+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-29856 | |||||||||
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Title | C3HR3_9r_shift4: Extendable repeat protein fiber | |||||||||
Map data | Sharpened map | |||||||||
Sample |
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Keywords | Oligomer / repeat protein / DE NOVO PROTEIN | |||||||||
Biological species | unidentified (others) / synthetic construct (others) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.92 Å | |||||||||
Authors | Bethel NP / Borst AJ | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Chem / Year: 2023 Title: Precisely patterned nanofibres made from extendable protein multiplexes. Authors: Neville P Bethel / Andrew J Borst / Fabio Parmeggiani / Matthew J Bick / T J Brunette / Hannah Nguyen / Alex Kang / Asim K Bera / Lauren Carter / Marcos C Miranda / Ryan D Kibler / Mila Lamb ...Authors: Neville P Bethel / Andrew J Borst / Fabio Parmeggiani / Matthew J Bick / T J Brunette / Hannah Nguyen / Alex Kang / Asim K Bera / Lauren Carter / Marcos C Miranda / Ryan D Kibler / Mila Lamb / Xinting Li / Banumathi Sankaran / David Baker / Abstract: Molecular systems with coincident cyclic and superhelical symmetry axes have considerable advantages for materials design as they can be readily lengthened or shortened by changing the length of the ...Molecular systems with coincident cyclic and superhelical symmetry axes have considerable advantages for materials design as they can be readily lengthened or shortened by changing the length of the constituent monomers. Among proteins, alpha-helical coiled coils have such symmetric, extendable architectures, but are limited by the relatively fixed geometry and flexibility of the helical protomers. Here we describe a systematic approach to generating modular and rigid repeat protein oligomers with coincident C to C and superhelical symmetry axes that can be readily extended by repeat propagation. From these building blocks, we demonstrate that a wide range of unbounded fibres can be systematically designed by introducing hydrophilic surface patches that force staggering of the monomers; the geometry of such fibres can be precisely tuned by varying the number of repeat units in the monomer and the placement of the hydrophilic patches. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_29856.map.gz | 87 MB | EMDB map data format | |
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Header (meta data) | emd-29856-v30.xml emd-29856.xml | 17.3 KB 17.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_29856_fsc.xml | 11.8 KB | Display | FSC data file |
Images | emd_29856.png | 55.3 KB | ||
Filedesc metadata | emd-29856.cif.gz | 5.4 KB | ||
Others | emd_29856_additional_1.map.gz emd_29856_half_map_1.map.gz emd_29856_half_map_2.map.gz | 14.1 MB 157 MB 157 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-29856 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-29856 | HTTPS FTP |
-Validation report
Summary document | emd_29856_validation.pdf.gz | 1.3 MB | Display | EMDB validaton report |
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Full document | emd_29856_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | emd_29856_validation.xml.gz | 20.6 KB | Display | |
Data in CIF | emd_29856_validation.cif.gz | 26.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29856 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29856 | HTTPS FTP |
-Related structure data
Related structure data | 8g8iMC 8eovC 8eoxC 8eozC 8erwC 8ga9C 8gaaC 8gaqC C: citing same article (ref.) M: atomic model generated by this map |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_29856.map.gz / Format: CCP4 / Size: 169.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Sharpened map | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.885 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Unsharpened map
File | emd_29856_additional_1.map | ||||||||||||
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Annotation | Unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map A
File | emd_29856_half_map_1.map | ||||||||||||
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Annotation | Half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map B
File | emd_29856_half_map_2.map | ||||||||||||
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Annotation | Half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : C3HR3_8r
Entire | Name: C3HR3_8r |
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Components |
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-Supramolecule #1: C3HR3_8r
Supramolecule | Name: C3HR3_8r / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: unidentified (others) |
Molecular weight | Theoretical: 141 KDa |
-Macromolecule #1: C3HR3_9r_shift4
Macromolecule | Name: C3HR3_9r_shift4 / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 55.922121 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MVYERLKELI EENPEIQEIL ELWKFIGRED VVEKLFEVIK WAVEEGGNNM VFISLLKEIL SNPEIFEILL KWVDIGREDV VKKLFSVIK QAVEDGGNNM VFLSLLKELL SNPEIFEILL LWVEINREDV VKKFFDVIKW AVERGGNNPK FLSLLKLILS N PEIFKILL ...String: MVYERLKELI EENPEIQEIL ELWKFIGRED VVEKLFEVIK WAVEEGGNNM VFISLLKEIL SNPEIFEILL KWVDIGREDV VKKLFSVIK QAVEDGGNNM VFLSLLKELL SNPEIFEILL LWVEINREDV VKKFFDVIKW AVERGGNNPK FLSLLKLILS N PEIFKILL LWVYENKEEV VKKLFDVLLY AVKEGGDNEK FLELLKEILS NPEIFEILLE WVEENKEDVV KKLFDVIKYA VE RGGDNEK FYELLKLLLS NPEIFKILLE WVEINKEDVV KKFFDVIKWA VEEGGDNPVF YRLLKLILSN PEIFKILLEW VDI NNEDVV KKLFSVIKQA VEDGGNNMVF IDLLELILSN PEIFEILLLW VHINREDVVK KLFDVIKWAV EDGGNNMVFI HLLR KLLSN PEIFEILLLW VDIGREEVVK KFFEKVLEAV KEGGNDMIEI KKLEEILLDP EKFEELLLEV GSLEHHHHHH |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS GLACIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm |