8R59 | pdb_00008r59

Structure of the Co(II) triggered TRAP (S33HK35H) protein cage (levo form)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.86 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Designed, Programmable Protein Cages Utilizing Diverse Metal Coordination Geometries Show Reversible, pH-Dependent Assembly.

Osinski, N.Majsterkiewicz, K.Pakosz-Stepien, Z.Azuma, Y.Biela, A.P.Gawel, S.Heddle, J.G.

(2025) Macromol Rapid Commun 46: e2400712-e2400712

  • DOI: https://doi.org/10.1002/marc.202400712
  • Primary Citation of Related Structures:  
    8R59, 8R5A

  • PubMed Abstract: 

    The rational design and production of a novel series of engineered protein cages are presented, which have emerged as versatile and adaptable platforms with significant applications in biomedicine. These protein cages are assembled from multiple protein subunits, and precise control over their interactions is crucial for regulating assembly and disassembly, such as the on-demand release of encapsulated therapeutic agents. This approach employs a homo-undecameric, ring-shaped protein scaffold with strategically positioned metal binding sites. These engineered proteins can self-assemble into highly stable cages in the presence of cobalt or zinc ions. Furthermore, the cages can be disassembled on demand by employing external triggers such as chelating agents and changes in pH. Interestingly, for certain triggers, the disassembly process is reversible, allowing the cages to reassemble upon reversal or outcompeting of triggering conditions/agents. This work offers a promising platform for the development of advanced drug delivery systems and other biomedical applications.


  • Organizational Affiliation
    • Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, Kraków, 30387, Poland.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription attenuation protein MtrB
A,
AA [auth k],
AB [auth 9],
AC [auth YA],
AD [auth xA],
AE [auth MB],
AF [auth lB],
AG [auth AC],
AH [auth ZC],
AI [auth yC],
AJ [auth ND],
B [auth L],
BA [auth l],
BB [auth AA],
BC [auth ZA],
BD [auth yA],
BE [auth NB],
BF [auth mB],
BG [auth BC],
BH [auth aC],
BI [auth zC],
BJ [auth OD],
C [auth M],
CA [auth m],
CB [auth BA],
CC [auth aA],
CD [auth zA],
CE [auth OB],
CF [auth nB],
CG [auth CC],
CH [auth bC],
CI [auth 0C],
CJ [auth PD],
D [auth N],
DA [auth n],
DB [auth CA],
DC [auth bA],
DD [auth 0A],
DE [auth PB],
DF [auth oB],
DG [auth DC],
DH [auth cC],
DI [auth 1C],
DJ [auth QD],
E [auth O],
EA [auth o],
EB [auth DA],
EC [auth cA],
ED [auth 1A],
EE [auth QB],
EF [auth pB],
EG [auth EC],
EH [auth dC],
EI [auth 2C],
F [auth P],
FA [auth p],
FB [auth EA],
FC [auth dA],
FD [auth 2A],
FE [auth RB],
FF [auth qB],
FG [auth FC],
FH [auth eC],
FI [auth 3C],
G [auth Q],
GA [auth q],
GB [auth FA],
GC [auth eA],
GD [auth 3A],
GE [auth SB],
GF [auth rB],
GG [auth GC],
GH [auth fC],
GI [auth K],
H [auth R],
HA [auth r],
HB [auth GA],
HC [auth fA],
HD [auth 4A],
HE [auth TB],
HF [auth sB],
HG [auth HC],
HH [auth gC],
HI [auth 4C],
I [auth S],
IA [auth s],
IB [auth HA],
IC [auth gA],
ID [auth 5A],
IE [auth UB],
IF [auth tB],
IG [auth IC],
IH [auth J],
II [auth 5C],
J [auth T],
JA [auth t],
JB [auth IA],
JC [auth hA],
JD [auth 6A],
JE [auth VB],
JF [auth uB],
JG [auth JC],
JH [auth hC],
JI [auth 6C],
K [auth U],
KA [auth u],
KB [auth JA],
KC [auth iA],
KD [auth 7A],
KE [auth WB],
KF [auth vB],
KG [auth I],
KH [auth iC],
KI [auth 7C],
L [auth V],
LA [auth v],
LB [auth KA],
LC [auth jA],
LD [auth 8A],
LE [auth XB],
LF [auth wB],
LG [auth KC],
LH [auth jC],
LI [auth 8C],
M [auth W],
MA [auth w],
MB [auth LA],
MC [auth kA],
MD [auth 9A],
ME [auth YB],
MF [auth H],
MG [auth LC],
MH [auth kC],
MI [auth 9C],
N [auth Y],
NA [auth x],
NB [auth MA],
NC [auth lA],
ND [auth AB],
NE [auth ZB],
NF [auth xB],
NG [auth MC],
NH [auth lC],
NI [auth AD],
O [auth Z],
OA [auth y],
OB [auth NA],
OC [auth mA],
OD [auth BB],
OE [auth G],
OF [auth yB],
OG [auth NC],
OH [auth mC],
OI [auth BD],
P [auth a],
PA [auth z],
PB [auth OA],
PC [auth nA],
PD [auth CB],
PE [auth aB],
PF [auth zB],
PG [auth OC],
PH [auth nC],
PI [auth CD],
Q [auth b],
QA [auth 0],
QB [auth PA],
QC [auth oA],
QD [auth F],
QE [auth bB],
QF [auth 0B],
QG [auth PC],
QH [auth oC],
QI [auth DD],
R [auth c],
RA [auth 1],
RB [auth QA],
RC [auth pA],
RD [auth DB],
RE [auth cB],
RF [auth 1B],
RG [auth QC],
RH [auth pC],
RI [auth ED],
S [auth d],
SA [auth 2],
SB [auth RA],
SC [auth E],
SD [auth EB],
SE [auth dB],
SF [auth 2B],
SG [auth RC],
SH [auth qC],
SI [auth FD],
T [auth e],
TA [auth 3],
TB [auth SA],
TC [auth qA],
TD [auth FB],
TE [auth eB],
TF [auth 3B],
TG [auth SC],
TH [auth rC],
TI [auth GD],
U [auth f],
UA [auth 4],
UB [auth D],
UC [auth rA],
UD [auth GB],
UE [auth fB],
UF [auth 4B],
UG [auth TC],
UH [auth sC],
UI [auth HD],
V [auth g],
VA [auth 5],
VB [auth TA],
VC [auth sA],
VD [auth HB],
VE [auth gB],
VF [auth 5B],
VG [auth UC],
VH [auth tC],
VI [auth ID],
W [auth h],
WA [auth C],
WB [auth UA],
WC [auth tA],
WD [auth IB],
WE [auth hB],
WF [auth 6B],
WG [auth VC],
WH [auth uC],
WI [auth JD],
X [auth i],
XA [auth 6],
XB [auth VA],
XC [auth uA],
XD [auth JB],
XE [auth iB],
XF [auth 7B],
XG [auth WC],
XH [auth vC],
XI [auth KD],
Y [auth B],
YA [auth 7],
YB [auth WA],
YC [auth vA],
YD [auth KB],
YE [auth jB],
YF [auth 8B],
YG [auth XC],
YH [auth wC],
YI [auth LD],
Z [auth j],
ZA [auth 8],
ZB [auth XA],
ZC [auth wA],
ZD [auth LB],
ZE [auth kB],
ZF [auth 9B],
ZG [auth YC],
ZH [auth xC],
ZI [auth MD]
74Geobacillus stearothermophilusMutation(s): 2 
Gene Names: mtrB
UniProt
Find proteins for Q9X6J6 (Geobacillus stearothermophilus)
Explore Q9X6J6 
Go to UniProtKB:  Q9X6J6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9X6J6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CO (Subject of Investigation/LOI)
Query on CO

