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- PDB-6tba: Virion of native gene transfer agent (GTA) particle -

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Basic information

Entry
Database: PDB / ID: 6tba
TitleVirion of native gene transfer agent (GTA) particle
Components
  • (Uncharacterized ...) x 8
  • Phage major capsid protein, HK97 family
  • Phage major tail protein, TP901-1 family
  • Portal protein Rcc01684
KeywordsVIRUS / "virion" / "horizontal gene transfer" / "gene delivery" / "HK97"
Function / homology
Function and homology information


GTA TIM-barrel-like domain / : / GTA TIM-barrel-like domain / Rcc01698-like, C-terminal / Protein of unknown function DUF2460 / Conserved hypothetical protein 2217 (DUF2460) / Phage conserved hypothetical protein / Tail completion protein / Tail completion protein gp17 / Baseplate hub protein, N-terminal attachment domain ...GTA TIM-barrel-like domain / : / GTA TIM-barrel-like domain / Rcc01698-like, C-terminal / Protein of unknown function DUF2460 / Conserved hypothetical protein 2217 (DUF2460) / Phage conserved hypothetical protein / Tail completion protein / Tail completion protein gp17 / Baseplate hub protein, N-terminal attachment domain / Gene transfer agent, major tail protein / Phage portal protein, HK97 / Bacteriophage phiJL001, Gp84 / Bacteriophage phiJL001, Gp84, C-terminal / : / Phage conserved hypothetical protein BR0599 / Bacteriophage SPP1, head-tail adaptor superfamily / Bacteriophage SPP1, head-tail adaptor / Phage head completion protein / Tip attachment protein J / Putative phage tail protein / Phage major tail protein TP901-1 / Phage tail tube protein / Bacteriophage/Gene transfer agent portal protein / Phage portal protein / : / Phage capsid / Phage capsid family / Glycoside hydrolase superfamily
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / Uncharacterized protein / Uncharacterized protein / Phage portal protein, HK97 family / Phage major capsid protein, HK97 family / Gene transfer agent protein / Head-tail adaptor protein / DUF3168 domain-containing protein / Phage major tail protein, TP901-1 family / DUF2460 domain-containing protein ...IRON/SULFUR CLUSTER / Uncharacterized protein / Uncharacterized protein / Phage portal protein, HK97 family / Phage major capsid protein, HK97 family / Gene transfer agent protein / Head-tail adaptor protein / DUF3168 domain-containing protein / Phage major tail protein, TP901-1 family / DUF2460 domain-containing protein / Bacteriophage phiJL001 Gp84 C-terminal domain-containing protein / Host specificity protein
Similarity search - Component
Biological speciesRhodobacter capsulatus SB 1003 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.54 Å
AuthorsBardy, P. / Fuzik, T. / Hrebik, D. / Pantucek, R. / Beatty, J.T. / Plevka, P.
Funding support Czech Republic, 7items
OrganizationGrant numberCountry
Ministry of Education (MoE, Czech Republic)LQ1601 Czech Republic
European Regional Development FundCZ.1.05/1.1.00/02.0070 Czech Republic
Ministry of Education (MoE, Czech Republic)LM2011033 Czech Republic
Czech Science Foundation15-21631Y Czech Republic
Czech Science Foundation18-17810S Czech Republic
European Molecular Biology Organization (EMBO)3041 Czech Republic
Grant Agency of the Czech Republic18-13064S Czech Republic
CitationJournal: Nat Commun / Year: 2020
Title: Structure and mechanism of DNA delivery of a gene transfer agent.
Authors: Pavol Bárdy / Tibor Füzik / Dominik Hrebík / Roman Pantůček / J Thomas Beatty / Pavel Plevka /
Abstract: Alphaproteobacteria, which are the most abundant microorganisms of temperate oceans, produce phage-like particles called gene transfer agents (GTAs) that mediate lateral gene exchange. However, the ...Alphaproteobacteria, which are the most abundant microorganisms of temperate oceans, produce phage-like particles called gene transfer agents (GTAs) that mediate lateral gene exchange. However, the mechanism by which GTAs deliver DNA into cells is unknown. Here we present the structure of the GTA of Rhodobacter capsulatus (RcGTA) and describe the conformational changes required for its DNA ejection. The structure of RcGTA resembles that of a tailed phage, but it has an oblate head shortened in the direction of the tail axis, which limits its packaging capacity to less than 4,500 base pairs of linear double-stranded DNA. The tail channel of RcGTA contains a trimer of proteins that possess features of both tape measure proteins of long-tailed phages from the family Siphoviridae and tail needle proteins of short-tailed phages from the family Podoviridae. The opening of a constriction within the RcGTA baseplate enables the ejection of DNA into bacterial periplasm.
History
DepositionNov 1, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 7, 2021Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.process_site
Revision 1.2Jul 14, 2021Group: Derived calculations
Category: pdbx_struct_sheet_hbond / struct_sheet ...pdbx_struct_sheet_hbond / struct_sheet / struct_sheet_order / struct_sheet_range
Revision 1.3May 22, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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  • Deposited structure unit
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  • EMDB-10443
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Assembly

