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- PDB-6rvw: Structure of right-handed protein cage consisting of 24 eleven-me... -

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Basic information

Entry
Database: PDB / ID: 6rvw
TitleStructure of right-handed protein cage consisting of 24 eleven-membered ring proteins held together by gold (I) bridges.
ComponentsTranscription attenuation protein MtrB
KeywordsRNA BINDING PROTEIN / TRAP / protein cage / gold binding / snub cube
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: 3.7 Å
AuthorsMalay, A.D. / Miyazaki, N. / Biela, A.P. / Iwasaki, K. / Heddle, J.G.
Funding support Poland, Japan, 5items
OrganizationGrant numberCountry
Polish National Science CentreNCN 2016/20/W/NZ1/00095 Poland
Other governmentFNP Homing/2016-2/20 Poland
Japan Society for the Promotion of ScienceNo. 2556023 Japan
Other governmentMRPO.05.01.00-12-013/15 Poland
Japan Agency for Medical Research and Development (AMED) Japan
CitationJournal: Nature / Year: 2019
Title: An ultra-stable gold-coordinated protein cage displaying reversible assembly.
Authors: Ali D Malay / Naoyuki Miyazaki / Artur Biela / Soumyananda Chakraborti / Karolina Majsterkiewicz / Izabela Stupka / Craig S Kaplan / Agnieszka Kowalczyk / Bernard M A G Piette / Georg K A ...Authors: Ali D Malay / Naoyuki Miyazaki / Artur Biela / Soumyananda Chakraborti / Karolina Majsterkiewicz / Izabela Stupka / Craig S Kaplan / Agnieszka Kowalczyk / Bernard M A G Piette / Georg K A Hochberg / Di Wu / Tomasz P Wrobel / Adam Fineberg / Manish S Kushwah / Mitja Kelemen / Primož Vavpetič / Primož Pelicon / Philipp Kukura / Justin L P Benesch / Kenji Iwasaki / Jonathan G Heddle /
Abstract: Symmetrical protein cages have evolved to fulfil diverse roles in nature, including compartmentalization and cargo delivery, and have inspired synthetic biologists to create novel protein assemblies ...Symmetrical protein cages have evolved to fulfil diverse roles in nature, including compartmentalization and cargo delivery, and have inspired synthetic biologists to create novel protein assemblies via the precise manipulation of protein-protein interfaces. Despite the impressive array of protein cages produced in the laboratory, the design of inducible assemblies remains challenging. Here we demonstrate an ultra-stable artificial protein cage, the assembly and disassembly of which can be controlled by metal coordination at the protein-protein interfaces. The addition of a gold (I)-triphenylphosphine compound to a cysteine-substituted, 11-mer protein ring triggers supramolecular self-assembly, which generates monodisperse cage structures with masses greater than 2 MDa. The geometry of these structures is based on the Archimedean snub cube and is, to our knowledge, unprecedented. Cryo-electron microscopy confirms that the assemblies are held together by 120 S-Au-S staples between the protein oligomers, and exist in two chiral forms. The cage shows extreme chemical and thermal stability, yet it readily disassembles upon exposure to reducing agents. As well as gold, mercury(II) is also found to enable formation of the protein cage. This work establishes an approach for linking protein components into robust, higher-order structures, and expands the design space available for supramolecular assemblies to include previously unexplored geometries.
History
DepositionJun 3, 2019Deposition site: PDBE / Processing site: PDBE
SupersessionJun 12, 2019ID: 6IB4
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Assembly

