[English] 日本語
Yorodumi
- PDB-9op9: Two Component Protein Nano-Particle (T=3). De Novo Design, Comput... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9op9
TitleTwo Component Protein Nano-Particle (T=3). De Novo Design, Computationally Relaxed into Low Resolution Subtomogram Averaged CryoEM Map with Icosahedral Symmetry Applied
Components
  • C2-B
  • C3-A
KeywordsDE NOVO PROTEIN / Goldberg icosahedron / C60 / Fullerene
Biological speciessynthetic construct (others)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 31.6 Å
AuthorsDiMaio, F. / Chmielewski, D. / Weidle, C.
Funding support United States, France, 8items
OrganizationGrant numberCountry
Defense Threat Reduction Agency (DTRA)HDTRA1-19-1-0003 United States
Burroughs Wellcome Fund United States
Human Frontier Science Program (HFSP)RGP0061/2019 France
Bill & Melinda Gates FoundationINV-043758 United States
Bill & Melinda Gates FoundationOPP1156262 United States
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute on Aging (NIH/NIA)R01AG063845 United States
Department of Energy (DOE, United States)KP1607011 United States
CitationJournal: Nature / Year: 2026
Title: De novo design of quasisymmetric two-component protein cages.
Authors: Shunzhi Wang / Ying Xie / David Chemielewski / Connor Weidle / Tong Shu / Green Ahn / Ryan D Kibler / Cindy Hernandez / Wei Chen / David Camilo Duran / Ann Carr / Asim K Bera / Sangmin Lee / ...Authors: Shunzhi Wang / Ying Xie / David Chemielewski / Connor Weidle / Tong Shu / Green Ahn / Ryan D Kibler / Cindy Hernandez / Wei Chen / David Camilo Duran / Ann Carr / Asim K Bera / Sangmin Lee / Justin Decarreau / Alex Kang / Evans Brackenbrough / Emily Joyce / Kejia Wu / Andrew J Borst / Andrew Favor / Buwei Huang / Frank DiMaio / Liam J Holt / David Baker /
Abstract: Quasisymmetric icosahedral viral capsids achieve larger sizes than possible with strictly symmetric icosahedra by tessellating pentagons and hexagons using a single subunit that adopts different ...Quasisymmetric icosahedral viral capsids achieve larger sizes than possible with strictly symmetric icosahedra by tessellating pentagons and hexagons using a single subunit that adopts different conformations in symmetrically non-equivalent locations. Recapitulating such quasisymmetric architectures through computational design is a considerable challenge in nanomaterials engineering. Here we introduce a computational design strategy based on geometric frustration to generate two-component, quasisymmetric protein cages with customizable properties. We designed complementary trimeric and dimeric protein components that co-assemble into positively curved local hexagonal assemblies. Hexagonal lattices cannot tile spherical surfaces; instead, the components form closed sphere-like cage assemblies through incorporation of curvature-inducing pentagonal defects, as evidenced by electron microscopy. By designing dimers that encode different local curvatures, we programmed cage dimensions ranging from 40 to over 200 nm in diameter and with molecular weights from 2 MDa to over 50 MDa, comparable with natural virus capsids. We further functionalized these large cages with additional protein domains to enable ribonucleoprotein cargo loading and cellular uptake. Fluorescently labelled cage assemblies expressed in mammalian cells function as rheological probes and cargo recruiters, enabling a systematic study of size-dependent cytoplasmic diffusion and protein localization. Thus, the quasi-symmetry that has long fascinated structural biologists can now be achieved by computational protein design, with immediate applications to biologics delivery and molecular cell biology.