Deposited unit
C5: Phage major capsid protein, HK97 family
X4: Phage major capsid protein, HK97 family
Y4: Phage major capsid protein, HK97 family
Z4: Phage major capsid protein, HK97 family
A5: Phage major capsid protein, HK97 family
B5: Phage major capsid protein, HK97 family
N4: Phage major capsid protein, HK97 family
R4: Phage major capsid protein, HK97 family
M4: Phage major capsid protein, HK97 family
Q4: Phage major capsid protein, HK97 family
O4: Phage major capsid protein, HK97 family
P4: Phage major capsid protein, HK97 family
W4: Phage major capsid protein, HK97 family
U4: Phage major capsid protein, HK97 family
T4: Phage major capsid protein, HK97 family
S4: Phage major capsid protein, HK97 family
K4: Phage major capsid protein, HK97 family
J4: Phage major capsid protein, HK97 family
V4: Phage major capsid protein, HK97 family
L4: Phage major capsid protein, HK97 family
H4: Phage major capsid protein, HK97 family
I4: Phage major capsid protein, HK97 family
A4: Phage major capsid protein, HK97 family
D4: Phage major capsid protein, HK97 family
E4: Phage major capsid protein, HK97 family
F4: Phage major capsid protein, HK97 family
G4: Phage major capsid protein, HK97 family
B4: Phage major capsid protein, HK97 family
C4: Phage major capsid protein, HK97 family
E3: Uncharacterized protein
D3: Uncharacterized protein
A3: Uncharacterized protein
C3: Uncharacterized protein
B3: Uncharacterized protein
F3: Uncharacterized protein
A1: Uncharacterized protein
E2: Uncharacterized protein
D2: Uncharacterized protein
A2: Uncharacterized protein
C2: Uncharacterized protein
B2: Uncharacterized protein
F2: Uncharacterized protein
CP: Phage major capsid protein, HK97 family
XO: Phage major capsid protein, HK97 family
YO: Phage major capsid protein, HK97 family
ZO: Phage major capsid protein, HK97 family
AP: Phage major capsid protein, HK97 family
BP: Phage major capsid protein, HK97 family
NO: Phage major capsid protein, HK97 family
RO: Phage major capsid protein, HK97 family
MO: Phage major capsid protein, HK97 family
QO: Phage major capsid protein, HK97 family
OO: Phage major capsid protein, HK97 family
PO: Phage major capsid protein, HK97 family
WO: Phage major capsid protein, HK97 family
UO: Phage major capsid protein, HK97 family
TO: Phage major capsid protein, HK97 family
SO: Phage major capsid protein, HK97 family
KO: Phage major capsid protein, HK97 family
JO: Phage major capsid protein, HK97 family
VO: Phage major capsid protein, HK97 family
LO: Phage major capsid protein, HK97 family
HO: Phage major capsid protein, HK97 family
IO: Phage major capsid protein, HK97 family
AO: Phage major capsid protein, HK97 family
DO: Phage major capsid protein, HK97 family
EO: Phage major capsid protein, HK97 family
FO: Phage major capsid protein, HK97 family
GO: Phage major capsid protein, HK97 family
BO: Phage major capsid protein, HK97 family
CO: Phage major capsid protein, HK97 family
EN: Uncharacterized protein
DN: Uncharacterized protein
AN: Uncharacterized protein
CN: Uncharacterized protein
BN: Uncharacterized protein
FN: Uncharacterized protein
AL: Uncharacterized protein
EM: Uncharacterized protein
DM: Uncharacterized protein
AM: Uncharacterized protein
CM: Uncharacterized protein
BM: Uncharacterized protein
FM: Uncharacterized protein
CK: Phage major capsid protein, HK97 family
XJ: Phage major capsid protein, HK97 family
YJ: Phage major capsid protein, HK97 family
ZJ: Phage major capsid protein, HK97 family
AK: Phage major capsid protein, HK97 family
BK: Phage major capsid protein, HK97 family
NJ: Phage major capsid protein, HK97 family
RJ: Phage major capsid protein, HK97 family
MJ: Phage major capsid protein, HK97 family
QJ: Phage major capsid protein, HK97 family
