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- PDB-6zw5: C15 symmetry: Bacterial Vipp1 and PspA are members of the ancient... -

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Basic information

Entry
Database: PDB / ID: 6zw5
TitleC15 symmetry: Bacterial Vipp1 and PspA are members of the ancient ESCRT-III membrane-remodeling superfamily.
Componentsvipp1
KeywordsLIPID BINDING PROTEIN / membrane remodelling
Function / homologyPspA/IM30 / PspA/IM30 family / lipid binding / plasma membrane / Membrane-associated protein Vipp1
Function and homology information
Biological speciesNostoc punctiforme (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7 Å
AuthorsLiu, J.W. / Tassinari, M. / Souza, D.P. / Naskar, S. / Noel, J.K. / Bohuszewicz, O. / Buck, M. / Williams, T.A. / Baum, B. / Low, H.H.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: Cell / Year: 2021
Title: Bacterial Vipp1 and PspA are members of the ancient ESCRT-III membrane-remodeling superfamily.
Authors: Jiwei Liu / Matteo Tassinari / Diorge P Souza / Souvik Naskar / Jeffrey K Noel / Olga Bohuszewicz / Martin Buck / Tom A Williams / Buzz Baum / Harry H Low /
Abstract: Membrane remodeling and repair are essential for all cells. Proteins that perform these functions include Vipp1/IM30 in photosynthetic plastids, PspA in bacteria, and ESCRT-III in eukaryotes. Here, ...Membrane remodeling and repair are essential for all cells. Proteins that perform these functions include Vipp1/IM30 in photosynthetic plastids, PspA in bacteria, and ESCRT-III in eukaryotes. Here, using a combination of evolutionary and structural analyses, we show that these protein families are homologous and share a common ancient evolutionary origin that likely predates the last universal common ancestor. This homology is evident in cryo-electron microscopy structures of Vipp1 rings from the cyanobacterium Nostoc punctiforme presented over a range of symmetries. Each ring is assembled from rungs that stack and progressively tilt to form dome-shaped curvature. Assembly is facilitated by hinges in the Vipp1 monomer, similar to those in ESCRT-III proteins, which allow the formation of flexible polymers. Rings have an inner lumen that is able to bind and deform membranes. Collectively, these data suggest conserved mechanistic principles that underlie Vipp1, PspA, and ESCRT-III-dependent membrane remodeling across all domains of life.
History
DepositionJul 27, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 19, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2May 4, 2022Group: Structure summary / Category: audit_author / struct / Item: _struct.title
Revision 1.3Jul 10, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Structure visualization

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Assembly

Deposited unit
A: vipp1
B: vipp1
C: vipp1
D: vipp1
E: vipp1
F: vipp1
G: vipp1
H: vipp1
I: vipp1
J: vipp1
K: vipp1
L: vipp1
M: vipp1
N: vipp1
O: vipp1
P: vipp1
Q: vipp1
R: vipp1
S: vipp1
T: vipp1
V: vipp1
W: vipp1
X: vipp1
Y: vipp1
Z: vipp1
AA: vipp1
BA: vipp1
CA: vipp1
DA: vipp1
EA: vipp1
FA: vipp1
GA: vipp1
HA: vipp1
IA: vipp1
JA: vipp1
KA: vipp1
LA: vipp1
MA: vipp1
NA: vipp1
OA: vipp1
PA: vipp1
QA: vipp1
RA: vipp1
SA: vipp1
TA: vipp1
UA: vipp1
VA: vipp1
WA: vipp1
XA: vipp1
YA: vipp1
ZA: vipp1
AB: vipp1
BB: vipp1
CB: vipp1
DB: vipp1
EB: vipp1
FB: vipp1
GB: vipp1
HB: vipp1
IB: vipp1
JB: vipp1
KB: vipp1
LB: vipp1
MB: vipp1
NB: vipp1
OB: vipp1
PB: vipp1
QB: vipp1
RB: vipp1
SB: vipp1
TB: vipp1
UB: vipp1
VB: vipp1
WB: vipp1
XB: vipp1
YB: vipp1
ZB: vipp1
AC: vipp1
BC: vipp1
CC: vipp1
DC: vipp1
EC: vipp1
FC: vipp1
GC: vipp1
HC: vipp1
IC: vipp1
JC: vipp1
KC: vipp1
LC: vipp1
MC: vipp1


Theoretical massNumber of molelcules
Total (without water)2,587,09190
Polymers2,587,09190
Non-polymers00
Water00
1


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

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Components

#1: Protein ...
vipp1


Mass: 28745.461 Da / Num. of mol.: 90
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc punctiforme (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: B2J6D9

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: vipp1 c15 ring / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Nostoc punctiforme (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8.4
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: 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 FIELD
Image recordingElectron dose: 1.5 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.16_3549+SVNrefinement
PHENIX1.16_3549+SVNrefinement
EM softwareName: RELION / Category: 3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 18217 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 468.36 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.004686685
ELECTRON MICROSCOPYf_angle_d1.1141120810
ELECTRON MICROSCOPYf_chiral_restr0.051816815
ELECTRON MICROSCOPYf_plane_restr0.001217400
ELECTRON MICROSCOPYf_dihedral_angle_d1.176951030

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