History
DepositionMay 17, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2026Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update
Revision 1.1Jun 3, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin / Data content type: EM metadata / EM metadata / EM metadata
Item: _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
ZA: C2-B
YC: C2-B
YD: C3-A
ZY: C2-B
ZZ: C3-A
YE: C2-B
YF: C3-A
YG: C2-B
YH: C3-A
YI: C2-B
YJ: C3-A
YK: C2-B
YL: C3-A
YM: C2-B
YN: C3-A
YO: C2-B
YP: C3-A
YQ: C2-B
YR: C3-A
YS: C2-B
YT: C3-A
YU: C2-B
YV: C3-A
AA: C2-B
AB: C3-A
YW: C2-B
YX: C3-A
ZB: C3-A
YY: C2-B
YZ: C3-A
AC: C2-B
AD: C3-A
AE: C2-B
AF: C3-A
AG: C2-B
AH: C3-A
AI: C2-B
AJ: C3-A
AK: C2-B
AL: C3-A
AM: C2-B
AN: C3-A
AO: C3-A
AP: C2-B
AQ: C3-A
AR: C2-B
AS: C2-B
AT: C3-A
AU: C2-B
AV: C3-A
AW: C2-B
AX: C3-A
AY: C2-B
AZ: C3-A
ZC: C2-B
BA: C2-B
BB: C3-A
BC: C2-B
BD: C3-A
BE: C2-B
BF: C3-A
BG: C2-B
BH: C3-A
BI: C2-B
BJ: C3-A
BK: C2-B
BL: C3-A
BM: C2-B
BN: C3-A
BO: C2-B
BP: C3-A
BQ: C2-B
BR: C3-A
BS: C2-B
BT: C3-A
BU: C2-B
BV: C3-A
BW: C2-B
BX: C3-A
BY: C2-B
BZ: C3-A
ZD: C3-A
CA: C2-B
CB: C3-A
CC: C2-B
CD: C3-A
CE: C2-B
CF: C3-A
CG: C2-B
CH: C3-A
CI: C2-B
CJ: C3-A
CK: C2-B
CL: C3-A
CM: C2-B
CN: C3-A
CO: C2-B
CP: C3-A
CQ: C2-B
CR: C3-A
CS: C2-B
CT: C3-A
CU: C2-B
CV: C3-A
CW: C2-B
CX: C3-A
CY: C2-B
CZ: C3-A
ZE: C2-B
DA: C2-B
DB: C3-A
DC: C2-B
DD: C3-A
DE: C2-B
DF: C3-A
DG: C2-B
DH: C3-A
DI: C2-B
DJ: C3-A
DK: C2-B
DL: C3-A
DM: C2-B
DN: C3-A
DO: C2-B
DP: C3-A
DQ: C2-B
DR: C3-A
DS: C2-B
DT: C3-A
DU: C2-B
DW: C3-A
DX: C2-B
DY: C3-A
DZ: C2-B
EA: C3-A
ZF: C3-A
EB: C2-B
EC: C3-A
ED: C2-B
EE: C3-A
EF: C2-B
EG: C3-A
EH: C2-B
EI: C3-A
EJ: C2-B
EK: C3-A
EL: C2-B
EM: C3-A
EN: C2-B
EO: C3-A
EP: C2-B
EQ: C3-A
ER: C2-B
ES: C3-A
ET: C2-B
EU: C3-A
EV: C2-B
EW: C3-A
EX: C2-B
EY: C3-A
EZ: C2-B
FA: C3-A
ZG: C2-B
FB: C2-B
FC: C3-A
FD: C2-B
FE: C3-A
FF: C2-B
FG: C3-A
FH: C2-B
FI: C3-A
FJ: C2-B
FK: C3-A
FL: C2-B
FM: C3-A
FN: C2-B
FO: C3-A
FP: C2-B
FQ: C3-A
FR: C2-B
FS: C3-A
FT: C2-B
FU: C3-A
FV: C2-B
FW: C3-A
FX: C2-B
FY: C3-A
FZ: C2-B
GA: C3-A
ZH: C3-A
GB: C2-B
GC: C3-A
GD: C2-B
GE: C3-A
GF: C2-B
GG: C3-A
GH: C2-B
GI: C3-A
GJ: C2-B
GK: C3-A
GL: C2-B
GM: C3-A
GN: C2-B
GO: C3-A
GP: C2-B
GQ: C3-A
GR: C2-B
GS: C3-A
GT: C2-B
GU: C3-A
GV: C2-B
GW: C3-A
GX: C2-B
GY: C3-A
GZ: C2-B
HA: C3-A
ZI: C2-B
HB: C2-B
HC: C3-A
HD: C2-B
HE: C3-A
HF: C3-A
WB: C2-B
HG: C2-B
HH: C3-A
HI: C2-B
HJ: C3-A
HK: C3-A
WA: C2-B
HL: C2-B
HM: C3-A
HN: C2-B
HO: C3-A
HP: C2-B
HQ: C3-A
HR: C2-B
HS: C3-A
HT: C2-B
HU: C3-A
HV: C2-B
HW: C3-A
HX: C2-B
HY: C3-A
HZ: C2-B
IA: C3-A
ZJ: C3-A
IB: C3-A
WC: C2-B
IC: C2-B
ID: C3-A
IE: C2-B
IF: C3-A
IG: C3-A
IH: C2-B
II: C2-B
IJ: C3-A
IK: C2-B
IL: C3-A
IM: C2-B
IN: C3-A
IO: C2-B
IP: C3-A
IQ: C2-B
IR: C3-A
IS: C2-B
IT: C3-A
IU: C2-B
IV: C3-A
IW: C2-B
IX: C3-A
IY: C2-B
IZ: C3-A
JA: C2-B
ZK: C2-B
JB: C3-A
JC: C2-B
JD: C3-A
JE: C2-B
JF: C3-A
JG: C2-B
JH: C3-A
JI: C2-B
JJ: C3-A
JK: C2-B
JL: C3-A
JM: C2-B
JN: C3-A
JO: C2-B
JP: C3-A
JQ: C2-B
JR: C3-A
JS: C2-B
JT: C3-A
JU: C3-A
WD: C2-B
JV: C2-B
JW: C3-A
JX: C2-B
JY: C3-A
JZ: C2-B
KA: C3-A
ZL: C3-A
KB: C2-B
KC: C3-A
KD: C2-B
KE: C3-A
KF: C2-B
KG: C3-A
KH: C2-B
KI: C3-A
KJ: C2-B
KK: C3-A
KL: C2-B
KM: C3-A
KN: C2-B
KO: C3-A
KP: C2-B
KQ: C3-A
KR: C2-B
KS: C3-A
KT: C2-B
KU: C3-A
KV: C2-B
KW: C3-A
KX: C2-B
KY: C3-A
KZ: C2-B
LA: C3-A
ZM: C2-B
LB: C2-B
LC: C3-A
LD: C2-B
LE: C3-A
LF: C2-B
LG: C3-A
LH: C2-B
LI: C3-A
LJ: C2-B
LK: C3-A
LL: C2-B
LM: C3-A
LN: C2-B
LO: C3-A
LP: C2-B
LQ: C3-A
LR: C2-B
LS: C3-A
ZN: C3-A
ZO: C2-B
ZP: C3-A
ZQ: C2-B
ZR: C3-A
ZS: C2-B
ZT: C3-A
ZU: C2-B
ZV: C3-A
ZW: C2-B
ZX: C3-A
YA: C2-B
YB: C3-A


