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- PDB-9hzs: 200 A SynPspA rod after incubation with EPL -

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Basic information

Entry
Database: PDB / ID: 9hzs
Title200 A SynPspA rod after incubation with EPL
ComponentsChloroplast membrane-associated 30 kD protein
KeywordsLIPID BINDING PROTEIN / Nucleotide binding / Helical assembly / ESCRT-III fold / Membrane remodeling
Function / homologyPspA/IM30 / PspA/IM30 family / Chloroplast membrane-associated 30 kD protein
Function and homology information
Biological speciesSynechocystis sp. PCC 6803 (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 4.7 Å
AuthorsHudina, E. / Junglas, B. / Sachse, C.
Funding support Germany, 5items
OrganizationGrant numberCountry
German Research Foundation (DFG)SA 1882/6-1 Germany
German Research Foundation (DFG)SCHN 690/16-1 Germany
German Research Foundation (DFG)SFB1551 Germany
German Research Foundation (DFG)SFB1552 Germany
German Research Foundation (DFG)SFB1208 Germany
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: The bacterial ESCRT-III PspA rods thin lipid tubules and increase membrane curvature through helix α0 interactions.
Authors: Esther Hudina / Stephan Schott-Verdugo / Benedikt Junglas / Mirka Kutzner / Ilona Ritter / Nadja Hellmann / Dirk Schneider / Holger Gohlke / Carsten Sachse /
Abstract: The phage shock protein A (PspA), a bacterial member of the endosomal sorting complexes required for transport (ESCRT)-III superfamily, forms rod-shaped helical assemblies that internalize membrane ...The phage shock protein A (PspA), a bacterial member of the endosomal sorting complexes required for transport (ESCRT)-III superfamily, forms rod-shaped helical assemblies that internalize membrane tubules. The N-terminal helix α0 of PspA (and other ESCRT-III members) has been suggested to act as a membrane anchor; the detailed mechanism, however, of how it binds to membranes and eventually triggers membrane fusion and/or fission events remains unclear. By solving a total of 15 cryoelectron microscopy (cryo-EM) structures of PspA and a truncation lacking the N-terminal helix α0 in the presence of polar lipid membranes, we show in molecular detail how PspA interacts with and remodels membranes: Binding of the N-terminal helix α0 in the outer tubular membrane leaflet induces membrane curvature, supporting membrane tubulation by PspA. Detailed molecular dynamics simulations and free energy computations of interactions between the helix α0 and negatively charged membranes suggest a compensating mechanism between helix-membrane interactions and the energy contributions required for membrane bending. The energetic considerations are in line with the membrane structures observed in the cryo-EM images of tubulated membrane vesicles, fragmented vesicles inside tapered PspA rods, and shedded vesicles emerging at the thinner PspA rod ends. Our results provide insights into the molecular determinants and a potential mechanism of vesicular membrane remodeling mediated by a member of the ESCRT-III superfamily.
History
DepositionJan 14, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
I: 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
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


Theoretical massNumber of molelcules
Total (without water)1,685,86560
Polymers1,685,86560
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "O"
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 "S"
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_1OO
d_2TT
d_3UU
d_4VV
d_5WW
d_6XX
d_7YY
d_8ZZ
d_9aAA
d_10bBA
d_110AB
d_121BB
d_132CB
d_143DB
d_154EB
d_165FB
d_176GB
d_187HB
d_19AB
d_20BC
d_21CD
d_22DE
d_23EF
d_24FG
d_25GH
d_26HI
d_27IA
d_28JJ
d_29KK
d_30LL
d_31MM
d_32NN
d_33SS
d_34PP
d_35QQ
d_36RR
d_37cCA
d_38dDA
d_39eEA
d_40fFA
d_41gGA
d_42hHA
d_43iIA
d_44jJA
d_45kKA
d_46lLA
d_47mMA
d_48nNA
d_49oOA
d_50pPA
d_51qQA
d_52rRA
d_53sSA
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
Has ligand of interestY
Has protein modificationN

