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- EMDB-22204: Streptococcus Pneumoniae IgA1 Protease with IgA1 substrate -

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Basic information

Entry
Database: EMDB / ID: EMD-22204
TitleStreptococcus Pneumoniae IgA1 Protease with IgA1 substrate
Map dataIgA1 Protease with IgA1 substrate
Sample
  • Complex: IgA1 Protease and IgA1 substrate
    • Complex: Immunoglobulin A1 protease
      • Protein or peptide: Immunoglobulin A1 protease
    • Complex: Immunoglobulin heavy constant alpha 1, Immunoglobulin alpha-1 light chain, Immunoglobulin alpha-1 heavy chain
      • Protein or peptide: Immunoglobulin heavy constant alpha 1
      • Protein or peptide: Immunoglobulin alpha-1 light chain
      • Protein or peptide: Immunoglobulin alpha-1 heavy chain
KeywordsIgA1 / Complex / Protease / metalloprotease / IMMUNE SYSTEM
Function / homology
Function and homology information


IgA-specific metalloendopeptidase / secretory dimeric IgA immunoglobulin complex / monomeric IgA immunoglobulin complex / secretory IgA immunoglobulin complex / IgA immunoglobulin complex / glomerular filtration / IgG immunoglobulin complex / immunoglobulin complex, circulating / positive regulation of respiratory burst / complement activation, classical pathway ...IgA-specific metalloendopeptidase / secretory dimeric IgA immunoglobulin complex / monomeric IgA immunoglobulin complex / secretory IgA immunoglobulin complex / IgA immunoglobulin complex / glomerular filtration / IgG immunoglobulin complex / immunoglobulin complex, circulating / positive regulation of respiratory burst / complement activation, classical pathway / Scavenging of heme from plasma / antigen binding / Cell surface interactions at the vascular wall / B cell receptor signaling pathway / metalloendopeptidase activity / antibacterial humoral response / blood microparticle / adaptive immune response / immune response / proteolysis / extracellular space / extracellular exosome / extracellular region / zinc ion binding / membrane / plasma membrane
Similarity search - Function
Peptidase M26, N-terminal domain / GLUG / Peptidase M26, C-terminal domain / M26 IgA1-specific Metallo-endopeptidase N-terminal region / M26 IgA1-specific Metallo-endopeptidase C-terminal region / The GLUG motif / G5 domain / G5 domain / G5 domain profile. / G5 ...Peptidase M26, N-terminal domain / GLUG / Peptidase M26, C-terminal domain / M26 IgA1-specific Metallo-endopeptidase N-terminal region / M26 IgA1-specific Metallo-endopeptidase C-terminal region / The GLUG motif / G5 domain / G5 domain / G5 domain profile. / G5 / YSIRK type signal peptide / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Immunoglobulin / Immunoglobulin domain / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / : / Neutral zinc metallopeptidases, zinc-binding region signature. / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Immunoglobulin heavy constant alpha 1 / Immunoglobulin A1 protease
Similarity search - Component
Biological speciesStreptococcus pneumoniae (strain ATCC BAA-255 / R6) (bacteria) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsEisenmesser EZ / Zheng H
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21 AI146295 United States
CitationJournal: Nat Commun / Year: 2020
Title: Mechanism and inhibition of Streptococcus pneumoniae IgA1 protease.
Authors: Zhiming Wang / Jeremy Rahkola / Jasmina S Redzic / Ying-Chih Chi / Norman Tran / Todd Holyoak / Hongjin Zheng / Edward Janoff / Elan Eisenmesser /
Abstract: Opportunistic pathogens such as Streptococcus pneumoniae secrete a giant metalloprotease virulence factor responsible for cleaving host IgA1, yet the molecular mechanism has remained unknown since ...Opportunistic pathogens such as Streptococcus pneumoniae secrete a giant metalloprotease virulence factor responsible for cleaving host IgA1, yet the molecular mechanism has remained unknown since their discovery nearly 30 years ago despite the potential for developing vaccines that target these enzymes to block infection. Here we show through a series of cryo-electron microscopy single particle reconstructions how the Streptococcus pneumoniae IgA1 protease facilitates IgA1 substrate recognition and how this can be inhibited. Specifically, the Streptococcus pneumoniae IgA1 protease subscribes to an active-site-gated mechanism where a domain undergoes a 10.0 Å movement to facilitate cleavage. Monoclonal antibody binding inhibits this conformational change, providing a direct means to block infection at the host interface. These structural studies explain decades of biological and biochemical studies and provides a general strategy to block Streptococcus pneumoniae IgA1 protease activity to potentially prevent infection.
History
DepositionJun 23, 2020-
Header (metadata) releaseJan 20, 2021-
Map releaseJan 20, 2021-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.15
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.15
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6xja
  • Surface level: 0.15
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22204.png

