[English] 日本語
Yorodumi
- PDB-8aks: 215 A SynPspA rod after incubation with ATP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8aks
Title215 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: 3.9 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Buried area338130 Å2
ΔGint-2368 kcal/mol
Surface area651420 Å2
MethodPISA
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "N"
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 "y"
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 "S"
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

-
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) / Gene: im30 / Plasmid: pET50del
Details (production host): Based on pET50b(+) with deletion of NusA tag
Production host: Escherichia coli K-12 (bacteria) / Strain (production host): BL21(DE3) / 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

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Phage shock protein A (PspA) / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 111.2 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

-
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)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 130.2 ° / Axial rise/subunit: 2.52 Å / Axial symmetry: C1
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 48854 / Symmetry type: HELICAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 43.75 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0017191760
ELECTRON MICROSCOPYf_angle_d0.4397347520
ELECTRON MICROSCOPYf_chiral_restr0.024514160
ELECTRON MICROSCOPYf_plane_restr0.001928500
ELECTRON MICROSCOPYf_dihedral_angle_d10.207553520
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2OELECTRON MICROSCOPYNCS constraints2.12819517485E-12
ens_1d_3OELECTRON MICROSCOPYNCS constraints1.6733907394E-11
ens_1d_4OELECTRON MICROSCOPYNCS constraints7.05027187027E-12
ens_1d_5OELECTRON MICROSCOPYNCS constraints2.23995295687E-12
ens_1d_6OELECTRON MICROSCOPYNCS constraints1.87020612608E-12
ens_1d_7OELECTRON MICROSCOPYNCS constraints3.63332315571E-12
ens_1d_8OELECTRON MICROSCOPYNCS constraints2.12195886396E-12
ens_1d_9OELECTRON MICROSCOPYNCS constraints5.28676902095E-12
ens_1d_10OELECTRON MICROSCOPYNCS constraints1.82850753129E-12
ens_1d_11OELECTRON MICROSCOPYNCS constraints4.34296520393E-12
ens_1d_12OELECTRON MICROSCOPYNCS constraints1.89519153703E-12
ens_1d_13OELECTRON MICROSCOPYNCS constraints1.71527641039E-12
ens_1d_14OELECTRON MICROSCOPYNCS constraints4.5405948948E-12
ens_1d_15OELECTRON MICROSCOPYNCS constraints2.04329361322E-12
ens_1d_16OELECTRON MICROSCOPYNCS constraints3.0180629359E-12
ens_1d_17OELECTRON MICROSCOPYNCS constraints6.23733237507E-12
ens_1d_18OELECTRON MICROSCOPYNCS constraints2.04829505675E-12
ens_1d_19OELECTRON MICROSCOPYNCS constraints2.26421330104E-12
ens_1d_20OELECTRON MICROSCOPYNCS constraints4.74011963126E-12
ens_1d_21OELECTRON MICROSCOPYNCS constraints1.52300623198E-12
ens_1d_22OELECTRON MICROSCOPYNCS constraints1.83404809917E-12
ens_1d_23OELECTRON MICROSCOPYNCS constraints4.54751202436E-12
ens_1d_24OELECTRON MICROSCOPYNCS constraints1.96575469873E-12
ens_1d_25OELECTRON MICROSCOPYNCS constraints2.77412120592E-12
ens_1d_26OELECTRON MICROSCOPYNCS constraints4.1959106835E-12
ens_1d_27OELECTRON MICROSCOPYNCS constraints1.90410130062E-10
ens_1d_28OELECTRON MICROSCOPYNCS constraints3.00393541559E-12
ens_1d_29OELECTRON MICROSCOPYNCS constraints6.43099688107E-12
ens_1d_30OELECTRON MICROSCOPYNCS constraints1.80687008284E-12
ens_1d_31OELECTRON MICROSCOPYNCS constraints5.98032902059E-12
ens_1d_32OELECTRON MICROSCOPYNCS constraints9.23148366933E-13
ens_1d_33OELECTRON MICROSCOPYNCS constraints1.73018641323E-12
ens_1d_34OELECTRON MICROSCOPYNCS constraints4.76088924487E-12
ens_1d_35OELECTRON MICROSCOPYNCS constraints1.95529056943E-12
ens_1d_36OELECTRON MICROSCOPYNCS constraints8.17762472067E-13
ens_1d_37OELECTRON MICROSCOPYNCS constraints9.11461788979E-13
ens_1d_38OELECTRON MICROSCOPYNCS constraints3.41834892778E-12
ens_1d_39OELECTRON MICROSCOPYNCS constraints1.81588119581E-12
ens_1d_40OELECTRON MICROSCOPYNCS constraints4.84234092294E-12
ens_1d_41OELECTRON MICROSCOPYNCS constraints4.91779987893E-12
ens_1d_42OELECTRON MICROSCOPYNCS constraints2.35003362286E-12
ens_1d_43OELECTRON MICROSCOPYNCS constraints1.95318709963E-11
ens_1d_44OELECTRON MICROSCOPYNCS constraints6.26715522238E-12
ens_1d_45OELECTRON MICROSCOPYNCS constraints1.76103058845E-12
ens_1d_46OELECTRON MICROSCOPYNCS constraints4.89968584907E-12
ens_1d_47OELECTRON MICROSCOPYNCS constraints1.8180621659E-12
ens_1d_48OELECTRON MICROSCOPYNCS constraints1.19587784806E-12
ens_1d_49OELECTRON MICROSCOPYNCS constraints2.98920351738E-12
ens_1d_50OELECTRON MICROSCOPYNCS constraints1.0326610594E-12
ens_1d_51OELECTRON MICROSCOPYNCS constraints2.48992504269E-12
ens_1d_52OELECTRON MICROSCOPYNCS constraints4.08089871573E-12
ens_1d_53OELECTRON MICROSCOPYNCS constraints2.41812411476E-12
ens_1d_54OELECTRON MICROSCOPYNCS constraints3.13035878625E-12
ens_1d_55OELECTRON MICROSCOPYNCS constraints6.30304861442E-12
ens_1d_56OELECTRON MICROSCOPYNCS constraints5.88953290571E-12
ens_1d_57OELECTRON MICROSCOPYNCS constraints2.21004316237E-12
ens_1d_58OELECTRON MICROSCOPYNCS constraints5.65183633212E-12
ens_1d_59OELECTRON MICROSCOPYNCS constraints3.46503044081E-12
ens_1d_60OELECTRON MICROSCOPYNCS constraints1.74824130831E-12

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more