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- EMDB-29602: Three component pH responsive antibody octahedra escape lysosomal... -

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Basic information

Entry
Database: EMDB / ID: EMD-29602
TitleThree component pH responsive antibody octahedra escape lysosomal degradation
Map dataBfactor sharpening -230
Sample
  • Complex: O432-17
    • Other: ECYplug059A
    • Other: ECYplug59B
Keywordsoctahedra / oligomer / de novo design / rosetta / cryoEM / interface / cellular delivery / DE NOVO PROTEIN
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.05 Å
AuthorsBorst AJ / Baker D
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: To Be Published
Title: Three component pH responsive antibody octahedra escape lysosomal degradation
Authors: Yang EC / Divine R / Miranda M / Borst AJ / Baker D
History
DepositionJan 27, 2023-
Header (metadata) releaseJan 31, 2024-
Map releaseJan 31, 2024-
UpdateJan 31, 2024-
Current statusJan 31, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29602.png

Downloads & links

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Map

FileDownload / File: emd_29602.map.gz / Format: CCP4 / Size: 137.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBfactor sharpening -230
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.68 Å/pix.
x 330 pix.
= 554.4 Å		1.68 Å/pix.
x 330 pix.
= 554.4 Å		1.68 Å/pix.
x 330 pix.
= 554.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.68 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.162
Minimum - Maximum-0.11840915 - 0.367165
Average (Standard dev.)0.00075662456 (±0.023002576)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions330330330
Spacing330330330
CellA=B=C: 554.39996 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Un-sharpened Map

Fileemd_29602_additional_1.map
AnnotationUn-sharpened Map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Auto-sharpened map

Fileemd_29602_additional_2.map
AnnotationAuto-sharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_29602_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_29602_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : O432-17

EntireName: O432-17
Components
  • Complex: O432-17
    • Other: ECYplug059A
    • Other: ECYplug59B

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Supramolecule #1: O432-17

SupramoleculeName: O432-17 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: synthetic construct (others)

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Macromolecule #1: ECYplug059A

MacromoleculeName: ECYplug059A / type: other / ID: 1 / Classification: other
SequenceString: 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

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Macromolecule #2: ECYplug59B

MacromoleculeName: ECYplug59B / type: other / ID: 2 / Classification: other
SequenceString: 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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.4 mg/mL
BufferpH: 7.5
GridModel: C-flat-1.2/1.3 / Support film - Material: CARBON
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 63.775 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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

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Image processing

Particle selectionNumber selected: 88357
Startup modelType of model: NONE / Details: Ab initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.05 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 50017
Initial angle assignmentType: NOT APPLICABLE / Software - Name: cryoSPARC (ver. 3.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1.2)
FSC plot (resolution estimation)

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