9CM1 | pdb_00009cm1

Novel designed icosahedral nanoparticle I3-D12

PDB DOI: https://doi.org/10.2210/pdb9CM1/pdb
EM Map EMD-45736: EMDB EMDataResource

Classification: VIRUS LIKE PARTICLE
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-07-12 Released: 2025-07-16
Deposition Author(s): Haas, C.M., Jasti, N., Dosey, A.M., Gillespie, R., McGowan, J., Allen, J.D., Leaf, E.M., Crispin, M., DeForest, C., Kanekiyo, M., King, N.P.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Computational design of protein nanoparticle vaccine scaffolds from sequence alone

Haas, C.M., Jasti, N., Dosey, A.M., Gillespie, R., Allen, J.D., Leaf, E.M., Crispin, M., DeForest, C., Kanekiyo, M., King, N.P.

To be published.

Macromolecule Content

Total Structure Weight: 1,753.7 kDa
Atom Count: 112,620
Modeled Residue Count: 14,220
Deposited Residue Count: 15,540
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphosulfolactate synthase	A [auth 0] AA [auth Q] AB [auth s] B [auth 1] BA [auth R] A [auth 0], AA [auth Q], AB [auth s], B [auth 1], BA [auth R], BB [auth t], C [auth 2], CA [auth S], CB [auth u], D [auth 3], DA [auth T], DB [auth v], E [auth 4], EA [auth U], EB [auth w], F [auth 5], FA [auth V], FB [auth x], G [auth 6], GA [auth W], GB [auth y], H [auth 7], HA [auth X], HB [auth z], I [auth 8], IA [auth Y], J [auth 9], JA [auth Z], K [auth A], KA [auth c], L [auth B], LA [auth d], M [auth C], MA [auth e], N [auth D], NA [auth f], O [auth E], OA [auth g], P [auth F], PA [auth h], Q [auth G], QA [auth i], R [auth H], RA [auth j], S [auth I], SA [auth k], T [auth J], TA [auth l], U [auth K], UA [auth m], V [auth L], VA [auth n], W [auth M], WA [auth o], X [auth N], XA [auth p], Y [auth O], YA [auth q], Z [auth P], ZA [auth r]	259	Escherichia coli	Mutation(s): 0 Gene Names: comA EC: 4.4.1.19
UniProt
Find proteins for Q57703 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore Q57703 Go to UniProtKB: Q57703
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q57703
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-07-16

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History (Full details and data files)

Version 1.0: 2025-07-16
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.