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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: Nat Struct Mol Biol / Year: 2025
Title: Structural plasticity of bacterial ESCRT-III protein PspA in higher-order assemblies.
Authors: Benedikt Junglas / Esther Hudina / Philipp Schönnenbeck / Ilona Ritter / Anja Heddier / Beatrix Santiago-Schübel / Pitter F Huesgen / Dirk Schneider / Carsten Sachse /
Abstract: Eukaryotic members of the endosome sorting complex required for transport-III (ESCRT-III) family have been shown to form diverse higher-order assemblies. The bacterial phage shock protein A (PspA) ...Eukaryotic members of the endosome sorting complex required for transport-III (ESCRT-III) family have been shown to form diverse higher-order assemblies. The bacterial phage shock protein A (PspA) has been identified as a member of the ESCRT-III superfamily, and PspA homo-oligomerizes to form rod-shaped assemblies. As observed for eukaryotic ESCRT-III, PspA forms tubular assemblies of varying diameters. Using electron cryo-electron microscopy, we determined 61 Synechocystis PspA structures and observed in molecular detail how the structural plasticity of PspA rods is mediated by conformational changes at three hinge regions in the monomer and by the fixed and changing molecular contacts between protomers. Moreover, we reduced and increased the structural plasticity of PspA rods by removing the loop connecting helices α3/α4 and the addition of nucleotides, respectively. Based on our analysis of PspA-mediated membrane remodeling, we suggest that the observed mode of structural plasticity is a prerequisite for the biological function of ESCRT-III members.
History
DepositionJul 31, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 14, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2024Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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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
Water00
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


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 FIELD / 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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