9K7Z | pdb_00009k7z

Cryo-EM structure of designed zinc-induced icosahedron Cage-i53-Zn1-HEHE-16

• PDB DOI: https://doi.org/10.2210/pdb9K7Z/pdb
• EM Map EMD-62155: EMDB EMDataResource

• Classification: METAL BINDING PROTEIN
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-10-24 Released: 2025-10-29 
• Deposition Author(s): Qu, Y.N., Cao, L.X.
• Funding Organization(s): Ministry of Science and Technology (MoST, China)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.65 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

De novo design of metal ion regulated protein assemblies

Qu, Y.N., Cao, L.X.

To be published.

Biological Assembly 1  

Global Symmetry: Icosahedral - I  (Explore in 3D)
Global Stoichiometry: Homo 60-mer - A60 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 1,796.43 kDa 
• Atom Count: 114,900 
• Modeled Residue Count: 14,040 
• Deposited Residue Count: 15,480 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cage-i53-Zn1-HEHE-16	A, AA [auth U], AB [auth k], B, BA [auth f], BB [auth v], C, CA [auth q], CB [auth 6], D, DA [auth 1], DB [auth P], E, EA [auth K], EB [auth a], F, FA [auth V], FB [auth l], G [auth Q], GA [auth g], GB [auth w], H [auth b], HA [auth r], HB [auth 7], I [auth m], IA [auth 2], J [auth x], JA [auth L], K [auth G], KA [auth W], L [auth R], LA [auth h], M [auth c], MA [auth s], N [auth n], NA [auth 3], O [auth y], OA [auth M], P [auth H], PA [auth X], Q [auth S], QA [auth i], R [auth d], RA [auth t], S [auth o], SA [auth 4], T [auth z], TA [auth N], U [auth I], UA [auth Y], V [auth T], VA [auth j], W [auth e], WA [auth u], X [auth p], XA [auth 5], Y [auth 0], YA [auth O], Z [auth J], ZA [auth Z]	258	Escherichia coli	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	AC [auth m], AD [auth e], AE [auth L], AF [auth u], BC [auth x], BD [auth e], BE [auth L], BF [auth 5], CC [auth G], CD [auth p], CE [auth W], CF [auth 5], DC [auth G], DD [auth 0], DE [auth W], DF [auth 5], EC [auth G], ED [auth 0], EE [auth h], EF [auth O], FC [auth R], FD [auth 0], FE [auth h], FF [auth O], GC [auth R], GD [auth J], GE [auth s], GF [auth Z], HC [auth c], HD [auth J], HE [auth 3], HF [auth Z], IB [auth A], IC [auth c], ID [auth U], IE [auth 3], IF [auth k], JB [auth A], JC [auth n], JD [auth U], JE [auth 3], JF [auth k], KB [auth A], KC [auth n], KD [auth f], KE [auth M], KF [auth v], LB [auth B], LC [auth y], LD [auth f], LE [auth M], LF [auth 6], MB [auth B], MC [auth H], MD [auth q], ME [auth X], MF [auth 6], NB [auth C], NC [auth H], ND [auth 1], NE [auth X], NF [auth 6], OB [auth C], OC [auth H], OD [auth 1], OE [auth i], OF [auth P], PB [auth D], PC [auth S], PD [auth 1], PE [auth i], PF [auth P], QB [auth D], QC [auth S], QD [auth K], QE [auth t], QF [auth a], RB [auth E], RC [auth d], RD [auth K], RE [auth 4], RF [auth a], SB [auth F], SC [auth d], SD [auth V], SE [auth 4], SF [auth l], TB [auth F], TC [auth o], TD [auth V], TE [auth 4], TF [auth l], UB [auth F], UC [auth o], UD [auth g], UE [auth N], UF [auth w], VB [auth Q], VC [auth z], VD [auth g], VE [auth N], VF [auth 7], WB [auth Q], WC [auth I], WD [auth r], WE [auth Y], WF [auth 7], XB [auth b], XC [auth I], XD [auth 2], XE [auth Y], XF [auth 7], YB [auth b], YC [auth T], YD [auth 2], YE [auth j], ZB [auth m], ZC [auth T], ZD [auth 2], ZE [auth j]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.65 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-10-29 
Deposition Author(s): Qu, Y.N., Cao, L.X.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	--

Revision History  

• Version 1.0: 2025-10-29
  Type: Initial release