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- PDB-8r5a: Structure of the Co(II) triggered TRAP (S33HK35H) protein cage (d... -

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Basic information

Entry
Database: PDB / ID: 8r5a
TitleStructure of the Co(II) triggered TRAP (S33HK35H) protein cage (dextro form)
ComponentsTranscription attenuation protein MtrB
KeywordsVIRUS LIKE PARTICLE / TRAP protein / protein cage
Function / homology
Function and homology information


DNA-templated transcription termination / regulation of DNA-templated transcription / RNA binding / identical protein binding
Similarity search - Function
Transcription attenuation protein MtrB / Tryptophan RNA-binding attenuator protein domain / Tryptophan RNA-binding attenuator protein / Tryptophan RNA-binding attenuator protein-like domain superfamily
Similarity search - Domain/homology
: / Transcription attenuation protein MtrB
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.84 Å
AuthorsBiela, A.P. / Heddle, J.G.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science Centre2019/34/A/NZ1/00196 Poland
CitationJournal: Macromol Rapid Commun / Year: 2024
Title: Designed, Programmable Protein Cages Utilizing Diverse Metal Coordination Geometries Show Reversible, pH-Dependent Assembly.
Authors: Norbert Osiński / Karolina Majsterkiewicz / Zuzanna Pakosz-Stępień / Yusuke Azuma / Artur P Biela / Szymon Gaweł / Jonathan G Heddle /
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. ...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.
History
DepositionNov 16, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 25, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcription attenuation protein MtrB
L: Transcription attenuation protein MtrB
M: Transcription attenuation protein MtrB
N: Transcription attenuation protein MtrB
O: Transcription attenuation protein MtrB
P: Transcription attenuation protein MtrB
Q: Transcription attenuation protein MtrB
R: Transcription attenuation protein MtrB
S: Transcription attenuation protein MtrB
T: Transcription attenuation protein MtrB
U: Transcription attenuation protein MtrB
V: Transcription attenuation protein MtrB
W: Transcription attenuation protein MtrB
Y: Transcription attenuation protein MtrB
Z: Transcription attenuation protein MtrB
a: Transcription attenuation protein MtrB
b: Transcription attenuation protein MtrB
c: Transcription attenuation protein MtrB
d: Transcription attenuation protein MtrB
e: Transcription attenuation protein MtrB
f: Transcription attenuation protein MtrB
g: Transcription attenuation protein MtrB
h: Transcription attenuation protein MtrB
i: Transcription attenuation protein MtrB
B: Transcription attenuation protein MtrB
j: Transcription attenuation protein MtrB
k: Transcription attenuation protein MtrB
l: Transcription attenuation protein MtrB
m: Transcription attenuation protein MtrB
n: Transcription attenuation protein MtrB
o: Transcription attenuation protein MtrB
p: Transcription attenuation protein MtrB
q: Transcription attenuation protein MtrB
r: Transcription attenuation protein MtrB
s: Transcription attenuation protein MtrB
t: Transcription attenuation protein MtrB
u: Transcription attenuation protein MtrB
v: Transcription attenuation protein MtrB
w: Transcription attenuation protein MtrB
x: Transcription attenuation protein MtrB
y: Transcription attenuation protein MtrB
z: Transcription attenuation protein MtrB
0: Transcription attenuation protein MtrB
1: Transcription attenuation protein MtrB
2: Transcription attenuation protein MtrB
3: Transcription attenuation protein MtrB
4: Transcription attenuation protein MtrB
5: Transcription attenuation protein MtrB
C: Transcription attenuation protein MtrB
6: Transcription attenuation protein MtrB
7: Transcription attenuation protein MtrB
8: Transcription attenuation protein MtrB
9: Transcription attenuation protein MtrB
AA: Transcription attenuation protein MtrB
BA: Transcription attenuation protein MtrB
CA: Transcription attenuation protein MtrB
DA: Transcription attenuation protein MtrB
EA: Transcription attenuation protein MtrB
FA: Transcription attenuation protein MtrB
GA: Transcription attenuation protein MtrB
HA: Transcription attenuation protein MtrB
IA: Transcription attenuation protein MtrB
JA: Transcription attenuation protein MtrB
KA: Transcription attenuation protein MtrB
LA: Transcription attenuation protein MtrB
MA: Transcription attenuation protein MtrB
NA: Transcription attenuation protein MtrB
OA: Transcription attenuation protein MtrB
PA: Transcription attenuation protein MtrB
QA: Transcription attenuation protein MtrB
RA: Transcription attenuation protein MtrB
SA: Transcription attenuation protein MtrB
D: Transcription attenuation protein MtrB
TA: Transcription attenuation protein MtrB
UA: Transcription attenuation protein MtrB
VA: Transcription attenuation protein MtrB
WA: Transcription attenuation protein MtrB
XA: Transcription attenuation protein MtrB
YA: Transcription attenuation protein MtrB
ZA: Transcription attenuation protein MtrB
aA: Transcription attenuation protein MtrB
bA: Transcription attenuation protein MtrB
cA: Transcription attenuation protein MtrB
dA: Transcription attenuation protein MtrB
eA: Transcription attenuation protein MtrB
fA: Transcription attenuation protein MtrB
gA: Transcription attenuation protein MtrB
hA: Transcription attenuation protein MtrB
iA: Transcription attenuation protein MtrB
jA: Transcription attenuation protein MtrB
kA: Transcription attenuation protein MtrB
lA: Transcription attenuation protein MtrB
mA: Transcription attenuation protein MtrB
nA: Transcription attenuation protein MtrB
oA: Transcription attenuation protein MtrB
pA: Transcription attenuation protein MtrB
E: Transcription attenuation protein MtrB
qA: Transcription attenuation protein MtrB
rA: Transcription attenuation protein MtrB
sA: Transcription attenuation protein MtrB
tA: Transcription attenuation protein MtrB
uA: Transcription attenuation protein MtrB
vA: Transcription attenuation protein MtrB
wA: Transcription attenuation protein MtrB
xA: Transcription attenuation protein MtrB
yA: Transcription attenuation protein MtrB
zA: Transcription attenuation protein MtrB
0A: Transcription attenuation protein MtrB
1A: Transcription attenuation protein MtrB
2A: Transcription attenuation protein MtrB
3A: Transcription attenuation protein MtrB
4A: Transcription attenuation protein MtrB
5A: Transcription attenuation protein MtrB
6A: Transcription attenuation protein MtrB
7A: Transcription attenuation protein MtrB
8A: Transcription attenuation protein MtrB
9A: Transcription attenuation protein MtrB
AB: Transcription attenuation protein MtrB
BB: Transcription attenuation protein MtrB
CB: Transcription attenuation protein MtrB
F: Transcription attenuation protein MtrB
DB: Transcription attenuation protein MtrB
EB: Transcription attenuation protein MtrB
FB: Transcription attenuation protein MtrB
GB: Transcription attenuation protein MtrB
HB: Transcription attenuation protein MtrB
IB: Transcription attenuation protein MtrB
JB: Transcription attenuation protein MtrB
KB: Transcription attenuation protein MtrB
LB: Transcription attenuation protein MtrB
MB: Transcription attenuation protein MtrB
NB: Transcription attenuation protein MtrB
OB: Transcription attenuation protein MtrB
PB: Transcription attenuation protein MtrB
QB: Transcription attenuation protein MtrB
RB: Transcription attenuation protein MtrB
SB: Transcription attenuation protein MtrB
TB: Transcription attenuation protein MtrB
UB: Transcription attenuation protein MtrB
VB: Transcription attenuation protein MtrB
WB: Transcription attenuation protein MtrB
XB: Transcription attenuation protein MtrB
YB: Transcription attenuation protein MtrB
ZB: Transcription attenuation protein MtrB
G: Transcription attenuation protein MtrB
aB: Transcription attenuation protein MtrB
bB: Transcription attenuation protein MtrB
cB: Transcription attenuation protein MtrB
dB: Transcription attenuation protein MtrB
eB: Transcription attenuation protein MtrB
fB: Transcription attenuation protein MtrB
gB: Transcription attenuation protein MtrB
hB: Transcription attenuation protein MtrB
iB: Transcription attenuation protein MtrB
jB: Transcription attenuation protein MtrB
kB: Transcription attenuation protein MtrB
lB: Transcription attenuation protein MtrB
mB: Transcription attenuation protein MtrB
nB: Transcription attenuation protein MtrB
oB: Transcription attenuation protein MtrB
pB: Transcription attenuation protein MtrB
qB: Transcription attenuation protein MtrB
rB: Transcription attenuation protein MtrB
sB: Transcription attenuation protein MtrB
tB: Transcription attenuation protein MtrB
uB: Transcription attenuation protein MtrB
vB: Transcription attenuation protein MtrB
wB: Transcription attenuation protein MtrB
H: Transcription attenuation protein MtrB
xB: Transcription attenuation protein MtrB
yB: Transcription attenuation protein MtrB
zB: Transcription attenuation protein MtrB
0B: Transcription attenuation protein MtrB
1B: Transcription attenuation protein MtrB
2B: Transcription attenuation protein MtrB
3B: Transcription attenuation protein MtrB
4B: Transcription attenuation protein MtrB
5B: Transcription attenuation protein MtrB
6B: Transcription attenuation protein MtrB
7B: Transcription attenuation protein MtrB
8B: Transcription attenuation protein MtrB
9B: Transcription attenuation protein MtrB
AC: Transcription attenuation protein MtrB
BC: Transcription attenuation protein MtrB
CC: Transcription attenuation protein MtrB
DC: Transcription attenuation protein MtrB
EC: Transcription attenuation protein MtrB
FC: Transcription attenuation protein MtrB
GC: Transcription attenuation protein MtrB
