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- PDB-8akt: 235 A SynPspA rod after incubation with ATP -

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Basic information

Entry
Database: PDB / ID: 8akt
Title235 A SynPspA rod after incubation with ATP
ComponentsChloroplast membrane-associated 30 kD protein
KeywordsLIPID BINDING PROTEIN / Nucleotide binding / Helical assembly / ESCRT-III fold / Membrane remodeling
Function / homologyPspA/IM30 / PspA/IM30 family / ADENOSINE-5'-DIPHOSPHATE / Chloroplast membrane-associated 30 kD protein
Function and homology information
Biological speciesSynechocystis sp. PCC 6803 (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsJunglas, B. / Hudina, E. / Schoennenbeck, P. / Ritter, I. / Santiago-Schuebel, B. / Huesgen, P. / Sachse, C.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Union (EU)European Union
CitationJournal: To Be Published
Title: Non-canonical ATPase activity drives PspA membrane constriction
Authors: Junglas, B. / Hudina, E. / Schoennenbeck, P. / Ritter, I. / Santiago-Schuebel, B. / Huesgen, P. / Sachse, C.
History
DepositionJul 31, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 14, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
0: Chloroplast membrane-associated 30 kD protein
1: Chloroplast membrane-associated 30 kD protein
2: Chloroplast membrane-associated 30 kD protein
3: Chloroplast membrane-associated 30 kD protein
4: Chloroplast membrane-associated 30 kD protein
5: Chloroplast membrane-associated 30 kD protein
6: Chloroplast membrane-associated 30 kD protein
7: Chloroplast membrane-associated 30 kD protein
A: Chloroplast membrane-associated 30 kD protein
B: Chloroplast membrane-associated 30 kD protein
C: Chloroplast membrane-associated 30 kD protein
D: Chloroplast membrane-associated 30 kD protein
E: Chloroplast membrane-associated 30 kD protein
F: Chloroplast membrane-associated 30 kD protein
G: Chloroplast membrane-associated 30 kD protein
H: Chloroplast membrane-associated 30 kD protein
I: Chloroplast membrane-associated 30 kD protein
J: Chloroplast membrane-associated 30 kD protein
K: Chloroplast membrane-associated 30 kD protein
L: Chloroplast membrane-associated 30 kD protein
M: Chloroplast membrane-associated 30 kD protein
N: Chloroplast membrane-associated 30 kD protein
O: Chloroplast membrane-associated 30 kD protein
P: Chloroplast membrane-associated 30 kD protein
Q: Chloroplast membrane-associated 30 kD protein
R: Chloroplast membrane-associated 30 kD protein
S: Chloroplast membrane-associated 30 kD protein
T: Chloroplast membrane-associated 30 kD protein
U: Chloroplast membrane-associated 30 kD protein
V: Chloroplast membrane-associated 30 kD protein
W: Chloroplast membrane-associated 30 kD protein
X: Chloroplast membrane-associated 30 kD protein
Y: Chloroplast membrane-associated 30 kD protein
Z: Chloroplast membrane-associated 30 kD protein
a: Chloroplast membrane-associated 30 kD protein
b: Chloroplast membrane-associated 30 kD protein
c: Chloroplast membrane-associated 30 kD protein
d: Chloroplast membrane-associated 30 kD protein
e: Chloroplast membrane-associated 30 kD protein
f: Chloroplast membrane-associated 30 kD protein
g: Chloroplast membrane-associated 30 kD protein
h: Chloroplast membrane-associated 30 kD protein
i: Chloroplast membrane-associated 30 kD protein
j: Chloroplast membrane-associated 30 kD protein
k: Chloroplast membrane-associated 30 kD protein
l: Chloroplast membrane-associated 30 kD protein
m: Chloroplast membrane-associated 30 kD protein
n: Chloroplast membrane-associated 30 kD protein
o: Chloroplast membrane-associated 30 kD protein
p: Chloroplast membrane-associated 30 kD protein
q: Chloroplast membrane-associated 30 kD protein
r: Chloroplast membrane-associated 30 kD protein
s: Chloroplast membrane-associated 30 kD protein
t: Chloroplast membrane-associated 30 kD protein
u: Chloroplast membrane-associated 30 kD protein
v: Chloroplast membrane-associated 30 kD protein
w: Chloroplast membrane-associated 30 kD protein
x: Chloroplast membrane-associated 30 kD protein
y: Chloroplast membrane-associated 30 kD protein
z: Chloroplast membrane-associated 30 kD protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,711,498120
Polymers1,685,86560
Non-polymers25,63260
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "Y"
d_2ens_1chain "T"
d_3ens_1chain "U"
d_4ens_1chain "V"
d_5ens_1chain "W"
d_6ens_1chain "X"
d_7ens_1chain "S"
d_8ens_1chain "Z"
d_9ens_1chain "a"
d_10ens_1chain "b"
d_11ens_1chain "0"
d_12ens_1chain "1"
d_13ens_1chain "2"
d_14ens_1chain "3"
d_15ens_1chain "4"
d_16ens_1chain "5"
d_17ens_1chain "6"
d_18ens_1chain "7"
d_19ens_1chain "A"
d_20ens_1chain "B"
d_21ens_1chain "C"
d_22ens_1chain "D"
d_23ens_1chain "E"
d_24ens_1chain "F"
d_25ens_1chain "G"
d_26ens_1chain "H"
d_27ens_1chain "I"
d_28ens_1chain "J"
d_29ens_1chain "K"
d_30ens_1chain "L"
d_31ens_1chain "M"
d_32ens_1chain "N"
d_33ens_1chain "O"
d_34ens_1chain "P"
d_35ens_1chain "Q"
d_36ens_1chain "R"
d_37ens_1chain "c"
d_38ens_1chain "d"
d_39ens_1chain "e"
d_40ens_1chain "f"
d_41ens_1chain "g"
d_42ens_1chain "h"
d_43ens_1chain "i"
d_44ens_1chain "j"
d_45ens_1chain "k"
d_46ens_1chain "l"
d_47ens_1chain "m"
d_48ens_1chain "n"
d_49ens_1chain "o"
d_50ens_1chain "p"
d_51ens_1chain "q"
d_52ens_1chain "r"
d_53ens_1chain "s"
d_54ens_1chain "t"
d_55ens_1chain "u"
d_56ens_1chain "v"
d_57ens_1chain "w"
d_58ens_1chain "x"
d_59ens_1chain "y"
d_60ens_1chain "z"

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: SER / End label comp-ID: SER / Auth seq-ID: 22 - 217 / Label seq-ID: 45 - 240

Dom-IDAuth asym-IDLabel asym-ID
d_10A
d_21B
d_32C
d_43D
d_54E
d_65F
d_76G
d_87H
d_9AI
d_10BJ
d_11CK
d_12DL
d_13EM
d_14FN
d_15GO
d_16HP
d_17IQ
d_18JR
d_19KS
d_20LT
d_21MU
d_22NV
d_23OW
d_24PX
d_25QY
d_26RZ
d_27SAA
d_28TBA
d_29UCA
d_30VDA
d_31WEA
d_32XFA
d_33YGA
d_34ZHA
d_35aIA
d_36bJA
d_37cKA
d_38dLA
d_39eMA
d_40fNA
d_41gOA
d_42hPA
d_43iQA
d_44jRA
d_45kSA
d_46lTA
d_47mUA
d_48nVA
d_49oWA
d_50pXA
d_51qYA
d_52rZA
d_53sAB
d_54tBB
d_55uCB
d_56vDB
d_57wEB
d_58xFB
d_59yGB
d_60zHB

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Components

#1: Protein ...
Chloroplast membrane-associated 30 kD protein


Mass: 28097.758 Da / Num. of mol.: 60
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC 6803 / Kazusa / Gene: im30 / Plasmid: pET50del
Details (production host): Based on pET50b(+) with deletion of NusA tag
Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: P74717
#2: Chemical...
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 60 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Phage shock protein A (PspA) / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 120.7 kDa/nm / Experimental value: NO
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria) / Plasmid: pET50del
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 4000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 58 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 28.3 ° / Axial rise/subunit: 6.97 Å / Axial symmetry: C3
3D reconstructionResolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 46597 / Symmetry type: HELICAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 141.56 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0023191820
ELECTRON MICROSCOPYf_angle_d0.4429347640
ELECTRON MICROSCOPYf_chiral_restr0.024514160
ELECTRON MICROSCOPYf_plane_restr0.001928560
ELECTRON MICROSCOPYf_dihedral_angle_d7.496228320
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2ZELECTRON MICROSCOPYNCS constraints7.64586223686E-12
ens_1d_3ZELECTRON MICROSCOPYNCS constraints6.75432023337E-12
ens_1d_4ZELECTRON MICROSCOPYNCS constraints3.87630365777E-12
ens_1d_5ZELECTRON MICROSCOPYNCS constraints2.82113321094E-12
ens_1d_6ZELECTRON MICROSCOPYNCS constraints1.05065222492E-12
ens_1d_7ZELECTRON MICROSCOPYNCS constraints3.8023300804E-12
ens_1d_8ZELECTRON MICROSCOPYNCS constraints6.36130023409E-13
ens_1d_9ZELECTRON MICROSCOPYNCS constraints5.65149410771E-13
ens_1d_10ZELECTRON MICROSCOPYNCS constraints7.76523221374E-13
ens_1d_11ZELECTRON MICROSCOPYNCS constraints2.05204352023E-12
ens_1d_12ZELECTRON MICROSCOPYNCS constraints2.58023853864E-13
ens_1d_13ZELECTRON MICROSCOPYNCS constraints2.91874732236E-13
ens_1d_14ZELECTRON MICROSCOPYNCS constraints1.82262497048E-12
ens_1d_15ZELECTRON MICROSCOPYNCS constraints3.67002387948E-13
ens_1d_16ZELECTRON MICROSCOPYNCS constraints1.15195139916E-12
ens_1d_17ZELECTRON MICROSCOPYNCS constraints5.29133320195E-12
ens_1d_18ZELECTRON MICROSCOPYNCS constraints2.68127949611E-11
ens_1d_19ZELECTRON MICROSCOPYNCS constraints5.08517056525E-12
ens_1d_20ZELECTRON MICROSCOPYNCS constraints1.42681274446E-11
ens_1d_21ZELECTRON MICROSCOPYNCS constraints4.61547294873E-13
ens_1d_22ZELECTRON MICROSCOPYNCS constraints8.06424016077E-12
ens_1d_23ZELECTRON MICROSCOPYNCS constraints7.07524020603E-12
ens_1d_24ZELECTRON MICROSCOPYNCS constraints4.21222067388E-12
ens_1d_25ZELECTRON MICROSCOPYNCS constraints2.96924513781E-12
ens_1d_26ZELECTRON MICROSCOPYNCS constraints1.72991267395E-12
ens_1d_27ZELECTRON MICROSCOPYNCS constraints1.35661928258E-10
ens_1d_28ZELECTRON MICROSCOPYNCS constraints4.91483392179E-13
ens_1d_29ZELECTRON MICROSCOPYNCS constraints5.40117335742E-13
ens_1d_30ZELECTRON MICROSCOPYNCS constraints3.58354003697E-13
ens_1d_31ZELECTRON MICROSCOPYNCS constraints1.93559520238E-12
ens_1d_32ZELECTRON MICROSCOPYNCS constraints5.85190901802E-12
ens_1d_33ZELECTRON MICROSCOPYNCS constraints1.07913026607E-11
ens_1d_34ZELECTRON MICROSCOPYNCS constraints8.52796838306E-12
ens_1d_35ZELECTRON MICROSCOPYNCS constraints7.93549212944E-12
ens_1d_36ZELECTRON MICROSCOPYNCS constraints6.63466029499E-12
ens_1d_37ZELECTRON MICROSCOPYNCS constraints3.2869738063E-12
ens_1d_38ZELECTRON MICROSCOPYNCS constraints1.79566160793E-11
ens_1d_39ZELECTRON MICROSCOPYNCS constraints3.56209270351E-13
ens_1d_40ZELECTRON MICROSCOPYNCS constraints7.96905848761E-12
ens_1d_41ZELECTRON MICROSCOPYNCS constraints7.95598305011E-12
ens_1d_42ZELECTRON MICROSCOPYNCS constraints6.18048956972E-12
ens_1d_43ZELECTRON MICROSCOPYNCS constraints3.24485329075E-12
ens_1d_44ZELECTRON MICROSCOPYNCS constraints2.23139701455E-12
ens_1d_45ZELECTRON MICROSCOPYNCS constraints3.31840219797E-13
ens_1d_46ZELECTRON MICROSCOPYNCS constraints5.54401715509E-13
ens_1d_47ZELECTRON MICROSCOPYNCS constraints1.26943996462E-12
ens_1d_48ZELECTRON MICROSCOPYNCS constraints4.32373619152E-13
ens_1d_49ZELECTRON MICROSCOPYNCS constraints3.05724766046E-13
ens_1d_50ZELECTRON MICROSCOPYNCS constraints1.8514184388E-12
ens_1d_51ZELECTRON MICROSCOPYNCS constraints2.65124003983E-13
ens_1d_52ZELECTRON MICROSCOPYNCS constraints1.00175812081E-12
ens_1d_53ZELECTRON MICROSCOPYNCS constraints4.66578332924E-12
ens_1d_54ZELECTRON MICROSCOPYNCS constraints2.18764912389E-11
ens_1d_55ZELECTRON MICROSCOPYNCS constraints1.33150907695E-12
ens_1d_56ZELECTRON MICROSCOPYNCS constraints2.87226496989E-13
ens_1d_57ZELECTRON MICROSCOPYNCS constraints8.18626100265E-12
ens_1d_58ZELECTRON MICROSCOPYNCS constraints7.54942410159E-12
ens_1d_59ZELECTRON MICROSCOPYNCS constraints5.96696415459E-12
ens_1d_60ZELECTRON MICROSCOPYNCS constraints3.13221396965E-12

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