Deposited unit
AA: Transcription attenuation protein MtrB
AB: Transcription attenuation protein MtrB
AC: Transcription attenuation protein MtrB
AD: Transcription attenuation protein MtrB
AE: Transcription attenuation protein MtrB
AF: Transcription attenuation protein MtrB
AG: Transcription attenuation protein MtrB
AH: Transcription attenuation protein MtrB
AI: Transcription attenuation protein MtrB
AJ: Transcription attenuation protein MtrB
AK: Transcription attenuation protein MtrB
BA: Transcription attenuation protein MtrB
BB: Transcription attenuation protein MtrB
BC: Transcription attenuation protein MtrB
BD: Transcription attenuation protein MtrB
BE: Transcription attenuation protein MtrB
BF: Transcription attenuation protein MtrB
BG: Transcription attenuation protein MtrB
BH: Transcription attenuation protein MtrB
BI: Transcription attenuation protein MtrB
BJ: Transcription attenuation protein MtrB
BK: Transcription attenuation protein MtrB
CA: Transcription attenuation protein MtrB
CB: Transcription attenuation protein MtrB
CC: Transcription attenuation protein MtrB
CD: Transcription attenuation protein MtrB
CE: Transcription attenuation protein MtrB
CF: Transcription attenuation protein MtrB
CG: Transcription attenuation protein MtrB
CH: Transcription attenuation protein MtrB
CI: Transcription attenuation protein MtrB
CJ: Transcription attenuation protein MtrB
CK: Transcription attenuation protein MtrB
DA: Transcription attenuation protein MtrB
DB: Transcription attenuation protein MtrB
DC: Transcription attenuation protein MtrB
DD: Transcription attenuation protein MtrB
DE: Transcription attenuation protein MtrB
DF: Transcription attenuation protein MtrB
DG: Transcription attenuation protein MtrB
DH: Transcription attenuation protein MtrB
DI: Transcription attenuation protein MtrB
DJ: Transcription attenuation protein MtrB
DK: Transcription attenuation protein MtrB
EA: Transcription attenuation protein MtrB
EB: Transcription attenuation protein MtrB
EC: Transcription attenuation protein MtrB
ED: Transcription attenuation protein MtrB
EE: Transcription attenuation protein MtrB
EF: Transcription attenuation protein MtrB
EG: Transcription attenuation protein MtrB
EH: Transcription attenuation protein MtrB
EI: Transcription attenuation protein MtrB
EJ: Transcription attenuation protein MtrB
EK: Transcription attenuation protein MtrB
FA: Transcription attenuation protein MtrB
FB: Transcription attenuation protein MtrB
FC: Transcription attenuation protein MtrB
FD: Transcription attenuation protein MtrB
FE: Transcription attenuation protein MtrB
FF: Transcription attenuation protein MtrB
FG: Transcription attenuation protein MtrB
FH: Transcription attenuation protein MtrB
FI: Transcription attenuation protein MtrB
FJ: Transcription attenuation protein MtrB
FK: Transcription attenuation protein MtrB
GA: Transcription attenuation protein MtrB
GB: Transcription attenuation protein MtrB
GC: Transcription attenuation protein MtrB
GD: Transcription attenuation protein MtrB
GE: Transcription attenuation protein MtrB
GF: Transcription attenuation protein MtrB
GG: Transcription attenuation protein MtrB
GH: Transcription attenuation protein MtrB
GI: Transcription attenuation protein MtrB
GJ: Transcription attenuation protein MtrB
GK: Transcription attenuation protein MtrB
HA: Transcription attenuation protein MtrB
HB: Transcription attenuation protein MtrB
HC: Transcription attenuation protein MtrB
HD: Transcription attenuation protein MtrB
HE: Transcription attenuation protein MtrB
HF: Transcription attenuation protein MtrB
HG: Transcription attenuation protein MtrB
HH: Transcription attenuation protein MtrB
HI: Transcription attenuation protein MtrB
HJ: Transcription attenuation protein MtrB
HK: Transcription attenuation protein MtrB
IA: Transcription attenuation protein MtrB
IB: Transcription attenuation protein MtrB
IC: Transcription attenuation protein MtrB
ID: Transcription attenuation protein MtrB
IE: Transcription attenuation protein MtrB
IF: Transcription attenuation protein MtrB
IG: Transcription attenuation protein MtrB
IH: Transcription attenuation protein MtrB
II: Transcription attenuation protein MtrB
IJ: Transcription attenuation protein MtrB
IK: Transcription attenuation protein MtrB
JA: Transcription attenuation protein MtrB
JB: Transcription attenuation protein MtrB
JC: Transcription attenuation protein MtrB