Download Ideal Coordinates CCD File 
AK [auth YB]
AL [auth I]
AM [auth iC]
AN [auth 7C]
BK [auth ZB]
AK [auth YB],
AL [auth I],
AM [auth iC],
AN [auth 7C],
BK [auth ZB],
BL [auth KC],
BM [auth jC],
BN [auth 8C],
CK [auth G],
CL [auth LC],
CM [auth kC],
CN [auth 9C],
DK [auth aB],
DL [auth MC],
DM [auth lC],
DN [auth AD],
EJ [auth F],
EK [auth bB],
EL [auth NC],
EM [auth mC],
EN [auth BD],
FJ [auth DB],
FK [auth cB],
FL [auth OC],
FM [auth nC],
FN [auth CD],
GJ [auth EB],
GK [auth dB],
GL [auth PC],
GM [auth oC],
GN [auth DD],
HJ [auth FB],
HK [auth eB],
HL [auth QC],
HM [auth pC],
HN [auth ED],
IJ [auth GB],
IK [auth fB],
IL [auth RC],
IM [auth qC],
IN [auth FD],
JJ [auth HB],
JK [auth gB],
JL [auth SC],
JM [auth rC],
JN [auth GD],
KJ [auth IB],
KK [auth hB],
KL [auth TC],
KM [auth sC],
KN [auth HD],
LJ [auth JB],
LK [auth iB],
LL [auth UC],
LM [auth tC],
LN [auth ID],
MJ [auth KB],
MK [auth jB],
ML [auth VC],
MM [auth uC],
MN [auth JD],
NJ [auth LB],
NK [auth kB],
NL [auth WC],
NM [auth vC],
NN [auth KD],
OJ [auth MB],
OK [auth lB],
OL [auth XC],
OM [auth wC],
ON [auth LD],
PJ [auth NB],
PK [auth mB],
PL [auth YC],
PM [auth xC],
PN [auth MD],
QJ [auth OB],
QK [auth nB],
QL [auth ZC],
QM [auth yC],
QN [auth ND],
RJ [auth PB],
RK [auth oB],
RL [auth aC],
RM [auth zC],
RN [auth OD],
SJ [auth QB],
SK [auth pB],
SL [auth bC],
SM [auth 0C],
SN [auth PD],
TJ [auth RB],
TK [auth qB],
TL [auth cC],
TM [auth 1C],
TN [auth QD],
UJ [auth SB],
UK [auth rB],
UL [auth dC],
UM [auth 2C],
VJ [auth TB],
VK [auth sB],
VL [auth eC],
VM [auth 3C],
WJ [auth UB],
WK [auth tB],
WL [auth fC],
WM [auth K],
XJ [auth VB],
XK [auth uB],
XL [auth gC],
XM [auth 4C],
YJ [auth WB],
YK [auth vB],
YL [auth J],
YM [auth 5C],
ZJ [auth XB],
ZK [auth wB],
ZL [auth hC],
ZM [auth 6C]
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.86 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Polish National Science CentrePoland2019/34/A/NZ1/00196

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-25
    Type: Initial release
  • Version 1.1: 2025-04-02
    Changes: Data collection, Database references