OJ: Phage major capsid protein, HK97 family
PJ: Phage major capsid protein, HK97 family
WJ: Phage major capsid protein, HK97 family
UJ: Phage major capsid protein, HK97 family
TJ: Phage major capsid protein, HK97 family
SJ: Phage major capsid protein, HK97 family
KJ: Phage major capsid protein, HK97 family
JJ: Phage major capsid protein, HK97 family
VJ: Phage major capsid protein, HK97 family
LJ: Phage major capsid protein, HK97 family
HJ: Phage major capsid protein, HK97 family
IJ: Phage major capsid protein, HK97 family
AJ: Phage major capsid protein, HK97 family
DJ: Phage major capsid protein, HK97 family
EJ: Phage major capsid protein, HK97 family
FJ: Phage major capsid protein, HK97 family
GJ: Phage major capsid protein, HK97 family
BJ: Phage major capsid protein, HK97 family
CJ: Phage major capsid protein, HK97 family
EI: Uncharacterized protein
DI: Uncharacterized protein
AI: Uncharacterized protein
CI: Uncharacterized protein
BI: Uncharacterized protein
FI: Uncharacterized protein
AG: Uncharacterized protein
EH: Uncharacterized protein
DH: Uncharacterized protein
AH: Uncharacterized protein
CH: Uncharacterized protein
BH: Uncharacterized protein
FH: Uncharacterized protein
CF: Phage major capsid protein, HK97 family
XE: Phage major capsid protein, HK97 family
YE: Phage major capsid protein, HK97 family
ZE: Phage major capsid protein, HK97 family
AF: Phage major capsid protein, HK97 family
BF: Phage major capsid protein, HK97 family
NE: Phage major capsid protein, HK97 family
RE: Phage major capsid protein, HK97 family
ME: Phage major capsid protein, HK97 family
QE: Phage major capsid protein, HK97 family
OE: Phage major capsid protein, HK97 family
PE: Phage major capsid protein, HK97 family
WE: Phage major capsid protein, HK97 family
UE: Phage major capsid protein, HK97 family
TE: Phage major capsid protein, HK97 family
SE: Phage major capsid protein, HK97 family
KE: Phage major capsid protein, HK97 family
JE: Phage major capsid protein, HK97 family
VE: Phage major capsid protein, HK97 family
LE: Phage major capsid protein, HK97 family
HE: Phage major capsid protein, HK97 family
IE: Phage major capsid protein, HK97 family
AE: Phage major capsid protein, HK97 family
DE: Phage major capsid protein, HK97 family
EE: Phage major capsid protein, HK97 family
FE: Phage major capsid protein, HK97 family
GE: Phage major capsid protein, HK97 family
BE: Phage major capsid protein, HK97 family
CE: Phage major capsid protein, HK97 family
ED: Uncharacterized protein
DD: Uncharacterized protein
AD: Uncharacterized protein
CD: Uncharacterized protein
BD: Uncharacterized protein
FD: Uncharacterized protein
AB: Uncharacterized protein
EC: Uncharacterized protein
DC: Uncharacterized protein
AC: Uncharacterized protein
CC: Uncharacterized protein
BC: Uncharacterized protein
FC: Uncharacterized protein
CA: Phage major capsid protein, HK97 family
X9: Phage major capsid protein, HK97 family
Y9: Phage major capsid protein, HK97 family
Z9: Phage major capsid protein, HK97 family
AA: Phage major capsid protein, HK97 family
BA: Phage major capsid protein, HK97 family
N9: Phage major capsid protein, HK97 family
R9: Phage major capsid protein, HK97 family
M9: Phage major capsid protein, HK97 family
Q9: Phage major capsid protein, HK97 family
O9: Phage major capsid protein, HK97 family
P9: Phage major capsid protein, HK97 family
W9: Phage major capsid protein, HK97 family
U9: Phage major capsid protein, HK97 family
T9: Phage major capsid protein, HK97 family
S9: Phage major capsid protein, HK97 family
K9: Phage major capsid protein, HK97 family
J9: Phage major capsid protein, HK97 family
V9: Phage major capsid protein, HK97 family
L9: Phage major capsid protein, HK97 family
