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- EMDB-58714: Disulfide linked complex of T. ramosa IgA peptidase (IgAse2-4) wi... -

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Basic information

Entry
Database: EMDB / ID: EMD-58714
TitleDisulfide linked complex of T. ramosa IgA peptidase (IgAse2-4) with human IgA2 Fab' in recognition conformation
Map data
Sample
  • Complex: Disulfide linked complex of T. ramosa IgA peptidase (IgAse) with human IgA2 Fab
    • Complex: Monomeric IgA peptidase (E330-T806) with mutations E540A C414S D434C C476S C591S
      • Protein or peptide: IgA protease
    • Complex: IgA2 Heavy Chain alfa domain 1 and 2 including the hinge region (V2-P225).
      • Protein or peptide: IgA2(m1) Immunoglobulin Heavy Alpha Chain domains 1 and 2 including the hinge region (V2-P225).
    • Complex: IgA2 Lambda Light Chain domains 1 and 2 (S2-T214) with mutations S127C C216S.
      • Protein or peptide: IgA2 Lambda Light Chain domains 1 and 2 (S2-T214) with mutations S127C C216S
  • Ligand: ZINC ION
  • Ligand: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
  • Ligand: CHLORIDE ION
  • Ligand: GLYCINE
  • Ligand: water
KeywordsProtease / Metallopeptidase / Metzincin / HYDROLASE
Function / homology
Function and homology information


metallopeptidase activity
Similarity search - Function
Domain of unknown function DUF6273 / Domain of unknown function (DUF6273) / Peptidase M64, IgA / IgA Peptidase M64 / Carbohydrate binding X2 domain / Carbohydrate binding domain X2 / LPXTG cell wall anchor motif / LPXTG cell wall anchor domain / Metallopeptidase, catalytic domain superfamily / Immunoglobulin E-set / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesThomasclavelia ramosa (bacteria) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 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: Disulfide linked complex of T. ramosa IgA peptidase (IgAse2-4) with human IgA2 Fab' in recognition conformation
Authors: Ramirez-Larrota JS / Gragera M / Eckhard U / Gomis-Ruth FX
History
DepositionJun 29, 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_58714.png

Downloads & links

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Map

FileDownload / File: emd_58714.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
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: 0.000781
Minimum - Maximum-0.004472185 - 0.008005544
Average (Standard dev.)0.0000016031081 (±0.0001413149)
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_58714_additional_1.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 (E330-T806) with mutations E540A C414S D434C C476S C591S
      • Protein or peptide: IgA protease
    • Complex: IgA2 Heavy Chain alfa domain 1 and 2 including the hinge region (V2-P225).
      • Protein or peptide: IgA2(m1) Immunoglobulin Heavy Alpha Chain domains 1 and 2 including the hinge region (V2-P225).
    • Complex: IgA2 Lambda Light Chain domains 1 and 2 (S2-T214) with mutations S127C C216S.
      • Protein or peptide: IgA2 Lambda Light Chain domains 1 and 2 (S2-T214) with mutations S127C C216S
  • Ligand: ZINC ION
  • Ligand: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
  • Ligand: CHLORIDE ION
  • Ligand: GLYCINE
  • Ligand: water

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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 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 (E330-T806) with mutations E540A C414S D4...

SupramoleculeName: Monomeric IgA peptidase (E330-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 Heavy Chain alfa domain 1 and 2 including the hinge region (...

SupramoleculeName: IgA2 Heavy Chain alfa domain 1 and 2 including the hinge region (V2-P225).
type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: IgA2 Lambda Light Chain domains 1 and 2 (S2-T214) with mutations ...

SupramoleculeName: IgA2 Lambda Light Chain domains 1 and 2 (S2-T214) with mutations S127C C216S.
type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: IgA protease