HC: Transcription attenuation protein MtrB
IC: Transcription attenuation protein MtrB
JC: Transcription attenuation protein MtrB
I: Transcription attenuation protein MtrB
KC: Transcription attenuation protein MtrB
LC: Transcription attenuation protein MtrB
MC: Transcription attenuation protein MtrB
NC: Transcription attenuation protein MtrB
OC: Transcription attenuation protein MtrB
PC: Transcription attenuation protein MtrB
QC: Transcription attenuation protein MtrB
RC: Transcription attenuation protein MtrB
SC: Transcription attenuation protein MtrB
TC: Transcription attenuation protein MtrB
UC: Transcription attenuation protein MtrB
VC: Transcription attenuation protein MtrB
WC: Transcription attenuation protein MtrB
XC: Transcription attenuation protein MtrB
YC: Transcription attenuation protein MtrB
ZC: Transcription attenuation protein MtrB
aC: Transcription attenuation protein MtrB
bC: Transcription attenuation protein MtrB
cC: Transcription attenuation protein MtrB
dC: Transcription attenuation protein MtrB
eC: Transcription attenuation protein MtrB
fC: Transcription attenuation protein MtrB
gC: Transcription attenuation protein MtrB
J: Transcription attenuation protein MtrB
hC: Transcription attenuation protein MtrB
iC: Transcription attenuation protein MtrB
jC: Transcription attenuation protein MtrB
kC: Transcription attenuation protein MtrB
lC: Transcription attenuation protein MtrB
mC: Transcription attenuation protein MtrB
nC: Transcription attenuation protein MtrB
oC: Transcription attenuation protein MtrB
pC: Transcription attenuation protein MtrB
qC: Transcription attenuation protein MtrB
rC: Transcription attenuation protein MtrB
sC: Transcription attenuation protein MtrB
tC: Transcription attenuation protein MtrB
uC: Transcription attenuation protein MtrB
vC: Transcription attenuation protein MtrB
wC: Transcription attenuation protein MtrB
xC: Transcription attenuation protein MtrB
yC: Transcription attenuation protein MtrB
zC: Transcription attenuation protein MtrB
0C: Transcription attenuation protein MtrB
1C: Transcription attenuation protein MtrB
2C: Transcription attenuation protein MtrB
3C: Transcription attenuation protein MtrB
K: Transcription attenuation protein MtrB
4C: Transcription attenuation protein MtrB
5C: Transcription attenuation protein MtrB
6C: Transcription attenuation protein MtrB
7C: Transcription attenuation protein MtrB
8C: Transcription attenuation protein MtrB
9C: Transcription attenuation protein MtrB
AD: Transcription attenuation protein MtrB
BD: Transcription attenuation protein MtrB
CD: Transcription attenuation protein MtrB
DD: Transcription attenuation protein MtrB
ED: Transcription attenuation protein MtrB
FD: Transcription attenuation protein MtrB
GD: Transcription attenuation protein MtrB
HD: Transcription attenuation protein MtrB
ID: Transcription attenuation protein MtrB
JD: Transcription attenuation protein MtrB
KD: Transcription attenuation protein MtrB
LD: Transcription attenuation protein MtrB
MD: Transcription attenuation protein MtrB
ND: Transcription attenuation protein MtrB
OD: Transcription attenuation protein MtrB
PD: Transcription attenuation protein MtrB
QD: Transcription attenuation protein MtrB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,202,869384
Polymers2,195,797264
Non-polymers7,072120
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ...
Transcription attenuation protein MtrB / Trp RNA-binding attenuation protein / TRAP / Tryptophan RNA-binding attenuator protein


Mass: 8317.413 Da / Num. of mol.: 264 / Mutation: S33H,K35H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: mtrB / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X6J6
#2: Chemical...
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 120 / Source method: obtained synthetically / Formula: Co
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: TRAP(S33HK35C) protein cage / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 2.2 MDa / Experimental value: YES
Source (natural)Organism: Geobacillus stearothermophilus (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.9
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2EPUimage acquisition
4cryoSPARCCTF correction
7UCSF ChimeraXmodel fitting
9PHENIXmodel refinement
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: O (octahedral)
3D reconstructionResolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 161631 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 4v4f

4v4f


Accession code: 4v4f / Source name: PDB / Type: experimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 24.21 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0053144936
ELECTRON MICROSCOPYf_angle_d0.6549195360
ELECTRON MICROSCOPYf_chiral_restr0.053722440
ELECTRON MICROSCOPYf_plane_restr0.00325344
ELECTRON MICROSCOPYf_dihedral_angle_d5.679119272

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