H9: Phage major capsid protein, HK97 family
I9: Phage major capsid protein, HK97 family
A9: Phage major capsid protein, HK97 family
D9: Phage major capsid protein, HK97 family
E9: Phage major capsid protein, HK97 family
F9: Phage major capsid protein, HK97 family
G9: Phage major capsid protein, HK97 family
B9: Phage major capsid protein, HK97 family
C9: Phage major capsid protein, HK97 family
E8: Uncharacterized protein
D8: Uncharacterized protein
A8: Uncharacterized protein
C8: Uncharacterized protein
B8: Uncharacterized protein
F8: Uncharacterized protein
A6: Uncharacterized protein
E7: Uncharacterized protein
D7: Uncharacterized protein
A7: Uncharacterized protein
C7: Uncharacterized protein
B7: Uncharacterized protein
F7: Uncharacterized protein
2A: Uncharacterized protein
1A: Portal protein Rcc01684
1B: Portal protein Rcc01684
2B: Uncharacterized protein
4A: Uncharacterized protein
3A: Uncharacterized protein
5A: Phage major tail protein, TP901-1 family
5S: Phage major tail protein, TP901-1 family
5G: Phage major tail protein, TP901-1 family
5M: Phage major tail protein, TP901-1 family
2K: Uncharacterized protein
1K: Portal protein Rcc01684
1L: Portal protein Rcc01684
2L: Uncharacterized protein
4F: Uncharacterized protein
3F: Uncharacterized protein
5F: Phage major tail protein, TP901-1 family
5X: Phage major tail protein, TP901-1 family
5L: Phage major tail protein, TP901-1 family
5R: Phage major tail protein, TP901-1 family
2I: Uncharacterized protein
1I: Portal protein Rcc01684
1J: Portal protein Rcc01684
2J: Uncharacterized protein
4E: Uncharacterized protein
3E: Uncharacterized protein
5E: Phage major tail protein, TP901-1 family
5W: Phage major tail protein, TP901-1 family
5K: Phage major tail protein, TP901-1 family
5Q: Phage major tail protein, TP901-1 family
2G: Uncharacterized protein
1G: Portal protein Rcc01684
1H: Portal protein Rcc01684
2H: Uncharacterized protein
4D: Uncharacterized protein
3D: Uncharacterized protein
5D: Phage major tail protein, TP901-1 family
5V: Phage major tail protein, TP901-1 family
5J: Phage major tail protein, TP901-1 family
5P: Phage major tail protein, TP901-1 family
2E: Uncharacterized protein
1E: Portal protein Rcc01684
1F: Portal protein Rcc01684
2F: Uncharacterized protein
4C: Uncharacterized protein
3C: Uncharacterized protein
5C: Phage major tail protein, TP901-1 family
5U: Phage major tail protein, TP901-1 family
5I: Phage major tail protein, TP901-1 family
5O: Phage major tail protein, TP901-1 family
2C: Uncharacterized protein
1C: Portal protein Rcc01684
1D: Portal protein Rcc01684
2D: Uncharacterized protein
4B: Uncharacterized protein
3B: Uncharacterized protein
5B: Phage major tail protein, TP901-1 family
5T: Phage major tail protein, TP901-1 family
5H: Phage major tail protein, TP901-1 family
5N: Phage major tail protein, TP901-1 family
7A: Uncharacterized protein
8A: Uncharacterized protein
6B: Uncharacterized protein
6A: Uncharacterized protein
5Y: Phage major tail protein, TP901-1 family
5Z: Phage major tail protein, TP901-1 family
7C: Uncharacterized protein
8C: Uncharacterized protein
6F: Uncharacterized protein
6E: Uncharacterized protein
52: Phage major tail protein, TP901-1 family
53: Phage major tail protein, TP901-1 family
7B: Uncharacterized protein
8B: Uncharacterized protein
6D: Uncharacterized protein
6C: Uncharacterized protein
50: Phage major tail protein, TP901-1 family
51: Phage major tail protein, TP901-1 family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,765,993291
Polymers8,764,939288
Non-polymers1,0553
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 3 types, 187 molecules C5X4Y4Z4A5B5N4R4M4Q4O4P4W4U4T4S4K4J4V4L4H4I4A4D4E4F4G4B4C4CP...

