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- PDB-6ib4: Structure of right-handed protein cage consisting of 24 eleven-me... -

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Basic information

Entry
Database: PDB / ID: 6ib4
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 / homologyTranscription attenuation protein MtrB / Tryptophan RNA-binding attenuator protein-like domain superfamily / Tryptophan RNA-binding attenuator protein domain / Tryptophan RNA-binding attenuator protein / DNA-templated transcription, termination / regulation of transcription, DNA-templated / RNA binding / identical protein binding / Transcription attenuation protein MtrB
Function and homology information
Specimen sourceGeobacillus stearothermophilus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.7 Å resolution
AuthorsMalay, A.D. / Miyazaki, N. / Biela, A.P. / Iwasaki, K. / Heddle, J.G.
Funding supportPoland , Japan , 5 items
OrganizationGrant numberCountry
NCN 2016/20/W/NZ1/00095Poland
FNP Homing/2016-2/20Poland
Japan Society for the Promotion of ScienceNo. 2556023Japan
MRPO.05.01.00-12-013/15Poland
Japan Agency for Medical Research and Development (AMED)Japan
CitationJournal: To Be Published
Title: Structure of right-handed protein cage consisting of 24 eleven-membered ring proteins held together by gold (I) bridges.
Authors: Malay, A.D. / Miyazaki, N. / Biela, A.P. / Iwasaki, K. / Heddle, J.G.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 28, 2018 / Release: Mar 6, 2019

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Structure visualization

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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
Polyers2,154,563264
Non-polymers23,636120
Water0
1


  • idetical with deposited unit
  • defined by software
  • Evidence: gel filtration, mass spectrometry, native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)456380
ΔGint (kcal/M)-3538
Surface area (Å2)609440
MethodPISA

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Components

#1: Protein/peptide ...
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: (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 / Formula: Au / Gold

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Designed protein cage consisting of C11-symmetric TRAP proteins coordinated by Au+1 ionsDesign
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) / Plasmid: pET21b / Strain: BL21(DE3)
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 kelvins / Details: 3.0 s blotting time

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
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
9PHENIXmodel refinement
12RELIONclassification
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 176463 / Symmetry type: POINT
Atomic model buildingRef protocol: OTHER / Ref space: REAL
Target criteria: gradient-driven minimization of combined map and restraints target
Atomic model building
IDPDB-IDPdb chain ID 3D fitting ID
14V4FAA1
24V4FAB1
34V4FAC1
44V4FAD1
54V4FAE1
64V4FAF1
74V4FAG1
84V4FAH1
94V4FAI1
104V4FAJ1
114V4FAK1

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