[English] 日本語
Yorodumi
- PDB-6q3g: Structure of native bacteriophage P68 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6q3g
TitleStructure of native bacteriophage P68
Components
  • Arstotzka protein
  • Head fiber protein
  • Inner core proteinEarth's inner core
  • Lower collar protein
  • Major head protein
  • Minor structural protein
  • Portal protein
  • Tail fibre protein
KeywordsVIRUS / structural protein / bacteriophage / receptor binding protein / complex
Function / homology: / Phage 5-bladed beta propeller receptor binding platform domain / Uncharacterized protein / Uncharacterized protein / Major head protein / Lower collar protein / Minor structural protein
Function and homology information
Biological speciesStaphylococcus phage P68 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsDominik, H. / Karel, S. / Fuzik, T. / Plevka, P.
Funding support Czech Republic, 4items
OrganizationGrant numberCountry
Czech Science Foundation15-21631Y Czech Republic
Czech Science Foundation18-17810S Czech Republic
European Molecular Biology Organization3041 Czech Republic
16-29916A Czech Republic
CitationJournal: Sci Adv / Year: 2019
Title: Structure and genome ejection mechanism of phage P68.
Authors: Dominik Hrebík / Dana Štveráková / Karel Škubník / Tibor Füzik / Roman Pantůček / Pavel Plevka /
Abstract: Phages infecting can be used as therapeutics against antibiotic-resistant bacterial infections. However, there is limited information about the mechanism of genome delivery of phages that infect ...Phages infecting can be used as therapeutics against antibiotic-resistant bacterial infections. However, there is limited information about the mechanism of genome delivery of phages that infect Gram-positive bacteria. Here, we present the structures of native phage P68, genome ejection intermediate, and empty particle. The P68 head contains 72 subunits of inner core protein, 15 of which bind to and alter the structure of adjacent major capsid proteins and thus specify attachment sites for head fibers. Unlike in the previously studied phages, the head fibers of P68 enable its virion to position itself at the cell surface for genome delivery. The unique interaction of one end of P68 DNA with one of the 12 portal protein subunits is disrupted before the genome ejection. The inner core proteins are released together with the DNA and enable the translocation of phage genome across the bacterial membrane into the cytoplasm.
History
DepositionDec 4, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-4459
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-4459
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C1: Major head protein
A1: Major head protein
B1: Major head protein
D1: Major head protein
E1: Arstotzka protein
F1: Arstotzka protein
G1: Arstotzka protein
H1: Arstotzka protein
I1: Major head protein
J1: Major head protein
K1: Major head protein
L1: Major head protein
M1: Arstotzka protein
N1: Arstotzka protein
O1: Arstotzka protein
P1: Arstotzka protein
Q1: Major head protein
R1: Major head protein
S1: Major head protein
T1: Major head protein
U1: Arstotzka protein
V1: Arstotzka protein
W1: Arstotzka protein
X1: Major head protein
Y1: Major head protein
Z1: Major head protein
a1: Major head protein
b1: Arstotzka protein
c1: Arstotzka protein
d1: Arstotzka protein
e1: Arstotzka protein
f1: Major head protein
g1: Major head protein
h1: Major head protein
i1: Major head protein
j1: Arstotzka protein
k1: Arstotzka protein
l1: Arstotzka protein
m1: Arstotzka protein
A2: Portal protein
B2: Lower collar protein
D2: Minor structural protein
E2: Minor structural protein