Theoretical massNumber of molelcules
Total (without water)8,275,129360
Polymers8,275,129360
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

#1: Protein ...
C2-B


Mass: 12591.434 Da / Num. of mol.: 180
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21* (DE3)
#2: Protein ...
C3-A


Mass: 33381.504 Da / Num. of mol.: 180
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21* (DE3)
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: subtomogram averaging

-
Sample preparation

ComponentName: Protein structure is equivalent to a C60 fullerene and has the general shape of a soccer ball with 12 pentagonal and 20 hexagonal facets. There are a total of 60 vertices (C3-A) and 90 edges (C2-B)
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: synthetic construct (others)
Source (recombinant)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain: BL21* (DE3)
Buffer solutionpH: 8 / Details: 25 mM Tris-HCl and 300 mM NaCl (pH 8)
Buffer component
IDConc.NameFormulaBuffer-ID
125 mMtris(hydroxymethyl)aminomethane Hydrochloric AcidTris-HCl1
2300 mMSodium ChlorideNaCl1
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 15mA / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: C-flat-2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295.15 K

-
Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 22000 X / Nominal defocus max: 5000 nm / Nominal defocus min: 2000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 2.68 e/Å2 / Avg electron dose per subtomogram: 110 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum

-
Processing

EM software
IDNameVersionCategory
2SerialEMimage acquisition
4EMAN2CTF correction
7Rosettamodel fitting
9PHENIX1.21.2_5419model refinement
10cryoSPARCinitial Euler assignment
11EMAN2final Euler assignment
13EMAN23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 142674
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 31.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 462 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
EM volume selectionNum. of tomograms: 462 / Num. of volumes extracted: 599
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Atomic model buildingDetails: Computational Design / 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