Downloads & links

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Map

FileDownload / File: emd_22204.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIgA1 Protease with IgA1 substrate
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.59 Å/pix.
x 224 pix.
= 356.16 Å		1.59 Å/pix.
x 224 pix.
= 356.16 Å		1.59 Å/pix.
x 224 pix.
= 356.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.59 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15 / Movie #1: 0.15
Minimum - Maximum-0.4006242 - 0.75089216
Average (Standard dev.)0.00052375253 (±0.024103222)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions224224224
Spacing224224224
CellA=B=C: 356.15997 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.591.591.59
M x/y/z224224224
origin x/y/z0.0000.0000.000
length x/y/z356.160356.160356.160
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ350350350
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS224224224
D min/max/mean-0.4010.7510.001

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Supplemental data

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Sample components

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Entire : IgA1 Protease and IgA1 substrate

EntireName: IgA1 Protease and IgA1 substrate
Components
  • Complex: IgA1 Protease and IgA1 substrate
    • Complex: Immunoglobulin A1 protease
      • Protein or peptide: Immunoglobulin A1 protease
    • Complex: Immunoglobulin heavy constant alpha 1, Immunoglobulin alpha-1 light chain, Immunoglobulin alpha-1 heavy chain
      • Protein or peptide: Immunoglobulin heavy constant alpha 1
      • Protein or peptide: Immunoglobulin alpha-1 light chain
      • Protein or peptide: Immunoglobulin alpha-1 heavy chain

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Supramolecule #1: IgA1 Protease and IgA1 substrate

SupramoleculeName: IgA1 Protease and IgA1 substrate / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 300 KDa

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Supramolecule #2: Immunoglobulin A1 protease

SupramoleculeName: Immunoglobulin A1 protease / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Streptococcus pneumoniae (strain ATCC BAA-255 / R6) (bacteria)
Strain: ATCC BAA-255 / R6

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Supramolecule #3: Immunoglobulin heavy constant alpha 1, Immunoglobulin alpha-1 lig...

SupramoleculeName: Immunoglobulin heavy constant alpha 1, Immunoglobulin alpha-1 light chain, Immunoglobulin alpha-1 heavy chain
type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Immunoglobulin A1 protease

MacromoleculeName: Immunoglobulin A1 protease / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: IgA-specific metalloendopeptidase
Source (natural)Organism: Streptococcus pneumoniae (strain ATCC BAA-255 / R6) (bacteria)
Strain: ATCC BAA-255 / R6
Molecular weightTheoretical: 145.926625 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GNTTSENGQT EPEKKLELRN VSDIELYSQT NGTYRQHVSL DGIPENTDTY FVKVKSSAFK DVYIPVASIT EEKRNGQSVY KITAKAEKL QQELENKYVD NFTFYLDKKA KEENTNFTSF SNLVKAINQN PSGTYHLAAS LNANEVELGP DERSYIKDTF T GRLIGEKD ...String:
GNTTSENGQT EPEKKLELRN VSDIELYSQT NGTYRQHVSL DGIPENTDTY FVKVKSSAFK DVYIPVASIT EEKRNGQSVY KITAKAEKL QQELENKYVD NFTFYLDKKA KEENTNFTSF SNLVKAINQN PSGTYHLAAS LNANEVELGP DERSYIKDTF T GRLIGEKD GKNYAIYNLK KPLFENLSGA TVEKLSLKNV AISGKNDIGS LANEATNGTK IKQVHVDGVL AGERGVGGLL AK ADQSSIA ESSFKGRIVN TYETTDAYNI GGLVGHLTGK NASIAKSKAT VTISSNTNRS DQTVGGLAGL VDQDAHIQNS YAE GDINNV KHFGKVAGVA GYLWDRTSGE EKHAGELTNV LSDVNVTNGN AITGYHYTGM KVANTFSSKA NRVFNVTLEK DEVV SKESF EERGTMLDAS QIVSKKAEIN PLTLPTVEPL STSGKKDSDF SKIAHYQANR ALVYKNIEKL LPFYNKSTIV KYGNL VKEN SLLYQKELLS AVMMKDDQVI TDIVSNKQTA NKLLLHYNDH SSEKFDLKYQ TDFANLAEYN LGNTGLLYTP NQFLYD RDS IVKEVLPELQ KLDYQSDAIR KTLGISPEVK LTELYLEDQF SKTKQNLGDS LKKLLSADAG LASDNSVTRG YLVDKIK NN KEALLLGLTY LERWYNFNYG QVNVKDLVMY HPDFFGKGNT SPLDTLIELG KSGFNNLLAK NNVDTYGISL ASQHGATD L FSTLEHYRKV FLPNTSNNDW FKSETKAYIV EEKSTIEEVK TKQGLAGTKY SIGVYDRITS ATWKYRNMVL PLLTLPERS VFVISTMSSL GFGAYDRYRS SDHKAGKALN DFVEENARET AKRQRDHYDY WYRILDEQSR EKLYRTILLY DAYKFGDDTT SGKATAEAK FDSSNPAMKN FFGPVGNKVV HNQHGAYATG DGVYYMSYRM LDKDGAITYT HAMTHDSDQD IYLGGYGRRN G LGPEFFAK GLLQAPDQPS DATITINSIL KHSKSDSTEG SRLQVLDPTE RFQNAADLQN YVHNMFDLIY MMEYLEGQSI VN KLSVYQK MAALRKIENK YVKDPADGNE VYATNVVKEL TEAEARNLNS FESLIDHNIL SAREYQSGDY ERNGYYTIKL FAP IYSALS SEKGTPGDLM GRRIAYELLA AKGFKDGMVP YISNQYEEDA KQQGQTINLY GKERGLVTDE LVLKKVFDGK YKTW AEFKT AMYQERVDQF GNLKQVTFKD PTKPWPSYGT KTINNVDELQ ALMDQAVLKD AEGPRWSNYD PEIDSAVHKL KRAIF KAYL DQTNDFRSSI FENKK

