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- EMDB-26812: G. haemolysans IgA1 protease -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-26812
TitleG. haemolysans IgA1 protease
Map data
Sample
  • Complex: Gemella haemolysans IgA protease apo
    • Protein or peptide: IgA1 ProteaseIgA-specific metalloendopeptidase
Function / homology
Function and homology information


serine-type peptidase activity / metalloendopeptidase activity / proteolysis / zinc ion binding / extracellular region / membrane
Similarity search - Function
Peptidase M26, N-terminal domain / Peptidase M26, C-terminal domain / M26 IgA1-specific Metallo-endopeptidase N-terminal region / M26 IgA1-specific Metallo-endopeptidase C-terminal region / G5 domain / G5 domain / G5 domain profile. / G5 / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
LPXTG-motif cell wall anchor domain protein
Similarity search - Component
Biological speciesGemella haemolysans (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.28 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: Commun Biol / Year: 2022
Title: A substrate-induced gating mechanism is conserved among Gram-positive IgA1 metalloproteases.
Authors: Jasmina S Redzic / Jeremy Rahkola / Norman Tran / Todd Holyoak / Eunjeong Lee / Antonio Javier Martín-Galiano / Nancy Meyer / Hongjin Zheng / Elan Eisenmesser /
Abstract: The mucosal adaptive immune response is dependent on the production of IgA antibodies and particularly IgA1, yet opportunistic bacteria have evolved mechanisms to specifically block this response by ...The mucosal adaptive immune response is dependent on the production of IgA antibodies and particularly IgA1, yet opportunistic bacteria have evolved mechanisms to specifically block this response by producing IgA1 proteases (IgA1Ps). Our lab was the first to describe the structures of a metal-dependent IgA1P (metallo-IgA1P) produced from Gram-positive Streptococcus pneumoniae both in the absence and presence of its IgA1 substrate through cryo-EM single particle reconstructions. This prior study revealed an active-site gating mechanism reliant on substrate-induced conformational changes to the enzyme that begged the question of whether such a mechanism is conserved among the wider Gram-positive metallo-IgA1P subfamily of virulence factors. Here, we used cryo-EM to characterize the metallo-IgA1P of a more distantly related family member from Gemella haemolysans, an emerging opportunistic pathogen implicated in meningitis, endocarditis, and more recently bacteremia in the elderly. While the substrate-free structures of these two metallo-IgA1Ps exhibit differences in the relative starting positions of the domain responsible for gating substrate, the enzymes have similar domain orientations when bound to IgA1. Together with biochemical studies that indicate these metallo-IgA1Ps have similar binding affinities and activities, these data indicate that metallo-IgA1P binding requires the specific IgA1 substrate to open the enzymes for access to their active site and thus, largely conform to an "induced fit" model.
History
DepositionMay 2, 2022-
Header (metadata) releaseNov 23, 2022-
Map releaseNov 23, 2022-
UpdateNov 30, 2022-
Current statusNov 30, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26812.png

Downloads & links

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Map

FileDownload / File: emd_26812.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.83 Å
Density
Contour LevelBy AUTHOR: 0.43
Minimum - Maximum-1.1688576 - 1.7378294
Average (Standard dev.)0.0006574759 (±0.044905417)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 298.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_26812_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_26812_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 : Gemella haemolysans IgA protease apo

EntireName: Gemella haemolysans IgA protease apo
Components
  • Complex: Gemella haemolysans IgA protease apo
    • Protein or peptide: IgA1 ProteaseIgA-specific metalloendopeptidase

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Supramolecule #1: Gemella haemolysans IgA protease apo

SupramoleculeName: Gemella haemolysans IgA protease apo / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Gemella haemolysans (bacteria)

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Macromolecule #1: IgA1 Protease

MacromoleculeName: IgA1 Protease / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Gemella haemolysans (bacteria)
Molecular weightTheoretical: 246.235844 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MRKYLEEKYN KFSLRKLTVG VCSMTIGSFF LVSTVQPEDY VVKAADNAIV HYKYVGEDNL TDKEKELIKK EVPSVVSSKE ETYYLVFKP TKTTQLNKLP NTGLNYGVGS MLLGGMLGLV VVVVAKGKNK SRKILSILLV TSLGATTLEL PARAMEDLQL S VYNMDYNL ...String:
MRKYLEEKYN KFSLRKLTVG VCSMTIGSFF LVSTVQPEDY VVKAADNAIV HYKYVGEDNL TDKEKELIKK EVPSVVSSKE ETYYLVFKP TKTTQLNKLP NTGLNYGVGS MLLGGMLGLV VVVVAKGKNK SRKILSILLV TSLGATTLEL PARAMEDLQL S VYNMDYNL KVGDKLPEIS SIPGYSFVGF IKNEAETKKE NEEVKEQITS QQHNKKQPEL KENTDENVIE NKQENKTTLK IS DKKEDKK VIENINKKDE KKVQGVNTVN PQDEVLAGKL TKPELLYSDK IIETPLKYNQ IIESNDQLPE GTTRIKQQGK EGK KTEVIR MFTVEGKEVS RELISTKTEE PVSEIIEKGT KKAVSNVITK GQKLVKPAVE VKPEYTGVQA GAIVEPVKAE VPKE YTGVQ AGAIVEPAKV ETPKEYTGVQ AGAIVEPAKA EVSKEYTGVQ AGTIVEPAKA EVPKEYTGVQ AGAIVEPEKV EPQYG GVTS GALVKPEKIE APKEYTGVQA GAVVEPAKAE APKEYRGVQA GAIVEPEKIE SPKEYTGVQA GAVVEPAKAE VPKEYR GVQ AGAIVEPEKI ESPKEYTGEQ SGAIVEPEKV ETTKEYTGIQ AGALVEPEKV EAPKEYTGVQ AGAIVEPEKV EPPKEYT GV QAGAIVEPEK VEAPKEYTGK IEPLKTENPK PTVENNNTAE INNVPKNASA LLRMNFVKGN QVLSGTGSAT FIAPNVLL T VAHNFINNSA DNSTGEFIGD KSKNTYEWQT PDGQKGSFTS EDIHFYNKKD YPKGFIYDLA VITLPQSTRR QHANLVENY SKVNVNDKLN VYGYPRGEYA HLKDTTVEIE QKYANNTYGV QYQGGKAGMS GGGIFNSKGE VIGLHQNGAE NRSGGLILSP TQLDWIRSI IKGKEITPNY DALERHKDEK KDDIKEEKQV DKKLELRNIS NVELYTLENN KYRHVSSLSS VPTNPEAYFM K VKSENFKD VMLPVKSIES ARKDNQDVYK IVGQANDLIQ HENNITLENY TYYLPKTVNS ENGVYTSFKN LVDAMNINPY GT FRLGATM DAREVELSDG QESYINKEFS GKLIGENKGK YYAIYNLKKP LFKALSHATI QDLSIKEANV SSKEDAATIA KEA KNDTTI ANVHSSGVIA GERSIGGLIS QVTDSTISNS SFTGRITNTY DTTATYQIGG LVGKLSGVGA LIEKSISSID MATN ANTGD QVVGGVAGVV DKKATIRNSY VEGNLNNVKP FGKVGGVVGN LWDRETSEVS NSGNLTNVLS DVNVTNGNAI AGYDF NGIK ATNTYSNKNN KVVKVVQVDD EVLSKDSEEQ RGTVLENNIV LEKKIELVPK KNTKIEDFNF SSRYETDYKN LKDADV SRL RVYKNIEKLL PFYNRETIVK YGNLVDANNT LYTKDLVSVV PMKDKEVISD INKNKTSINK LLLHYSDNTS QTLDIKY LQ DFSKVAEYEI ANTKLIYTPN TLLHSYNNIV KAVLNDLKSV QYDSDAVRKV LDISSNIKLT ELYLDEQFTK TKANIEDS L SKLLSADAVI AENSNSIIDN YVIEKIKNNK EALLLGLTYL ERWYNFKYDN TSAKDLVLYH LDFFGKSNSS ALDNVIELG KSGFNNLLAK NNVITYNVLL SKNYGTEGLF KALEGYRKVF LPNVSNNDWF KTQSKAYIVE EKSTIPEVSS KQSKQGTEHS IGVYDRLTS PSWKYQSMVL PLLTLPEEKM IFMIANISTI GFGAYDRYRS SEYPKGDKLN RFVEENAQAA AKRFRDHYDY W YKILDKEN KEKLFRSVLV YDAFRFGNDT NKETQEANFE TNNPVIKNFF GPAGNNVVHN KHGAYATGDA FYYMAYRMLD KS GAVTYTH EMTHNSDREI YLGGYGRRSG LGPEFYAKGL LQAPDHSYDP TITINSVLKY DDSENSTRLQ IADPTQRFTN VED LHNYMH NMFDLIYTLE ILEGRAVAKL DYNEKNDLLR KIENIYKKDP DGNSVYATNA VRRLTSDEIK NLTSFDKLIE NDVI TRRGY IDQGEYERNG YHTINLFSPI YSALSSKIGT PGDLMGRRMA FELLAAKGYK EGMVPYISNQ YEKEAKDRGS KIRSY GKEI GLVTDDLVLE KVFNKKYGSW VEFKKDMYKE RVEQFSKLNR VSFFDPNGPW GRQKNVTVNN ISVLEKMIET AVREDA EDF TAQVYPDTNS RVLKLKKAIF KAYLDQTKDF RTSIFGGK

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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

Concentration5 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
300.0 mMNaClSodium chloridesodium choloride
20.0 mMHEPES2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonic acid
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Electron beamAcceleration voltage: 300 kV / Electron source: OTHER
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.2 µm
Image recordingFilm or detector model: GATAN K2 BASE (4k x 4k) / Average electron dose: 30.0 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6xjb

Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 443908

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