F2: Minor structural protein
G2: Tail fibre protein
H2: Tail fibre protein
I2: Tail fibre protein
J2: Tail fibre protein
K2: Tail fibre protein
L2: Tail fibre protein
C2: Minor structural protein
N2: Minor structural protein
O2: Minor structural protein
C3: Major head protein
A3: Major head protein
B3: Major head protein
D3: Major head protein
E3: Arstotzka protein
F3: Arstotzka protein
G3: Arstotzka protein
H3: Arstotzka protein
I3: Major head protein
J3: Major head protein
K3: Major head protein
L3: Major head protein
M3: Arstotzka protein
N3: Arstotzka protein
O3: Arstotzka protein
P3: Arstotzka protein
Q3: Major head protein
R3: Major head protein
S3: Major head protein
T3: Major head protein
U3: Arstotzka protein
V3: Arstotzka protein
W3: Arstotzka protein
X3: Arstotzka protein
Y3: Major head protein
Z3: Arstotzka protein
a3: Arstotzka protein
b3: Major head protein
c3: Arstotzka protein
d3: Arstotzka protein
C4: Major head protein
A4: Major head protein
B4: Major head protein
D4: Major head protein
E4: Arstotzka protein
F4: Arstotzka protein
G4: Arstotzka protein
H4: Arstotzka protein
I4: Major head protein
J4: Major head protein
K4: Major head protein
L4: Major head protein
M4: Arstotzka protein
N4: Arstotzka protein
O4: Arstotzka protein
P4: Arstotzka protein
Q4: Major head protein
R4: Major head protein
S4: Major head protein
T4: Major head protein
U4: Arstotzka protein
V4: Arstotzka protein
W4: Arstotzka protein
X4: Major head protein
Y4: Major head protein
Z4: Major head protein
a4: Major head protein
b4: Arstotzka protein
c4: Arstotzka protein
d4: Arstotzka protein
e4: Arstotzka protein
f4: Major head protein
g4: Major head protein
h4: Major head protein
i4: Major head protein
j4: Arstotzka protein
k4: Arstotzka protein
l4: Arstotzka protein
A5: Portal protein
B5: Lower collar protein
D5: Minor structural protein
E5: Minor structural protein
F5: Minor structural protein
G5: Tail fibre protein
H5: Tail fibre protein
I5: Tail fibre protein
J5: Tail fibre protein
K5: Tail fibre protein
L5: Tail fibre protein
C5: Minor structural protein
N5: Minor structural protein
O5: Minor structural protein
C6: Major head protein
A6: Major head protein
B6: Major head protein
D6: Major head protein
E6: Arstotzka protein
F6: Arstotzka protein
G6: Arstotzka protein
H6: Arstotzka protein
I6: Major head protein
J6: Major head protein
K6: Major head protein
L6: Major head protein
M6: Arstotzka protein
N6: Arstotzka protein
O6: Arstotzka protein
P6: Arstotzka protein
Q6: Major head protein
R6: Major head protein
S6: Major head protein
T6: Major head protein
U6: Arstotzka protein
V6: Arstotzka protein
W6: Arstotzka protein
X6: Arstotzka protein
Y6: Major head protein
Z6: Major head protein
a6: Major head protein
b6: Major head protein
c6: Arstotzka protein
d6: Arstotzka protein
e6: Arstotzka protein
f6: Arstotzka protein
g6: Major head protein
h6: Major head protein
i6: Major head protein
j6: Major head protein
k6: Arstotzka protein
l6: Arstotzka protein
m6: Arstotzka protein
n6: Arstotzka protein
C7: Major head protein
A7: Major head protein
B7: Major head protein
D7: Major head protein
E7: Arstotzka protein
F7: Arstotzka protein
G7: Arstotzka protein
H7: Arstotzka protein
I7: Major head protein
J7: Major head protein
K7: Major head protein
L7: Major head protein
M7: Arstotzka protein
N7: Arstotzka protein
O7: Arstotzka protein
P7: Arstotzka protein
Q7: Major head protein
R7: Major head protein
S7: Major head protein
T7: Major head protein
U7: Arstotzka protein
V7: Arstotzka protein
W7: Arstotzka protein
X7: Arstotzka protein
Y7: Major head protein
Z7: Major head protein
a7: Major head protein
