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- EMDB-58685: Raw map of the disulfide linked complex of T. ramosa IgA peptidas... -

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Basic information

Entry
Database: EMDB / ID: EMD-58685
TitleRaw map of the disulfide linked complex of T. ramosa IgA peptidase (IgAse2-4) with human IgA2 Fab' in precatalytic conformation
Map dataRaw map used for composite generation
Sample
  • Complex: Disulfide linked complex of T. ramosa IgA peptidase (IgAse) with human IgA2 Fab
    • Complex: Monomeric IgA peptidase S328-T806 with mutations E540A C414S D434C C476S C591S
    • Complex: IgA2(m1) Heavy-chain alpha domains 1 and 2 including the hinge region (Q1-P226).
    • Complex: IgA Lambda Light-chain domains 1 and 2 (Q1-T214) with mutations S127C and C216S.
KeywordsProtease-substrate complex / Metallopeptidase / Metzincin / HYDROLASE
Biological speciesThomasclavelia ramosa (bacteria) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsRamirez-Larrota JS / Gragera M / Eckhard U / Gomis-Ruth FX
Funding support Spain, 4 items
OrganizationGrant numberCountry
Agencia Estatal de Investigacion (AEI)PRE2020-096731 Spain
Agencia Estatal de Investigacion (AEI)PID2019-107725RB-I00 Spain
Agencia Estatal de Investigacion (AEI)RYC2020-029773-I Spain
Agencia Estatal de Investigacion (AEI)CNS2024-154537 Spain
CitationJournal: To Be Published
Title: Raw map of the disulfide linked complex of T. ramosa IgA peptidase (IgAse2-4) with human IgA2 Fab' in precatalytic conformation
Authors: Ramirez-Larrota JS / Gragera M / Eckhard U / Gomis-Ruth FX
History
DepositionJun 25, 2026-
Header (metadata) releaseOct 14, 2026-
Map releaseOct 14, 2026-
UpdateOct 14, 2026-
Current statusOct 14, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_58685.png

Downloads & links

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Map

FileDownload / File: emd_58685.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRaw map used for composite generation
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 360 pix.
= 262.8 Å		0.73 Å/pix.
x 360 pix.
= 262.8 Å		0.73 Å/pix.
x 360 pix.
= 262.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.73 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0009
Minimum - Maximum-0.003985056 - 0.007922518
Average (Standard dev.)0.000001566905 (±0.00014296235)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 262.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_58685_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_58685_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_58685_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Disulfide linked complex of T. ramosa IgA peptidase (IgAse) with ...

EntireName: Disulfide linked complex of T. ramosa IgA peptidase (IgAse) with human IgA2 Fab
Components
  • Complex: Disulfide linked complex of T. ramosa IgA peptidase (IgAse) with human IgA2 Fab
    • Complex: Monomeric IgA peptidase S328-T806 with mutations E540A C414S D434C C476S C591S
    • Complex: IgA2(m1) Heavy-chain alpha domains 1 and 2 including the hinge region (Q1-P226).
    • Complex: IgA Lambda Light-chain domains 1 and 2 (Q1-T214) with mutations S127C and C216S.

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Supramolecule #1: Disulfide linked complex of T. ramosa IgA peptidase (IgAse) with ...

SupramoleculeName: Disulfide linked complex of T. ramosa IgA peptidase (IgAse) with human IgA2 Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Details: Human IgA2 recombinantly expressed in Expi293F cells and IgA peptidase recobinantly expressed in E. coli.
Source (natural)Organism: Thomasclavelia ramosa (bacteria)

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Supramolecule #2: Monomeric IgA peptidase S328-T806 with mutations E540A C414S D434...

SupramoleculeName: Monomeric IgA peptidase S328-T806 with mutations E540A C414S D434C C476S C591S
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Thomasclavelia ramosa (bacteria)

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Supramolecule #3: IgA2(m1) Heavy-chain alpha domains 1 and 2 including the hinge re...

SupramoleculeName: IgA2(m1) Heavy-chain alpha domains 1 and 2 including the hinge region (Q1-P226).
type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: IgA Lambda Light-chain domains 1 and 2 (Q1-T214) with mutations S...

SupramoleculeName: IgA Lambda Light-chain domains 1 and 2 (Q1-T214) with mutations S127C and C216S.
type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Homo sapiens (human)

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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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.7.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Scipion (ver. 3) / Number images used: 105795
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: PDB / Chain - Initial model type: experimental model

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