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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: Helical assembly of SynPspA after incubation with EPL / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 1.7 MDa / Experimental value: NO
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria) / Strain: C41 / 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: 3500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 44 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: 5.78 Å / Axial symmetry: C2
3D reconstructionResolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 45586 / Symmetry type: HELICAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 83.56 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002895640
ELECTRON MICROSCOPYf_angle_d0.3904128400
ELECTRON MICROSCOPYf_chiral_restr0.024514160
ELECTRON MICROSCOPYf_plane_restr0.003717160
ELECTRON MICROSCOPYf_dihedral_angle_d12.796238280
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2OELECTRON MICROSCOPYNCS constraints5.94681457262E-11
ens_1d_3OELECTRON MICROSCOPYNCS constraints2.03233595908E-10
ens_1d_4OELECTRON MICROSCOPYNCS constraints2.42834226438E-10
ens_1d_5OELECTRON MICROSCOPYNCS constraints1.1898719245E-10
ens_1d_6OELECTRON MICROSCOPYNCS constraints8.38099428651E-11
ens_1d_7OELECTRON MICROSCOPYNCS constraints3.51087203577E-11
ens_1d_8OELECTRON MICROSCOPYNCS constraints2.85874343291E-11
ens_1d_9OELECTRON MICROSCOPYNCS constraints6.66084735711E-11
ens_1d_10OELECTRON MICROSCOPYNCS constraints6.04415850845E-11
ens_1d_11OELECTRON MICROSCOPYNCS constraints5.92264474113E-11
ens_1d_12OELECTRON MICROSCOPYNCS constraints1.92064734944E-11
ens_1d_13OELECTRON MICROSCOPYNCS constraints5.48457016451E-11
ens_1d_14OELECTRON MICROSCOPYNCS constraints1.83373320984E-10
ens_1d_15OELECTRON MICROSCOPYNCS constraints2.38474242933E-10
ens_1d_16OELECTRON MICROSCOPYNCS constraints2.35754873523E-10
ens_1d_17OELECTRON MICROSCOPYNCS constraints9.33971280946E-11
ens_1d_18OELECTRON MICROSCOPYNCS constraints1.71856107515E-10
ens_1d_19OELECTRON MICROSCOPYNCS constraints2.42609864231E-10
ens_1d_20OELECTRON MICROSCOPYNCS constraints1.21243320127E-12
ens_1d_21OELECTRON MICROSCOPYNCS constraints8.75480426348E-11
ens_1d_22OELECTRON MICROSCOPYNCS constraints3.68709307589E-11
ens_1d_23OELECTRON MICROSCOPYNCS constraints2.67313021071E-11
ens_1d_24OELECTRON MICROSCOPYNCS constraints6.24262912538E-11
ens_1d_25OELECTRON MICROSCOPYNCS constraints6.08788220761E-11
ens_1d_26OELECTRON MICROSCOPYNCS constraints5.29493514403E-11
ens_1d_27OELECTRON MICROSCOPYNCS constraints2.19011860317E-11
ens_1d_28OELECTRON MICROSCOPYNCS constraints8.29705640741E-11
ens_1d_29OELECTRON MICROSCOPYNCS constraints2.29273705693E-10
ens_1d_30OELECTRON MICROSCOPYNCS constraints2.42863303921E-10
ens_1d_31OELECTRON MICROSCOPYNCS constraints1.05310082373E-10
ens_1d_32OELECTRON MICROSCOPYNCS constraints6.15671045452E-11
ens_1d_33OELECTRON MICROSCOPYNCS constraints4.76738450067E-12
ens_1d_34OELECTRON MICROSCOPYNCS constraints4.19811096476E-11
ens_1d_35OELECTRON MICROSCOPYNCS constraints6.47304574297E-11
ens_1d_36OELECTRON MICROSCOPYNCS constraints9.18243793525E-11
ens_1d_37OELECTRON MICROSCOPYNCS constraints2.23433383063E-11
ens_1d_38OELECTRON MICROSCOPYNCS constraints3.53530367426E-11
ens_1d_39OELECTRON MICROSCOPYNCS constraints6.82355197593E-11
ens_1d_40OELECTRON MICROSCOPYNCS constraints1.86550316429E-11
ens_1d_41OELECTRON MICROSCOPYNCS constraints2.25119797004E-11
ens_1d_42OELECTRON MICROSCOPYNCS constraints4.86110618022E-11
ens_1d_43OELECTRON MICROSCOPYNCS constraints1.80711606744E-10
ens_1d_44OELECTRON MICROSCOPYNCS constraints2.34282035268E-10
ens_1d_45OELECTRON MICROSCOPYNCS constraints2.36264038022E-10
ens_1d_46OELECTRON MICROSCOPYNCS constraints9.61460733068E-11
ens_1d_47OELECTRON MICROSCOPYNCS constraints4.33037035322E-11
ens_1d_48OELECTRON MICROSCOPYNCS constraints7.52600234318E-12
ens_1d_49OELECTRON MICROSCOPYNCS constraints5.65179805573E-11
ens_1d_50OELECTRON MICROSCOPYNCS constraints6.87417796338E-11
ens_1d_51OELECTRON MICROSCOPYNCS constraints7.50280785185E-11
ens_1d_52OELECTRON MICROSCOPYNCS constraints1.79849141422E-11
ens_1d_53OELECTRON MICROSCOPYNCS constraints7.79863206144E-11
ens_1d_54OELECTRON MICROSCOPYNCS constraints2.21434024574E-10
ens_1d_55OELECTRON MICROSCOPYNCS constraints2.42034863847E-10
ens_1d_56OELECTRON MICROSCOPYNCS constraints1.11376721212E-10
ens_1d_57OELECTRON MICROSCOPYNCS constraints7.36524529155E-11
ens_1d_58OELECTRON MICROSCOPYNCS constraints1.38645530396E-11
ens_1d_59OELECTRON MICROSCOPYNCS constraints4.05397564244E-11
ens_1d_60OELECTRON MICROSCOPYNCS constraints6.95125279973E-11

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