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- PDB-8akr: 200 A SynPspA rod after incubation with ATP -

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Basic information

Entry
Database: PDB / ID: 8akr
Title200 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: 3.8 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
H: 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
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
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
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
Buried area345860 Å2
ΔGint-2166 kcal/mol
Surface area644680 Å2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "Q"
d_2ens_1chain "T"
d_3ens_1chain "U"
d_4ens_1chain "V"
d_5ens_1chain "W"
d_6ens_1chain "X"
d_7ens_1chain "Y"
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 "S"
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_1RR
d_2UU
d_3VV
d_4WW
d_5XX
d_6YY
d_7ZZ
d_8aAA
d_9bBA
d_10cCA
d_110AB
d_121BB
d_132CB
d_143DB
d_154EB
d_165FB
d_176GB
d_187HB
d_19BC
d_20CD
d_21DE
d_22EF
d_23FG
d_24GH
d_25II
d_26JJ
d_27HA
d_28KK
d_29LL
d_30MM
d_31NN
d_32OO
d_33PP
d_34QQ
d_35TT
d_36SS
d_37dDA
d_38eEA
d_39fFA
d_40gGA
d_41hHA
d_42iIA
d_43jJA
d_44kKA
d_45lLA
d_46mMA
d_47nNA
d_48oOA
d_49pPA
d_50qQA
d_51rRA
d_52sSA
d_53AB
d_54tTA
d_55uUA
d_56vVA
d_57wWA
d_58xXA
d_59yYA
d_60zZA

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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: 97.5 kDa/nm / Experimental value: NO
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)
Source (recombinant)Organism: Escherichia coli K-12 (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: 34.4 ° / Axial rise/subunit: 5.75 Å / Axial symmetry: C2
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 64979 / Symmetry type: HELICAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 81.03 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.001695640
ELECTRON MICROSCOPYf_angle_d0.3896128400
ELECTRON MICROSCOPYf_chiral_restr0.023814160
ELECTRON MICROSCOPYf_plane_restr0.00317160
ELECTRON MICROSCOPYf_dihedral_angle_d11.689738280
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2RELECTRON MICROSCOPYNCS constraints9.39199451276E-10
ens_1d_3RELECTRON MICROSCOPYNCS constraints5.14768868662E-13
ens_1d_4RELECTRON MICROSCOPYNCS constraints1.03919750592E-12
ens_1d_5RELECTRON MICROSCOPYNCS constraints7.67336727132E-13
ens_1d_6RELECTRON MICROSCOPYNCS constraints5.80250018432E-13
ens_1d_7RELECTRON MICROSCOPYNCS constraints6.99432282536E-13
ens_1d_8RELECTRON MICROSCOPYNCS constraints5.4869028536E-10
ens_1d_9RELECTRON MICROSCOPYNCS constraints1.48258542418E-10
ens_1d_10RELECTRON MICROSCOPYNCS constraints1.00629222209E-12
ens_1d_11RELECTRON MICROSCOPYNCS constraints1.50637418201E-10
ens_1d_12RELECTRON MICROSCOPYNCS constraints9.60238713641E-11
ens_1d_13RELECTRON MICROSCOPYNCS constraints2.78971091341E-10
ens_1d_14RELECTRON MICROSCOPYNCS constraints8.4381969144E-10
ens_1d_15RELECTRON MICROSCOPYNCS constraints8.30249541894E-13
ens_1d_16RELECTRON MICROSCOPYNCS constraints9.04862929363E-13
ens_1d_17RELECTRON MICROSCOPYNCS constraints8.86368440581E-13
ens_1d_18RELECTRON MICROSCOPYNCS constraints6.35520359945E-13
ens_1d_19RELECTRON MICROSCOPYNCS constraints7.61620511393E-13
ens_1d_20RELECTRON MICROSCOPYNCS constraints6.89894047165E-13
ens_1d_21RELECTRON MICROSCOPYNCS constraints6.9527557668E-13
ens_1d_22RELECTRON MICROSCOPYNCS constraints4.90987564938E-13
ens_1d_23RELECTRON MICROSCOPYNCS constraints5.43124541237E-10
ens_1d_24RELECTRON MICROSCOPYNCS constraints1.51162816042E-10
ens_1d_25RELECTRON MICROSCOPYNCS constraints1.18742197356E-12
ens_1d_26RELECTRON MICROSCOPYNCS constraints1.93244301627E-10
ens_1d_27RELECTRON MICROSCOPYNCS constraints9.92380210807E-10
ens_1d_28RELECTRON MICROSCOPYNCS constraints1.31271553462E-12
ens_1d_29RELECTRON MICROSCOPYNCS constraints6.88155003061E-13
ens_1d_30RELECTRON MICROSCOPYNCS constraints6.89025073764E-13
ens_1d_31RELECTRON MICROSCOPYNCS constraints6.38831934395E-13
ens_1d_32RELECTRON MICROSCOPYNCS constraints2.28206307776E-12
ens_1d_33RELECTRON MICROSCOPYNCS constraints7.80922458346E-10
ens_1d_34RELECTRON MICROSCOPYNCS constraints3.92877833417E-10
ens_1d_35RELECTRON MICROSCOPYNCS constraints4.98914692927E-10
ens_1d_36RELECTRON MICROSCOPYNCS constraints1.0536621684E-10
ens_1d_37RELECTRON MICROSCOPYNCS constraints2.29425827495E-10
ens_1d_38RELECTRON MICROSCOPYNCS constraints5.76426755702E-10
ens_1d_39RELECTRON MICROSCOPYNCS constraints1.47818896105E-10
ens_1d_40RELECTRON MICROSCOPYNCS constraints1.22010984592E-10
ens_1d_41RELECTRON MICROSCOPYNCS constraints2.4707665481E-10
ens_1d_42RELECTRON MICROSCOPYNCS constraints8.20234858414E-10
ens_1d_43RELECTRON MICROSCOPYNCS constraints6.48094532687E-13
ens_1d_44RELECTRON MICROSCOPYNCS constraints5.98952685737E-13
ens_1d_45RELECTRON MICROSCOPYNCS constraints7.39898725024E-13
ens_1d_46RELECTRON MICROSCOPYNCS constraints5.83806062415E-13
ens_1d_47RELECTRON MICROSCOPYNCS constraints1.8440803424E-12
ens_1d_48RELECTRON MICROSCOPYNCS constraints7.06367432748E-10
ens_1d_49RELECTRON MICROSCOPYNCS constraints1.30166279236E-10
ens_1d_50RELECTRON MICROSCOPYNCS constraints1.62405537157E-12
ens_1d_51RELECTRON MICROSCOPYNCS constraints9.44925556471E-11
ens_1d_52RELECTRON MICROSCOPYNCS constraints6.36165416351E-10
ens_1d_53RELECTRON MICROSCOPYNCS constraints7.33408667027E-13
ens_1d_54RELECTRON MICROSCOPYNCS constraints1.96740854094E-12
ens_1d_55RELECTRON MICROSCOPYNCS constraints5.75433591231E-13
ens_1d_56RELECTRON MICROSCOPYNCS constraints9.08634429973E-13
ens_1d_57RELECTRON MICROSCOPYNCS constraints9.63938266631E-13
ens_1d_58RELECTRON MICROSCOPYNCS constraints2.37147422897E-12
ens_1d_59RELECTRON MICROSCOPYNCS constraints7.6614851733E-13
ens_1d_60RELECTRON MICROSCOPYNCS constraints3.96117286047E-10

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