MacromoleculeName: IgA protease / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thomasclavelia ramosa (bacteria)
Molecular weightTheoretical: 63.825777 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSTEQSIQL TLGPWYSNDG KYSNPTIPVY TIQKTRSDTE NMVVVVCGEG YTKSQQGKFI NDVKRLWQDA MKYEPYRSYA DRFNVYALS TASESTFDNG GSTFFDVIVC KYNSPVISNN LHGSQWKNHI FERCIGPEFI EKIHDAHIKK KSDPNTIPSG S EYEPYYYV ...String:
MGSTEQSIQL TLGPWYSNDG KYSNPTIPVY TIQKTRSDTE NMVVVVCGEG YTKSQQGKFI NDVKRLWQDA MKYEPYRSYA DRFNVYALS TASESTFDNG GSTFFDVIVC KYNSPVISNN LHGSQWKNHI FERCIGPEFI EKIHDAHIKK KSDPNTIPSG S EYEPYYYV HDYIAQFAMV VNTKSDFGGA YNNREYGFHY FISPSDSYRA SKTFAHAFGH GLLGLGDEYS NGYLLDDKEL KS LNLSSVE DPEKIKWRQL LGFRNTYTSR NAYGSKMLVS SYECIMRDTN YQFCEVCRLQ GFKRMSQLVK DVDLYVATPE VKE YTGAYS KPSDFTDLET SSYYNYTYNR NDRLLSGNSK SRFNTNMNGK KIELRTVIQN ISDKNARQLK FKMWIKHSDG SVAT DSSGN PLQTVQTFDI PVWNDKANFW PLGALDHIKS DFNSGLKSCS LIYQIPSDAQ LKSGDTVAFQ VLDENGNVLA DDNTE TQRY TTVSIQYKFE DGSEIPNTAG GTFTVPYGTK LDLTPAKTLY DYEFIKVDGL NKPIVSDGTV VTYYYKNLEH HHHHH

UniProtKB: IgA protease

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Macromolecule #2: IgA2(m1) Immunoglobulin Heavy Alpha Chain domains 1 and 2 includi...

MacromoleculeName: IgA2(m1) Immunoglobulin Heavy Alpha Chain domains 1 and 2 including the hinge region (V2-P225).
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.768512 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLVQSGAE VRNPGASVKV SCKASGYTFT SYAIHWVRQA PGHRLEWVGR INTDNGNTKY SQKFHGRVAL SRDTSASTTY MDLSSLNSE DTAVYYCARA FYYSSGVMFD SWGQGALVTV SSASPTSPKV FPLSLDSTPQ DGNVVVACLV QGFFPQEPLS V TWSESGQN ...String:
QVQLVQSGAE VRNPGASVKV SCKASGYTFT SYAIHWVRQA PGHRLEWVGR INTDNGNTKY SQKFHGRVAL SRDTSASTTY MDLSSLNSE DTAVYYCARA FYYSSGVMFD SWGQGALVTV SSASPTSPKV FPLSLDSTPQ DGNVVVACLV QGFFPQEPLS V TWSESGQN VTARNFPPSQ DASGDLYTTS SQLTLPATQC PDGKSVTCHV KHYTNPSQDV TVPCPVPPPP PAIAHHHHHH

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Macromolecule #3: IgA2 Lambda Light Chain domains 1 and 2 (S2-T214) with mutations ...

MacromoleculeName: IgA2 Lambda Light Chain domains 1 and 2 (S2-T214) with mutations S127C C216S
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.786102 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QSALTQPPSV SGAPGQRVSI SCTGGSSNFG AGYDVHWYQQ LPATAPKLLI YGNNNRPSGV PDRFSGSKSG TSASLAITGL QAEDEGDYF CQSFDTSLSG WIFGGGTKLT VLGQPKAAPS VTLFPPSCEE LQANKATLVC LISDFYPGAV TVAWKADSSP V KAGVETTT ...String:
QSALTQPPSV SGAPGQRVSI SCTGGSSNFG AGYDVHWYQQ LPATAPKLLI YGNNNRPSGV PDRFSGSKSG TSASLAITGL QAEDEGDYF CQSFDTSLSG WIFGGGTKLT VLGQPKAAPS VTLFPPSCEE LQANKATLVC LISDFYPGAV TVAWKADSSP V KAGVETTT PSKQSNNKYA ASSYLSLTPE QWKSHRSYSC QVTHEGSTVE KTVAPTESS

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Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #5: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

MacromoleculeName: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / type: ligand / ID: 5 / Number of copies: 1 / Formula: TRS
Molecular weightTheoretical: 122.143 Da
Chemical component information

ChemComp-TRS:
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / pH buffer*YM

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Macromolecule #6: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: CL
Molecular weightTheoretical: 35.453 Da

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Macromolecule #7: GLYCINE

MacromoleculeName: GLYCINE / type: ligand / ID: 7 / Number of copies: 2 / Formula: GLY
Molecular weightTheoretical: 75.067 Da
Chemical component information

ChemComp-GLY:
GLYCINE

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Macromolecule #8: water

MacromoleculeName: water / type: ligand / ID: 8 / Number of copies: 80 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 3.1 Å / Resolution method: OTHER / Software - Name: Scipion (ver. 3) / Details: dFSC_model 0.5 / Number images used: 98115
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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