UniProtKB: Immunoglobulin A1 protease

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Macromolecule #2: Immunoglobulin heavy constant alpha 1

MacromoleculeName: Immunoglobulin heavy constant alpha 1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.887988 KDa
SequenceString: CCHPRLSLHR PALEDLLLGS EANLTCTLTG LRDASGVTFT WTPSSGKSAV QGPPERDLCG CYSVSSVLPG CAEPWNHGKT FTCTAAYPE SKTPLTATLS KSGNTFRPEV HLLPPPSEEL ALNELVTLTC LARGFSPKDV LVRWLQGSQE LPREKYLTWA S RQEPSQGT ...String:
CCHPRLSLHR PALEDLLLGS EANLTCTLTG LRDASGVTFT WTPSSGKSAV QGPPERDLCG CYSVSSVLPG CAEPWNHGKT FTCTAAYPE SKTPLTATLS KSGNTFRPEV HLLPPPSEEL ALNELVTLTC LARGFSPKDV LVRWLQGSQE LPREKYLTWA S RQEPSQGT TTFAVTSILR VAAEDWKKGD TFSCMVGHEA LPLAFTQKTI DR

UniProtKB: Immunoglobulin heavy constant alpha 1

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Macromolecule #3: Immunoglobulin alpha-1 light chain

MacromoleculeName: Immunoglobulin alpha-1 light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 21.947256 KDa
SequenceString: AAAMAQSPAS LSASAGAAAA IACRSSQAAA AAAAAAALAW YAAKPGAAPA ALIYAASAAA SAVPARFSGS GAGTDFAAAI AAVEAEDAA AYYCAQAAAA AATFGAGTRA EAKRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL Q SGNSQESV ...String:
AAAMAQSPAS LSASAGAAAA IACRSSQAAA AAAAAAALAW YAAKPGAAPA ALIYAASAAA SAVPARFSGS GAGTDFAAAI AAVEAEDAA AYYCAQAAAA AATFGAGTRA EAKRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL Q SGNSQESV TEQDSKDSTY SLSSTLTLSK ADYEKHKVYA CEVTHQGLSS PVTKSFNRGE C

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Macromolecule #4: Immunoglobulin alpha-1 heavy chain

MacromoleculeName: Immunoglobulin alpha-1 heavy chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 21.93048 KDa
SequenceString: AVALAASGAA AAAPGASLKL SCAASGATAA AAAAAWVRAA AGKALEWVAA IAAAAAAAAA AAAAAAAAAA AISADASAAA AALAAASLA AADTAAYYCA AAGAAAAAAW GQGTLVTVSS ASPTSPKVFP LSLCSTQPDG NVVIACLVQG FFPQEPLSVT W SESGQGVT ...String:
AVALAASGAA AAAPGASLKL SCAASGATAA AAAAAWVRAA AGKALEWVAA IAAAAAAAAA AAAAAAAAAA AISADASAAA AALAAASLA AADTAAYYCA AAGAAAAAAW GQGTLVTVSS ASPTSPKVFP LSLCSTQPDG NVVIACLVQG FFPQEPLSVT W SESGQGVT ARNFPPSQDA SGDLYTTSSQ LTLPATQCLA GKSVTCHVKH YTNPSQDVTV PCPAVPTPPT PSPS

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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: 7 / Details: 20 mM Hepes, pH 7 150 mM NaCl
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 3 SIGMA CUT-OFF / Number images used: 100000
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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