b7: Major head protein
c7: Arstotzka protein
d7: Arstotzka protein
e7: Arstotzka protein
f7: Arstotzka protein
g7: Major head protein
h7: Major head protein
i7: Major head protein
j7: Major head protein
k7: Arstotzka protein
l7: Arstotzka protein
m7: Arstotzka protein
n7: Arstotzka protein
C8: Major head protein
A8: Major head protein
B8: Major head protein
D8: Major head protein
E8: Arstotzka protein
F8: Arstotzka protein
G8: Arstotzka protein
H8: Arstotzka protein
I8: Major head protein
J8: Major head protein
K8: Major head protein
L8: Major head protein
M8: Arstotzka protein
N8: Arstotzka protein
O8: Arstotzka protein
P8: Arstotzka protein
Q8: Major head protein
R8: Major head protein
S8: Major head protein
T8: Major head protein
U8: Arstotzka protein
V8: Arstotzka protein
W8: Arstotzka protein
X8: Arstotzka protein
Y8: Major head protein
Z8: Major head protein
a8: Major head protein
b8: Major head protein
c8: Arstotzka protein
d8: Arstotzka protein
e8: Arstotzka protein
f8: Arstotzka protein
g8: Major head protein
h8: Major head protein
i8: Major head protein
j8: Major head protein
k8: Arstotzka protein
l8: Arstotzka protein
m8: Arstotzka protein
n8: Arstotzka protein
A9: Portal protein
B9: Lower collar protein
D9: Minor structural protein
E9: Minor structural protein
F9: Minor structural protein
G9: Tail fibre protein
H9: Tail fibre protein
I9: Tail fibre protein
J9: Tail fibre protein
K9: Tail fibre protein
L9: Tail fibre protein
C9: Minor structural protein
N9: Minor structural protein
O9: Minor structural protein
AA: Portal protein
BA: Lower collar protein
DA: Minor structural protein
EA: Minor structural protein
FA: Minor structural protein
GA: Tail fibre protein
HA: Tail fibre protein
IA: Tail fibre protein
JA: Tail fibre protein
KA: Tail fibre protein
LA: Tail fibre protein
CA: Minor structural protein
NA: Minor structural protein
OA: Minor structural protein
AB: Portal protein
BB: Lower collar protein
DB: Minor structural protein
EB: Minor structural protein
FB: Minor structural protein
GB: Tail fibre protein
HB: Tail fibre protein
IB: Tail fibre protein
JB: Tail fibre protein
KB: Tail fibre protein
LB: Tail fibre protein
CB: Minor structural protein
NB: Minor structural protein
OB: Minor structural protein
AC: Portal protein
BC: Lower collar protein
DC: Minor structural protein
EC: Minor structural protein
FC: Minor structural protein
GC: Tail fibre protein
HC: Tail fibre protein
IC: Tail fibre protein
JC: Tail fibre protein
KC: Tail fibre protein
LC: Tail fibre protein
CC: Minor structural protein
NC: Minor structural protein
OC: Minor structural protein
AD: Major head protein
BD: Major head protein
CD: Major head protein
DD: Major head protein
ED: Arstotzka protein
FD: Arstotzka protein
GD: Arstotzka protein
HD: Arstotzka protein
ID: Head fiber protein
KD: Major head protein
LD: Major head protein
MD: Arstotzka protein
ND: Arstotzka protein
OD: Head fiber protein
PD: Inner core protein
QD: Inner core protein
RD: Inner core protein
SD: Head fiber protein
DE: Major head protein
EE: Arstotzka protein
GE: Arstotzka protein
AE: Major head protein
BE: Major head protein
CE: Major head protein
FE: Major head protein
HE: Arstotzka protein
IE: Arstotzka protein
JE: Arstotzka protein
KE: Major head protein
LE: Major head protein
ME: Major head protein
NE: Major head protein
OE: Arstotzka protein
PE: Arstotzka protein
QE: Arstotzka protein
RE: Arstotzka protein
SE: Major head protein
TE: Major head protein
UE: Major head protein
VE: Major head protein
WE: Arstotzka protein
XE: Arstotzka protein
YE: Arstotzka protein
ZE: Arstotzka protein
aE: Major head protein