#1: Protein ...
Phage major capsid protein, HK97 family


Mass: 40894.988 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Source: (natural) Rhodobacter capsulatus SB 1003 (bacteria) / References: UniProt: D5ATZ3
#5: Protein
Portal protein Rcc01684


Mass: 42846.910 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Rhodobacter capsulatus SB 1003 (bacteria) / References: UniProt: D5ATZ0
#8: Protein ...
Phage major tail protein, TP901-1 family


Mass: 14420.007 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Source: (natural) Rhodobacter capsulatus SB 1003 (bacteria) / References: UniProt: D5ATZ7

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Uncharacterized ... , 8 types, 101 molecules E3D3A3C3B3A1E2D2A2C2B2ENDNANCNBNALEMDMAMCMBMEIDIAICIBIAGEHDH...

#2: Protein ...
Uncharacterized protein


Mass: 9104.348 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Source: (natural) Rhodobacter capsulatus SB 1003 (bacteria) / References: UniProt: D5AR33
#3: Protein
Uncharacterized protein


Mass: 32996.828 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Rhodobacter capsulatus SB 1003 (bacteria) / References: UniProt: D5AR34
#4: Protein
Uncharacterized protein


Mass: 20956.354 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Rhodobacter capsulatus SB 1003 (bacteria) / References: UniProt: D5ATZ4
#6: Protein
Uncharacterized protein


Mass: 13871.859 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Rhodobacter capsulatus SB 1003 (bacteria) / References: UniProt: D5ATZ6
#7: Protein
Uncharacterized protein


Mass: 12403.123 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Rhodobacter capsulatus SB 1003 (bacteria) / References: UniProt: D5ATZ5
#9: Protein Uncharacterized protein


