
OF: Decorator protein P03
OG: Decorator protein P03
OH: Decorator protein P03
OI: Scaffold protein
OJ: Scaffold protein
OK: Scaffold protein
OL: Major capsid protein
OM: Major capsid protein
ON: Major capsid protein
OO: Decorator protein P05
OP: Decorator protein P03
OQ: Decorator protein P03
OR: Scaffold protein
OS: Scaffold protein
OT: Scaffold protein
OU: Major capsid protein
OV: Major capsid protein
OW: Major capsid protein
OX: Scaffold protein
OY: Scaffold protein
OZ: Scaffold protein
PA: Portal protein
PB: Portal protein
PC: Portal protein
PD: Portal protein
PE: Portal protein
PF: Portal protein
PG: Portal protein
PH: Portal protein
PI: Portal protein
PJ: Portal protein
PK: Portal protein
PL: Portal protein
QA: Scaffold protein
QB: Scaffold protein
QC: Scaffold protein
QD: Scaffold protein
QE: Scaffold protein
QF: Scaffold protein
QG: Scaffold protein
QH: Scaffold protein
QI: Scaffold protein
QJ: Scaffold protein
RA: Scaffold protein
RB: Scaffold protein
SA: Scaffold protein
SB: Scaffold protein
SC: Scaffold protein
SD: Scaffold protein
SE: Scaffold protein
SF: Scaffold protein
SG: Scaffold protein
SH: Scaffold protein
SI: Scaffold protein
SJ: Scaffold protein
SK: Scaffold protein
SL: Scaffold protein
SM: Scaffold protein
SN: Scaffold protein
SO: Scaffold protein
TA: Scaffold protein
TB: Scaffold protein
TC: Scaffold protein
TD: Scaffold protein
TE: Scaffold protein
TF: Scaffold protein
TG: Scaffold protein
TH: Scaffold protein
TI: Scaffold protein
TJ: Scaffold protein
TK: Scaffold protein
TL: Scaffold protein
TM: Scaffold protein
TN: Scaffold protein
TO: Scaffold protein
TP: Scaffold protein
TQ: Scaffold protein
TR: Scaffold protein
TS: Scaffold protein
TT: Scaffold protein
TU: Scaffold protein
TV: Scaffold protein
TW: Scaffold protein
TX: Scaffold protein
TY: Scaffold protein
TZ: Scaffold protein
UA: Scaffold protein
UB: Scaffold protein
UC: Scaffold protein
UD: Scaffold protein
UE: Scaffold protein
UF: Scaffold protein
VA: Scaffold protein
VB: Scaffold protein
VC: Scaffold protein
VD: Scaffold protein
VE: Scaffold protein
VF: Scaffold protein
VG: Scaffold protein
VH: Scaffold protein
VI: Scaffold protein
VJ: Scaffold protein
VK: Scaffold protein
VL: Scaffold protein
VM: Scaffold protein
VN: Scaffold protein
VO: Scaffold protein
VP: Scaffold protein
VQ: Scaffold protein
VR: Scaffold protein
VS: Scaffold protein
VT: Scaffold protein
VU: Scaffold protein
VV: Scaffold protein
VW: Scaffold protein
VX: Scaffold protein
VY: Scaffold protein
VZ: Scaffold protein
WA: Scaffold protein
WB: Scaffold protein
WC: Scaffold protein
WD: Scaffold protein
WE: Scaffold protein
WF: Scaffold protein
XA: Scaffold protein
XB: Scaffold protein
XC: Scaffold protein
XD: Scaffold protein
XE: Scaffold protein
XF: Scaffold protein
XG: Scaffold protein
XH: Scaffold protein
XI: Scaffold protein
XJ: Scaffold protein
XK: Scaffold protein
XL: Scaffold protein
XM: Scaffold protein
XN: Scaffold protein
XO: Scaffold protein
XP: Scaffold protein
XQ: Scaffold protein
XR: Scaffold protein
XS: Scaffold protein
XT: Scaffold protein
XU: Scaffold protein
XV: Scaffold protein
XW: Scaffold protein
XX: Scaffold protein
XY: Scaffold protein
XZ: Scaffold protein
YA: Scaffold protein
YB: Scaffold protein
YC: Scaffold protein
YD: Scaffold protein
YE: Scaffold protein
YF: Scaffold protein


Theoretical massNumber of molelcules
Total (without water)14,423,035510
Polymers14,423,035510
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

-
Protein , 3 types, 395 molecules ABACAJAKALASATAUBBBCBDBKBLBMBTBUBVCCCDCECLCMCNCUCVCWDBDCDJDK...

#1: Protein ...
Major capsid protein


Mass: 36255.551 Da / Num. of mol.: 130
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
#4: Protein ...
Scaffold protein /


Mass: 26710.363 Da / Num. of mol.: 253
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
#6: Protein
Portal protein


Mass: 47095.508 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borreliella burgdorferi B31 (bacteria) / Gene: BB_L01 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): AI / References: UniProt: Q9R3K2

-
Decorator protein ... , 3 types, 115 molecules ADAOAWAXBFBGBNBOBWBXCFCGCHCPCQDDDODWDXEFEGENEOEWEXFFFGFHFPFQ...

#2: Protein ...
Decorator protein P03


Mass: 20026.479 Da / Num. of mol.: 75
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 P05


Mass: 21274.934 Da / Num. of mol.: 35
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
Decorator protein P04


Mass: 28067.344 Da / Num. of mol.: 5
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

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: The portal-containing cap of the Borrelia bacteriophage BB1 procapsid
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: C1 (asymmetric)
3D reconstructionResolution: 7.41 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