bE: Major head protein
cE: Major head protein
dE: Major head protein
eE: Arstotzka protein
fE: Arstotzka protein
gE: Arstotzka protein
hE: Arstotzka protein
AF: Portal protein
BF: Lower collar protein
DF: Minor structural protein
EF: Minor structural protein
FF: Minor structural protein
GF: Tail fibre protein
HF: Tail fibre protein
IF: Tail fibre protein
JF: Tail fibre protein
KF: Tail fibre protein
LF: Tail fibre protein
CF: Minor structural protein
NF: Minor structural protein
OF: Minor structural protein
CG: Major head protein
AG: Major head protein
BG: Major head protein
DG: Major head protein
EG: Arstotzka protein
FG: Arstotzka protein
GG: Arstotzka protein
HG: Arstotzka protein
IG: Major head protein
JG: Major head protein
KG: Major head protein
LG: Major head protein
MG: Arstotzka protein
NG: Arstotzka protein
OG: Arstotzka protein
PG: Arstotzka protein
QG: Major head protein
RG: Major head protein
SG: Major head protein
TG: Major head protein
UG: Arstotzka protein
VG: Arstotzka protein
WG: Arstotzka protein
XG: Arstotzka protein
YG: Major head protein
ZG: Major head protein
aG: Major head protein
bG: Major head protein
cG: Arstotzka protein
dG: Arstotzka protein
eG: Arstotzka protein
fG: Arstotzka protein
gG: Major head protein
hG: Major head protein
iG: Major head protein
jG: Major head protein
kG: Arstotzka protein
lG: Arstotzka protein
mG: Arstotzka protein
nG: Arstotzka protein
AH: Portal protein
BH: Lower collar protein
DH: Minor structural protein
EH: Minor structural protein
FH: Minor structural protein
GH: Tail fibre protein
HH: Tail fibre protein
IH: Tail fibre protein
JH: Tail fibre protein
KH: Tail fibre protein
LH: Tail fibre protein
CH: Minor structural protein
NH: Minor structural protein
OH: Minor structural protein
AI: Portal protein
BI: Lower collar protein
DI: Minor structural protein
EI: Minor structural protein
FI: Minor structural protein
GI: Tail fibre protein
HI: Tail fibre protein
II: Tail fibre protein
JI: Tail fibre protein
KI: Tail fibre protein
LI: Tail fibre protein
CI: Minor structural protein
NI: Minor structural protein
OI: Minor structural protein
AJ: Major head protein
BJ: Major head protein
CJ: Major head protein
DJ: Major head protein
EJ: Arstotzka protein
FJ: Arstotzka protein
GJ: Arstotzka protein
HJ: Arstotzka protein
IJ: Head fiber protein
KJ: Major head protein
LJ: Major head protein
MJ: Arstotzka protein
NJ: Arstotzka protein
OJ: Head fiber protein
PJ: Inner core protein
QJ: Inner core protein
RJ: Inner core protein
SJ: Head fiber protein
AK: Major head protein
BK: Major head protein
CK: Major head protein
DK: Major head protein
EK: Arstotzka protein
FK: Arstotzka protein
GK: Arstotzka protein
HK: Arstotzka protein
IK: Head fiber protein
KK: Major head protein
LK: Major head protein
MK: Arstotzka protein
NK: Arstotzka protein
OK: Head fiber protein
PK: Inner core protein
QK: Inner core protein
RK: Inner core protein
SK: Head fiber protein
CL: Major head protein
AL: Major head protein
BL: Major head protein
DL: Major head protein
EL: Arstotzka protein
FL: Arstotzka protein
GL: Arstotzka protein
HL: Arstotzka protein
IL: Major head protein
JL: Major head protein
KL: Major head protein
LL: Major head protein
ML: Arstotzka protein
NL: Arstotzka protein
OL: Arstotzka protein
PL: Arstotzka protein
QL: Major head protein
RL: Major head protein
SL: Major head protein
TL: Major head protein
UL: Arstotzka protein
VL: Arstotzka protein
WL: Arstotzka protein
XL: Arstotzka protein
YL: Major head protein
ZL: Major head protein
aL: Major head protein
bL: Major head protein
cL: Arstotzka protein
dL: Arstotzka protein
eL: Arstotzka protein