Mass: 31690.734 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Rhodobacter capsulatus SB 1003 (bacteria) / References: UniProt: D5AU02
#10: Protein Uncharacterized protein


Mass: 138527.359 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Rhodobacter capsulatus SB 1003 (bacteria) / References: UniProt: D5AU04
#11: Protein
Uncharacterized protein


Mass: 22985.713 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Rhodobacter capsulatus SB 1003 (bacteria) / References: UniProt: D5AU01

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Non-polymers , 1 types, 3 molecules

#12: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4

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Details

Has ligand of interestN

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Experimental details

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Experiment

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

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Sample preparation

Component
IDNameTypeDetailsEntity IDParent-IDSource
1Rhodobacter capsulatus DE442VIRUSphage-like particle mediating high-frequency horisontal gene transfer in Rhodobacterales species#1-#110NATURAL
2CapsidCOMPLEXOblate T=3 capsid#1-#31NATURAL
3Head spikeCOMPLEXpenton protrusion of the capsid#2-#31NATURAL
4ConnectorCOMPLEXspecial 5-fold vertex of the capsid, interconnecting capsid to tail#4-#51NATURAL
5TailCOMPLEXtubular structure interconnecting capsid to baseplate (host-recognition device)#6-#8, #111NATURAL
6BaseplateCOMPLEXhost-recognition device present at the tip of the tail#9-#101NATURAL
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
118.03 MDaNO
215.42 MDaNO
310.08 MDaNO
410.76 MDaNO
510.73 MDaNO
610.88 MDaNO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
21Rhodobacter capsulatus SB 1003 (bacteria)272942Gene transfer agent
32Rhodobacter capsulatus SB 1003 (bacteria)272942Gene transfer agent
43Rhodobacter capsulatus SB 1003 (bacteria)272942Gene transfer agent
54Rhodobacter capsulatus SB 1003 (bacteria)272942Gene transfer agent
65Rhodobacter capsulatus SB 1003 (bacteria)272942Gene transfer agent
76Rhodobacter capsulatus SB 1003 (bacteria)272942Gene transfer agent
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Rhodobacter capsulatus
Virus shellName: HK97-like oblate capsid / Diameter: 945 nm / Triangulation number (T number): 3
Buffer solutionpH: 7.8 / Details: G-buffer, doi: 10.1016/0003-9861(77)90508-2
Buffer component
IDConc.NameFormulaBuffer-ID
110 mMTris1
21 mMNaCl1
31 mMMgCl21
41 mMCaCl21
50.01 mg/mlBovine serum albumin1
SpecimenConc.: 20 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293.15 K

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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 FIELD / Nominal defocus max: -3000 nm / Nominal defocus min: -1000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 42.75 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k)
Image scansWidth: 4096 / Height: 4096

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Processing

EM software
IDNameVersionCategory
1RELION2.1particle selection
2EPU2.1image acquisition
4RELION2.1CTF correction
7Coot0.9model fitting
9PHENIX1.16model refinement
10RELION2.1initial Euler assignment
11RELION3final Euler assignment
12RELION3classification
13RELION33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 53432
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.54 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 27724 / Algorithm: BACK PROJECTION
Details: Map is generated from merged maps of GTA capsid (EMD-10442), neck (EMD-10477), tail tube (EMD-10478) and baseplate (EMD-10490). Internal map regions corresponds to the genome from asymmetric ...Details: Map is generated from merged maps of GTA capsid (EMD-10442), neck (EMD-10477), tail tube (EMD-10478) and baseplate (EMD-10490). Internal map regions corresponds to the genome from asymmetric reconstruction (EMD-10568) and tape-measure protein density from C3 reconstruction of tail tube (EMD-10570). Shown resoluton value corresponds to the map with lowest resolution (C3 tail tube).
Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL

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  • 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

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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

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