+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-29680 | |||||||||
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Title | C6HR1_8r: Extendable repeat protein heptamer | |||||||||
Map data | Sharpened map | |||||||||
Sample |
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Keywords | Oligomer / repeat protein / DE NOVO PROTEIN | |||||||||
Biological species | unidentified (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.18 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_29680.map.gz | 117.9 MB | EMDB map data format | |
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Header (meta data) | emd-29680-v30.xml emd-29680.xml | 15.8 KB 15.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_29680_fsc.xml | 10.6 KB | Display | FSC data file |
Images | emd_29680.png | 58.6 KB | ||
Filedesc metadata | emd-29680.cif.gz | 4.7 KB | ||
Others | emd_29680_additional_1.map.gz emd_29680_half_map_1.map.gz emd_29680_half_map_2.map.gz | 61.5 MB 116 MB 116 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-29680 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-29680 | HTTPS FTP |
-Validation report
Summary document | emd_29680_validation.pdf.gz | 954 KB | Display | EMDB validaton report |
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Full document | emd_29680_full_validation.pdf.gz | 953.6 KB | Display | |
Data in XML | emd_29680_validation.xml.gz | 19.1 KB | Display | |
Data in CIF | emd_29680_validation.cif.gz | 24.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29680 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29680 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_29680.map.gz / Format: CCP4 / Size: 125 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_29680_additional_1.map | ||||||||||||
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Annotation | Unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map B
File | emd_29680_half_map_1.map | ||||||||||||
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Annotation | Half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map A
File | emd_29680_half_map_2.map | ||||||||||||
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Annotation | Half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : C6HR1_8r
Entire | Name: C6HR1_8r |
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Components |
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-Supramolecule #1: C6HR1_8r
Supramolecule | Name: C6HR1_8r / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: unidentified (others) |
Molecular weight | Theoretical: 302.92 KDa |
-Macromolecule #1: C6HR1_8r
Macromolecule | Name: C6HR1_8r / type: protein_or_peptide / ID: 1 / Enantiomer: DEXTRO |
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Source (natural) | Organism: unidentified (others) |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MPEEVKRKIV EVYEAKEEGT PNEELIKRLK ELVEELVELA KEECDPSCVD LAIVCVYEMK ELGMPNEELI ELLEKLVKVL KTLALILCDP RVVDKAIVCV YEMKELGMPN EELIKLLKEL VKVLKILALI NSDPRVVDKA IVCVYEMKEL GMPNEELIKL LKELVKVLKI ...String: MPEEVKRKIV EVYEAKEEGT PNEELIKRLK ELVEELVELA KEECDPSCVD LAIVCVYEMK ELGMPNEELI ELLEKLVKVL KTLALILCDP RVVDKAIVCV YEMKELGMPN EELIKLLKEL VKVLKILALI NSDPRVVDKA IVCVYEMKEL GMPNEELIKL LKELVKVLKI LALINSDPRV VDKAIVCVYE MKELGMPNEE LIKLLKELVK VLKILALINS DPRVVDKAIV CVYEMKELGM PNEELIKLLK ELVKVLKILA LINSDPKVVD KAIVCVYEMK ELGEPNEELI KLLSELVKVL KTLALINKDP SVVEKALVCV EEMEELGMPE EELKKLYEEL VKVLEILEKI LFDERVRELA EKCRERIKGS WLEHHHHHH |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle 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: 1.8 µm / Nominal defocus min: 0.7000000000000001 µm |