fL: Arstotzka protein
gL: Major head protein
hL: Arstotzka protein
iL: Arstotzka protein
AM: Portal protein
BM: Lower collar protein
DM: Minor structural protein
EM: Minor structural protein
FM: Minor structural protein
GM: Tail fibre protein
HM: Tail fibre protein
IM: Tail fibre protein
JM: Tail fibre protein
KM: Tail fibre protein
LM: Tail fibre protein
CM: Minor structural protein
NM: Minor structural protein
OM: Minor structural protein
AN: Portal protein
BN: Lower collar protein
DN: Minor structural protein
EN: Minor structural protein
FN: Minor structural protein
GN: Tail fibre protein
HN: Tail fibre protein
IN: Tail fibre protein
JN: Tail fibre protein
KN: Tail fibre protein
LN: Tail fibre protein
CN: Minor structural protein
NN: Minor structural protein
ON: Minor structural protein
AO: Portal protein
BO: Lower collar protein
DO: Minor structural protein
EO: Minor structural protein
FO: Minor structural protein
GO: Tail fibre protein
HO: Tail fibre protein
IO: Tail fibre protein
JO: Tail fibre protein
KO: Tail fibre protein
LO: Tail fibre protein
CO: Minor structural protein
NO: Minor structural protein
OO: Minor structural protein
AP: Major head protein
BP: Major head protein
CP: Major head protein
DP: Major head protein
EP: Arstotzka protein
FP: Arstotzka protein
GP: Arstotzka protein
HP: Arstotzka protein
IP: Head fiber protein
KP: Major head protein
LP: Major head protein
MP: Arstotzka protein
NP: Arstotzka protein
OP: Head fiber protein
PP: Inner core protein
QP: Inner core protein
RP: Inner core protein
SP: Head fiber protein
CQ: Major head protein
AQ: Major head protein
BQ: Major head protein
DQ: Major head protein
EQ: Arstotzka protein
FQ: Arstotzka protein
GQ: Arstotzka protein
HQ: Arstotzka protein
IQ: Major head protein
JQ: Major head protein
KQ: Major head protein
LQ: Major head protein
MQ: Arstotzka protein
NQ: Arstotzka protein
OQ: Arstotzka protein
PQ: Arstotzka protein
QQ: Major head protein
RQ: Major head protein
SQ: Major head protein
TQ: Major head protein
UQ: Arstotzka protein
VQ: Arstotzka protein
WQ: Arstotzka protein
XQ: Arstotzka protein
YQ: Major head protein
ZQ: Arstotzka protein
aQ: Arstotzka protein
bQ: Major head protein
cQ: Major head protein
dQ: Major head protein
eQ: Major head protein
fQ: Arstotzka protein
gQ: Arstotzka protein
hQ: Arstotzka protein
iQ: Arstotzka protein
CR: Major head protein
AR: Major head protein
BR: Major head protein
DR: Major head protein
ER: Arstotzka protein
FR: Arstotzka protein
GR: Arstotzka protein
HR: Arstotzka protein
IR: Major head protein
JR: Major head protein
KR: Major head protein
LR: Major head protein
MR: Arstotzka protein
NR: Arstotzka protein
OR: Arstotzka protein
PR: Arstotzka protein
QR: Major head protein
RR: Major head protein
SR: Major head protein
TR: Major head protein
UR: Arstotzka protein
VR: Arstotzka protein
WR: Arstotzka protein
XR: Arstotzka protein
YR: Major head protein
ZR: Major head protein
aR: Major head protein
bR: Major head protein
cR: Arstotzka protein
dR: Arstotzka protein
eR: Arstotzka protein
fR: Arstotzka protein
gR: Major head protein
hR: Major head protein
iR: Major head protein
jR: Major head protein
kR: Arstotzka protein
lR: Arstotzka protein
mR: Arstotzka protein
AS: Major head protein
BS: Major head protein
CS: Major head protein
DS: Arstotzka protein
ES: Arstotzka protein
FS: Arstotzka protein
GS: Arstotzka protein
HS: Head fiber protein
IS: Major head protein
JS: Major head protein
KS: Major head protein
LS: Arstotzka protein
MS: Arstotzka protein
NS: Head fiber protein
PS: Inner core protein
QS: Inner core protein
RS: Inner core protein
SS: Head fiber protein


Theoretical massNumber of molelcules
Total (without water)20,029,043668
Polymers20,029,043668
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
MethodChimera

-
Components

-
Protein , 7 types, 653 molecules C1A1B1D1I1J1K1L1Q1R1S1T1X1Y1Z1a1f1g1h1i1C3A3B3D3I3J3K3L3Q3R3...

#1: Protein ...
Major head protein


Mass: 46954.941 Da / Num. of mol.: 235 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage P68 (virus) / References: UniProt: Q859I3
#2: Protein ...
Arstotzka protein


Mass: 6922.464 Da / Num. of mol.: 235 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage P68 (virus) / References: UniProt: Q859I2
#3: Protein
Portal protein


Mass: 37874.699 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage P68 (virus)
#4: Protein
Lower collar protein


Mass: 29164.445 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage P68 (virus) / References: UniProt: Q859I5
#5: Protein ...
Minor structural protein


Mass: 74833.750 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage P68 (virus) / References: UniProt: Q859I6
#6: Protein ...
Tail fibre protein


Mass: 15250.671 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Source: (natural) Staphylococcus phage P68 (virus) / References: UniProt: Q859I1
#7: Protein
Head fiber protein


Mass: 3927.292 Da / Num. of mol.: 15 / Source method: isolated from a natural source
Details: Poly-alanine chain fitted to the electron density of head fiber protein from five-fold symmetric reconstruction of native phage P68
Source: (natural) Staphylococcus phage P68 (virus)

-
Protein/peptide , 1 types, 15 molecules PDQDRDPJQJRJPKQKRKPPQPRPPSQSRS

#8: Protein/peptide
Inner core protein / Earth's inner core


Mass: 1226.338 Da / Num. of mol.: 15 / Source method: isolated from a natural source
Details: Poly-alanine chain fitted to a electron density of the inner core protein located at the hexon adjacent to portal from five-fold symmetric reconstruction of native phage P68
Source: (natural) Staphylococcus phage P68 (virus)

-
Experimental details

-
Experiment

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

-
Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Staphylococcus phage P68VIRUSall0NATURAL
2Capsid of native phage P68COMPLEX#1-#2, #71NATURAL
3Tail complexCOMPLEX#4-#51NATURAL
4Portal proteinCOMPLEX#31NATURAL
5Inner core proteinEarth's inner coreCOMPLEX#6, #81NATURAL
Molecular weightValue: 19.7 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
15Staphylococcus phage P68 (virus)204090
22Staphylococcus phage P68 (virus)204090
33Staphylococcus phage P68 (virus)204090
44Staphylococcus phage P68 (virus)204090
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Staphylococcus aureus / Strain: dTarM 4220
Virus shellName: Capsid / Diameter: 480 nm / Triangulation number (T number): 4
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMtris(hydroxymethyl)aminomethaneTris1
210 mMcalcium chlorideCaCl1
310 mMsodium chlorideNaClSodium chloride1
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293 K / Details: blot time 2s; blot force -2; 3.6 ul of sample

-
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: 75000 X / Nominal defocus max: 3 nm / Nominal defocus min: 1 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1 sec. / Electron dose: 21 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 2891
Image scansWidth: 4096 / Height: 4096 / Movie frames/image: 7 / Used frames/image: 1-7

-
Processing

EM software
IDNameVersionCategory
1EMAN22.1particle selection
2EPUimage acquisition
4CTFFIND4CTF correction
7UCSF Chimera2018-02-05model fitting
9RELION2.1initial Euler assignment
10RELION2.1final Euler assignment
11RELION2.1classification
12RELION2.13D reconstruction
13PHENIXdev:3042model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 37218
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 33612 / Algorithm: BACK PROJECTION
Details: The final map is combination of maps of individual parts of bacteriophage P68 as described in the assembly section.
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-correlation coefficient
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
16IAB

6iab

16IAB1PDBexperimental model
26IAT

6iat

16IAT2PDBexperimental model
36IAW

6iaw

16IAW3PDBexperimental model
46IAC

6iac

16IAC4PDBexperimental 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