[English] 日本語
Yorodumi
- PDB-7wkc: A prototype protein nanocage minimized from carboxysomes with gat... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7wkc
TitleA prototype protein nanocage minimized from carboxysomes with gated oxygen permeability
ComponentsCarboxysome shell vertex protein CcmL
KeywordsBIOSYNTHETIC PROTEIN / protein cages / quantum dots / Cryoelectron microscopy
Function / homology
Function and homology information


structural constituent of carboxysome shell / carboxysome / carbon fixation / photosynthesis
Similarity search - Function
Carboxysome shell vertex protein CcmL / Bacterial microcompartment vertex (BMV) domain profile. / Ethanolamine utilization protein EutN/carboxysome shell vertex protein CcmL / EutN/Ccml superfamily / Ethanolamine utilisation protein EutN/carboxysome
Similarity search - Domain/homology
Carboxysome shell vertex protein CcmL
Similarity search - Component
Biological speciesThermosynechococcus vestitus BP-1 (bacteria)
MethodSOLID-STATE NMR / simulated annealing
AuthorsTan, H. / Yang, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31771103, 91527302, 21425523 China
CitationJournal: Proc Natl Acad Sci U S A / Year: 2022
Title: A prototype protein nanocage minimized from carboxysomes with gated oxygen permeability.
Authors: Ruimin Gao / Huan Tan / Shanshan Li / Shaojie Ma / Yufu Tang / Kaiming Zhang / Zhiping Zhang / Quli Fan / Jun Yang / Xian-En Zhang / Feng Li /
Abstract: Protein nanocages (PNCs) in cells and viruses have inspired the development of self-assembling protein nanomaterials for various purposes. Despite the successful creation of artificial PNCs, the de ...Protein nanocages (PNCs) in cells and viruses have inspired the development of self-assembling protein nanomaterials for various purposes. Despite the successful creation of artificial PNCs, the de novo design of PNCs with defined permeability remains challenging. Here, we report a prototype oxygen-impermeable PNC (OIPNC) assembled from the vertex protein of the β-carboxysome shell, CcmL, with quantum dots as the template via interfacial engineering. The structure of the cage was solved at the atomic scale by combined solid-state NMR spectroscopy and cryoelectron microscopy, showing icosahedral assembly of CcmL pentamers with highly conserved interpentamer interfaces. Moreover, a gating mechanism was established by reversibly blocking the pores of the cage with molecular patches. Thus, the oxygen permeability, which was probed by an oxygen sensor inside the cage, can be completely controlled. The CcmL OIPNC represents a PNC platform for oxygen-sensitive or oxygen-responsive storage, catalysis, delivery, sensing, etc.
History
DepositionJan 8, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 16, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Carboxysome shell vertex protein CcmL
B: Carboxysome shell vertex protein CcmL
C: Carboxysome shell vertex protein CcmL
D: Carboxysome shell vertex protein CcmL
E: Carboxysome shell vertex protein CcmL


Theoretical massNumber of molelcules
Total (without water)57,7105
Polymers57,7105
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area5810 Å2
ΔGint-45 kcal/mol
Surface area26530 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)5 / 500structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein
Carboxysome shell vertex protein CcmL / Carbon dioxide concentrating mechanism protein CcmL


Mass: 11541.923 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosynechococcus vestitus BP-1 (bacteria)
Strain: BP-1 / Gene: ccmL, tll0945
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q8DKB4

-
Experimental details

-
Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111anisotropic13D CONCA
121anisotropic13D NCACX
131anisotropic13D NCOCX
152anisotropic12D 13C-13C PDSD
143anisotropic12D 13C-13C PDSD

-
Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
gel solid170 % w/w U-15N,13C 15N,13C_QD@HCcmL, 30% H2O15N,13C_QD@HCcmL was used to achieve the chemical shift assignment of QD@HCcmL.15N,13C_QD@HCcmL30% H2O
gel solid270 % w/w U-[2-13C] 2-13C_QD@HCcmL, 30% H2O2-13C_QD@HCcmL was used to obtain the structural constraints of HCcmL pentamer in QD@HCcmL assembly.2-13C_QD@HCcmL30% H2O
gel solid370 % w/w U-[2-13C] 2-13C_HCcmL, 30% H2O2-13C_HCcmL was used to obtain the structural constraints of HCcmL pentamer in QD@HCcmL assembly.2-13C_HCcmL30% H2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
70 % w/w15N,13C_QD@HCcmLU-15N,13C1
70 % w/w2-13C_QD@HCcmLU-[2-13C]2
70 % w/w2-13C_HCcmLU-[2-13C]3
Sample conditionsIonic strength: 200 mM / Label: 1 / pH: 8.0 / Pressure: 1.0 bar / Temperature: 288 K

-
NMR measurement

NMR spectrometerType: Bruker triple resonance / Manufacturer: Bruker / Model: triple resonance / Field strength: 800 MHz / Details: 3.2mm HCN-Efree probe

-
Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.6.2Bruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRFAM-SPARKYWoonghee Leechemical shift assignment
X-PLORBrungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 5

+
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://pdbjlvh1.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