[English] 日本語
Yorodumi
- PDB-11kc: Cryo-EM determined structure of designed nanoparticle O43-TM -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 11kc
TitleCryo-EM determined structure of designed nanoparticle O43-TM
Components
  • Designed nanoparticle O43-B
  • Designed nanoparticle O43-TM
KeywordsDE NOVO PROTEIN / De Novo / Membrane / Hydrophobic / Designed / Two Component / Octahedral / Micelle
Biological speciessynthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.07 Å
AuthorsCarr, K.D. / Borst, A.J. / Weidle, C.
Funding support United States, 2items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationINV-043758 United States
Bill & Melinda Gates FoundationINV-010680 United States
CitationJournal: To Be Published
Title: De Novo computational design and purification of two-component transmembrane nanoparticles
Authors: Zambrano, D.D.
History
DepositionFeb 27, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Additional map / Part number: 2 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Additional map / Part number: 3 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Additional map / Part number: 4 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Additional map / Part number: 5 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Additional map / Part number: 6 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Designed nanoparticle O43-TM
B: Designed nanoparticle O43-TM
C: Designed nanoparticle O43-TM
D: Designed nanoparticle O43-TM
E: Designed nanoparticle O43-TM
F: Designed nanoparticle O43-TM
G: Designed nanoparticle O43-TM
H: Designed nanoparticle O43-TM
I: Designed nanoparticle O43-TM
J: Designed nanoparticle O43-TM
K: Designed nanoparticle O43-TM
L: Designed nanoparticle O43-TM
M: Designed nanoparticle O43-TM
N: Designed nanoparticle O43-TM
O: Designed nanoparticle O43-TM
P: Designed nanoparticle O43-TM
Q: Designed nanoparticle O43-TM
R: Designed nanoparticle O43-TM
S: Designed nanoparticle O43-TM
T: Designed nanoparticle O43-TM
U: Designed nanoparticle O43-TM
V: Designed nanoparticle O43-TM
W: Designed nanoparticle O43-TM
X: Designed nanoparticle O43-TM
a: Designed nanoparticle O43-B
b: Designed nanoparticle O43-B
c: Designed nanoparticle O43-B
d: Designed nanoparticle O43-B
e: Designed nanoparticle O43-B
f: Designed nanoparticle O43-B
g: Designed nanoparticle O43-B
h: Designed nanoparticle O43-B
i: Designed nanoparticle O43-B
j: Designed nanoparticle O43-B
k: Designed nanoparticle O43-B
l: Designed nanoparticle O43-B
m: Designed nanoparticle O43-B
n: Designed nanoparticle O43-B
o: Designed nanoparticle O43-B
p: Designed nanoparticle O43-B
q: Designed nanoparticle O43-B
r: Designed nanoparticle O43-B
s: Designed nanoparticle O43-B
t: Designed nanoparticle O43-B
u: Designed nanoparticle O43-B
v: Designed nanoparticle O43-B
w: Designed nanoparticle O43-B
x: Designed nanoparticle O43-B


Theoretical massNumber of molelcules
Total (without water)1,160,28848
Polymers1,160,28848
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, assembled nanoparticles were observed by ns-EM and cryo-EM
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Protein ...
Designed nanoparticle O43-TM


Mass: 25101.250 Da / Num. of mol.: 24 / Fragment: Transmembrane domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Protein ...
Designed nanoparticle O43-B


Mass: 23244.084 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: two component de novo designed nanoparticle with trans-membrane domain O43-TM
Type: COMPLEX
Details: Designed two-component protein assembly with octahedral symmetry displaying a trans-membrane domain.
Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 1.180 MDa / Experimental value: NO
Source (natural)Organism: synthetic construct (others)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenConc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Particles were imaged in two datasets. The first was heterogeneous and contamined both the designed nanoparticle assembly and a co-eluting contaminant protein. The second was almost ...Details: Particles were imaged in two datasets. The first was heterogeneous and contamined both the designed nanoparticle assembly and a co-eluting contaminant protein. The second was almost completely pure with very little contaminant protein present.
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295.15 K
Details: Wait time: 7.5 seconds Blot time: 0.5 seconds Blot force: 0 seconds

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Image recording

Imaging-ID: 1 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

IDAverage exposure time (sec.)Electron dose (e/Å2)Num. of grids imagedNum. of real imagesDetails
154716211first dataset
247.326887second dataset
Image scans
WidthHeightIDImage recording-IDEntry-ID
576040921111KC
576040922211KC

-
Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARC4.4.1particle selection
2SerialEMimage acquisition
4cryoSPARC4.4.1CTF correction
7UCSF ChimeraXmodel fitting
9cryoSPARC4.4.1initial Euler assignment
10cryoSPARC4.4.1final Euler assignment
11cryoSPARC4.4.1classification
12cryoSPARC4.4.13D reconstructionglobal refinement
13cryoSPARC4.6.03D reconstructionlocal refinement
14ISOLDEmodel refinement
15PHENIXmodel refinement
16Cootmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: O (octahedral)
3D reconstructionResolution: 4.07 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 42340 / Symmetry type: POINT
Atomic model buildingB value: 163.2 / Protocol: OTHER / Space: REAL / Target criteria: Cross-correlation coefficient
Atomic model buildingDetails: Computationally designed model / Source name: Other / Type: in silico model

+
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