JD: Transcription attenuation protein MtrB
JE: Transcription attenuation protein MtrB
JF: Transcription attenuation protein MtrB
JG: Transcription attenuation protein MtrB
JH: Transcription attenuation protein MtrB
JI: Transcription attenuation protein MtrB
JJ: Transcription attenuation protein MtrB
JK: Transcription attenuation protein MtrB
KA: Transcription attenuation protein MtrB
KB: Transcription attenuation protein MtrB
KC: Transcription attenuation protein MtrB
KD: Transcription attenuation protein MtrB
KE: Transcription attenuation protein MtrB
KF: Transcription attenuation protein MtrB
KG: Transcription attenuation protein MtrB
KH: Transcription attenuation protein MtrB
KI: Transcription attenuation protein MtrB
KJ: Transcription attenuation protein MtrB
KK: Transcription attenuation protein MtrB
LA: Transcription attenuation protein MtrB
LB: Transcription attenuation protein MtrB
LC: Transcription attenuation protein MtrB
LD: Transcription attenuation protein MtrB
LE: Transcription attenuation protein MtrB
LF: Transcription attenuation protein MtrB
LG: Transcription attenuation protein MtrB
LH: Transcription attenuation protein MtrB
LI: Transcription attenuation protein MtrB
LJ: Transcription attenuation protein MtrB
LK: Transcription attenuation protein MtrB
MA: Transcription attenuation protein MtrB
MB: Transcription attenuation protein MtrB
MC: Transcription attenuation protein MtrB
MD: Transcription attenuation protein MtrB
ME: Transcription attenuation protein MtrB
MF: Transcription attenuation protein MtrB
MG: Transcription attenuation protein MtrB
MH: Transcription attenuation protein MtrB
MI: Transcription attenuation protein MtrB
MJ: Transcription attenuation protein MtrB
MK: Transcription attenuation protein MtrB
NA: Transcription attenuation protein MtrB
NB: Transcription attenuation protein MtrB
NC: Transcription attenuation protein MtrB
ND: Transcription attenuation protein MtrB
NE: Transcription attenuation protein MtrB
NF: Transcription attenuation protein MtrB
NG: Transcription attenuation protein MtrB
NH: Transcription attenuation protein MtrB
NI: Transcription attenuation protein MtrB
NJ: Transcription attenuation protein MtrB
NK: Transcription attenuation protein MtrB
OA: Transcription attenuation protein MtrB
OB: Transcription attenuation protein MtrB
OC: Transcription attenuation protein MtrB
OD: Transcription attenuation protein MtrB
OE: Transcription attenuation protein MtrB
OF: Transcription attenuation protein MtrB
OG: Transcription attenuation protein MtrB
OH: Transcription attenuation protein MtrB
OI: Transcription attenuation protein MtrB
OJ: Transcription attenuation protein MtrB
OK: Transcription attenuation protein MtrB
PA: Transcription attenuation protein MtrB
PB: Transcription attenuation protein MtrB
PC: Transcription attenuation protein MtrB
PD: Transcription attenuation protein MtrB
PE: Transcription attenuation protein MtrB
PF: Transcription attenuation protein MtrB
PG: Transcription attenuation protein MtrB
PH: Transcription attenuation protein MtrB
PI: Transcription attenuation protein MtrB
PJ: Transcription attenuation protein MtrB
PK: Transcription attenuation protein MtrB
QA: Transcription attenuation protein MtrB
QB: Transcription attenuation protein MtrB
QC: Transcription attenuation protein MtrB
QD: Transcription attenuation protein MtrB
QE: Transcription attenuation protein MtrB
QF: Transcription attenuation protein MtrB
QG: Transcription attenuation protein MtrB
QH: Transcription attenuation protein MtrB
QI: Transcription attenuation protein MtrB
QJ: Transcription attenuation protein MtrB
QK: Transcription attenuation protein MtrB
RA: Transcription attenuation protein MtrB
RB: Transcription attenuation protein MtrB
RC: Transcription attenuation protein MtrB
RD: Transcription attenuation protein MtrB
RE: Transcription attenuation protein MtrB
RF: Transcription attenuation protein MtrB
RG: Transcription attenuation protein MtrB
RH: Transcription attenuation protein MtrB
RI: Transcription attenuation protein MtrB
RJ: Transcription attenuation protein MtrB
RK: Transcription attenuation protein MtrB
SA: Transcription attenuation protein MtrB
SB: Transcription attenuation protein MtrB
SC: Transcription attenuation protein MtrB
SD: Transcription attenuation protein MtrB
SE: Transcription attenuation protein MtrB
SF: Transcription attenuation protein MtrB
SG: Transcription attenuation protein MtrB
SH: Transcription attenuation protein MtrB
SI: Transcription attenuation protein MtrB
SJ: Transcription attenuation protein MtrB
SK: Transcription attenuation protein MtrB
TA: Transcription attenuation protein MtrB
TB: Transcription attenuation protein MtrB
TC: Transcription attenuation protein MtrB
TD: Transcription attenuation protein MtrB
TE: Transcription attenuation protein MtrB
TF: Transcription attenuation protein MtrB
TG: Transcription attenuation protein MtrB
TH: Transcription attenuation protein MtrB
TI: Transcription attenuation protein MtrB
TJ: Transcription attenuation protein MtrB
TK: Transcription attenuation protein MtrB
UA: Transcription attenuation protein MtrB
UB: Transcription attenuation protein MtrB
UC: Transcription attenuation protein MtrB
UD: Transcription attenuation protein MtrB
UE: Transcription attenuation protein MtrB
UF: Transcription attenuation protein MtrB
UG: Transcription attenuation protein MtrB
UH: Transcription attenuation protein MtrB
UI: Transcription attenuation protein MtrB
UJ: Transcription attenuation protein MtrB
UK: Transcription attenuation protein MtrB
VA: Transcription attenuation protein MtrB
VB: Transcription attenuation protein MtrB
VC: Transcription attenuation protein MtrB
VD: Transcription attenuation protein MtrB
VE: Transcription attenuation protein MtrB
VF: Transcription attenuation protein MtrB
VG: Transcription attenuation protein MtrB
VH: Transcription attenuation protein MtrB
VI: Transcription attenuation protein MtrB
VJ: Transcription attenuation protein MtrB
VK: Transcription attenuation protein MtrB
WA: Transcription attenuation protein MtrB
WB: Transcription attenuation protein MtrB
WC: Transcription attenuation protein MtrB
WD: Transcription attenuation protein MtrB
WE: Transcription attenuation protein MtrB
WF: Transcription attenuation protein MtrB
WG: Transcription attenuation protein MtrB
WH: Transcription attenuation protein MtrB
WI: Transcription attenuation protein MtrB
WJ: Transcription attenuation protein MtrB
WK: Transcription attenuation protein MtrB
XA: Transcription attenuation protein MtrB
XB: Transcription attenuation protein MtrB
XC: Transcription attenuation protein MtrB
XD: Transcription attenuation protein MtrB
XE: Transcription attenuation protein MtrB
XF: Transcription attenuation protein MtrB
XG: Transcription attenuation protein MtrB
XH: Transcription attenuation protein MtrB
XI: Transcription attenuation protein MtrB
XJ: Transcription attenuation protein MtrB
XK: Transcription attenuation protein MtrB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,178,199384
Polymers2,154,563264
Non-polymers23,636120
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
MethodPISA

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Components

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


Mass: 8161.224 Da / Num. of mol.: 264 / Mutation: K35C, R64S
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-AU / GOLD ION


Mass: 196.967 Da / Num. of mol.: 120 / Source method: obtained synthetically / Formula: Au / Feature type: SUBJECT OF INVESTIGATION

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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: RH TRAP protein cage / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 2.16 MDa / Experimental value: YES
Source (natural)Organism: Geobacillus stearothermophilus (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenConc.: 0.89 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: 3.0 s blotting time

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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
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k)
Image scansWidth: 4096 / Height: 4096

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Processing

EM software
IDNameCategory
7PHENIXmodel fitting
11RELIONclassification
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 94388 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL
Target criteria: gradient-driven minimization of combined map and restraints target
Atomic model building

3D fitting-ID: 1 / Accession code: 4V4F / Initial refinement model-ID: 1 / PDB-ID: 4V4F

4v4f

/ Source name: PDB / Type: experimental model

IDPdb chain-ID
1AA
2AB
3AC
4AD
5AE
6AF
7AG
8AH
9AI
10AJ
11AK

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