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- EMDB-5341: Chemically controlled assembly of 1, 2 and 3-dimensional protein ... -

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Basic information

Entry
Database: EMDB / ID: EMD-5341
TitleChemically controlled assembly of 1, 2 and 3-dimensional protein arrays
Map dataThis is a surface rendered side-view of an engineered RIDC3 nanotube
Sample
  • Sample: an engineered cytochrome cb562, RIDC3
  • Protein or peptide: cytochrome cb562 variant
Keywordsnanotube / self assembly / protein array / ridc3 / metal coordination
Function / homologyCytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / electron transport chain / periplasmic space / electron transfer activity / iron ion binding / heme binding / Soluble cytochrome b562
Function and homology information
Biological speciesEscherichia coli (E. coli)
Methodhelical reconstruction / cryo EM / Resolution: 10.0 Å
AuthorsBrodin JD / Ambroggio XI / Tang C / Parent KN / Baker TS / Tezcan FA
CitationJournal: Nat Chem / Year: 2012
Title: Metal-directed, chemically tunable assembly of one-, two- and three-dimensional crystalline protein arrays.
Authors: Jeffrey D Brodin / X I Ambroggio / Chunyan Tang / Kristin N Parent / Timothy S Baker / F Akif Tezcan /
Abstract: Proteins represent the most sophisticated building blocks available to an organism and to the laboratory chemist. Yet, in contrast to nearly all other types of molecular building blocks, the designed ...Proteins represent the most sophisticated building blocks available to an organism and to the laboratory chemist. Yet, in contrast to nearly all other types of molecular building blocks, the designed self-assembly of proteins has largely been inaccessible because of the chemical and structural heterogeneity of protein surfaces. To circumvent the challenge of programming extensive non-covalent interactions to control protein self-assembly, we have previously exploited the directionality and strength of metal coordination interactions to guide the formation of closed, homoligomeric protein assemblies. Here, we extend this strategy to the generation of periodic protein arrays. We show that a monomeric protein with properly oriented coordination motifs on its surface can arrange, on metal binding, into one-dimensional nanotubes and two- or three-dimensional crystalline arrays with dimensions that collectively span nearly the entire nano- and micrometre scale. The assembly of these arrays is tuned predictably by external stimuli, such as metal concentration and pH.
History
DepositionSep 6, 2011-
Header (metadata) releaseNov 28, 2011-
Map releaseAug 1, 2012-
UpdateAug 1, 2012-
Current statusAug 1, 2012Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.154
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.154
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5341_1.png

Downloads & links

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Map

FileDownload / File: emd_5341.map.gz / Format: CCP4 / Size: 238.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a surface rendered side-view of an engineered RIDC3 nanotube
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.88 Å/pix.
x 400 pix.
= 1152. Å		2.88 Å/pix.
x 400 pix.
= 1152. Å		2.88 Å/pix.
x 400 pix.
= 1152. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.88 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.154 / Movie #1: 0.154
Minimum - Maximum-0.4174749 - 0.8219921
Average (Standard dev.)0.00576641 (±0.08015936)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 1152.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.882.882.88
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z1152.0001152.0001152.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-62-62-62
NX/NY/NZ125125125
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.4170.8220.006

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Supplemental data

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Sample components

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Entire : an engineered cytochrome cb562, RIDC3

EntireName: an engineered cytochrome cb562, RIDC3
Components
  • Sample: an engineered cytochrome cb562, RIDC3
  • Protein or peptide: cytochrome cb562 variant

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Supramolecule #1000: an engineered cytochrome cb562, RIDC3

SupramoleculeName: an engineered cytochrome cb562, RIDC3 / type: sample / ID: 1000 / Oligomeric state: The asymmetric unit is a tetramer / Number unique components: 1
Molecular weightExperimental: 124 KDa / Method: MALDI

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Macromolecule #1: cytochrome cb562 variant

MacromoleculeName: cytochrome cb562 variant / type: protein_or_peptide / ID: 1 / Name.synonym: ridc3 / Oligomeric state: dimer / Recombinant expression: Yes
Source (natural)Organism: Escherichia coli (E. coli) / synonym: Escherichia coli / Location in cell: periplasm
Molecular weightExperimental: 124 KDa / Theoretical: 124 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration1.2 mg/mL
BufferpH: 5.5 / Details: 20 mM MES, 10 mM ZnCl2
GridDetails: home-made lacey carbon with a thin layer of continuous carbon
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 89 K / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: manual plunge-freezer / Method: Blot for 5 seconds before freezing

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Electron microscopy

MicroscopeFEI POLARA 300
TemperatureMin: 90 K / Max: 90 K / Average: 90 K
Alignment procedureLegacy - Astigmatism: at working magnification
DateJun 23, 2011
Image recordingCategory: CCD / Film or detector model: GENERIC GATAN (4k x 4k) / Average electron dose: 15 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 52027 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.3 mm / Nominal defocus max: 3.675 µm / Nominal defocus min: 1.75 µm / Nominal magnification: 39000
Sample stageSpecimen holder: Polara Multi Specimen Holder / Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 25.7 Å
Applied symmetry - Helical parameters - Δ&Phi: 5.3 °
Applied symmetry - Helical parameters - Axial symmetry: C9 (9 fold cyclic)
Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 10.0 Å / Resolution method: OTHER / Software - Name: IHRSR
CTF correctionDetails: ROBEM and IHRSR

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