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- EMDB-29602: Three component pH responsive antibody octahedra escape lysosomal... -
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Open data
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Basic information
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Title | Three component pH responsive antibody octahedra escape lysosomal degradation | |||||||||
![]() | Bfactor sharpening -230 | |||||||||
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![]() | octahedra / oligomer / de novo design / rosetta / cryoEM / interface / cellular delivery / DE NOVO PROTEIN | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.05 Å | |||||||||
![]() | Borst AJ / Baker D | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Three component pH responsive antibody octahedra escape lysosomal degradation Authors: Yang EC / Divine R / Miranda M / Borst AJ / Baker D | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 68.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 17.8 KB 17.8 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 11 KB | Display | ![]() |
Images | ![]() | 61.5 KB | ||
Filedesc metadata | ![]() | 4.6 KB | ||
Others | ![]() ![]() ![]() ![]() | 65.9 MB 128.8 MB 126.9 MB 126.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 996.8 KB | Display | ![]() |
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Full document | ![]() | 996.4 KB | Display | |
Data in XML | ![]() | 19.3 KB | Display | |
Data in CIF | ![]() | 25 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | Bfactor sharpening -230 | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.68 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Un-sharpened Map
File | emd_29602_additional_1.map | ||||||||||||
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Annotation | Un-sharpened Map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Auto-sharpened map
File | emd_29602_additional_2.map | ||||||||||||
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Annotation | Auto-sharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map A
File | emd_29602_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_29602_half_map_2.map | ||||||||||||
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Annotation | Half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : O432-17
Entire | Name: O432-17 |
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Components |
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-Supramolecule #1: O432-17
Supramolecule | Name: O432-17 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: synthetic construct (others) |
-Macromolecule #1: ECYplug059A
Macromolecule | Name: ECYplug059A / type: other / ID: 1 / Classification: other |
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Sequence | String: MSEEKIEKLL EELTASTAEL KRATASLRAI TEELKKNPSE DALVEHNRAI VEHNAIIVEN NRIIATVLLA IVAAIATNEA TLAADKAKEA GASEVAKLAK KVLEEAEELA KENDSEEALK VVKAIADAAK AAAEAAREGK TEVAKLALKV LEEAIELAKE NRSEEALKVV ...String: MSEEKIEKLL EELTASTAEL KRATASLRAI TEELKKNPSE DALVEHNRAI VEHNAIIVEN NRIIATVLLA IVAAIATNEA TLAADKAKEA GASEVAKLAK KVLEEAEELA KENDSEEALK VVKAIADAAK AAAEAAREGK TEVAKLALKV LEEAIELAKE NRSEEALKVV REIARAALAA AQAAEEGKTE VAKLALKVLE EAIELAKENR SEEALKVVRE IARAALAAAQ AAEEEGKTEV AKLALEVLEQ AIEAAKLQRS ERALEMVREI ARAALEAARN AEGGRSDRAR AILASLKVSI IVVKLKSSGT SEEEILRIVL KIIKELRKTA KESGQSASYI ATMEAEIVKA IDYALDLSGT SGSWSGLEHH HHHH |
-Macromolecule #2: ECYplug59B
Macromolecule | Name: ECYplug59B / type: other / ID: 2 / Classification: other |
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Sequence | String: MFNKDQQSAF YEILNMPNLN EALRNGFIQL LKDDPSKSEV ILTAALIAAK LSEDIRTLKE SGSSYEEIAE RVARAVALLV ALLKTNGVSE DEIALAVALI ISAVIQTLKE SGSSYEVIAE IVARIVAEIV EALKRSGTSE DEIAEIVARV ISEVIRTLKE SGSSYEVIAE ...String: MFNKDQQSAF YEILNMPNLN EALRNGFIQL LKDDPSKSEV ILTAALIAAK LSEDIRTLKE SGSSYEEIAE RVARAVALLV ALLKTNGVSE DEIALAVALI ISAVIQTLKE SGSSYEVIAE IVARIVAEIV EALKRSGTSE DEIAEIVARV ISEVIRTLKE SGSSYEVIAE IVARIVAEIV EALKRSGTSE DEIAKIVARV IAEVLRTLKE SGSSEEVIKE IVARIITEIK EALKRSGTSE DEIELITLMI EAALEIAKLK SSGSEYEEIA EDVARRIAEL VEKLKRDGTS AVEIAKIVAA IISAVIAMLK ASGSSYEVIA EIVARIVAEI VEALKRSGTS AAIIALIVAL VISEVIRTLK ESGSSFEVIL EIVIRIVLEI IEALKRSGTS EQDVMLIVMA VLLVVLATLQ LSGSGSWSGL EHHHHHH |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.4 mg/mL |
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Buffer | pH: 7.5 |
Grid | Model: C-flat-1.2/1.3 / Support film - Material: CARBON |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 63.775 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |