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- EMDB-29245: Cryo-EM structure of native mosquito salivary gland surface prote... -

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Basic information

Entry
Database: EMDB / ID: EMD-29245
TitleCryo-EM structure of native mosquito salivary gland surface protein 1 (SGS1)
Map data
Sample
  • Complex: salivary gland surface protein 1 (SGS1)
    • Protein or peptide: salivary gland surface protein 1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Function / homologyTox-SGS domain / Salivary glad secreted protein domain toxin / Rhs repeat-associated core / membrane / AAEL009993-PA
Function and homology information
Biological speciesAedes aegypti (yellow fever mosquito) / yellow fever mosquito (yellow fever mosquito)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsLiu S / Xia X / Calvo E / Zhou ZH
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM071940 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI001246 United States
CitationJournal: Nat Commun / Year: 2023
Title: Native structure of mosquito salivary protein uncovers domains relevant to pathogen transmission.
Authors: Shiheng Liu / Xian Xia / Eric Calvo / Z Hong Zhou /
Abstract: Female mosquitoes inject saliva into vertebrate hosts during blood feeding. This process transmits mosquito-borne human pathogens that collectively cause ~1,000,000 deaths/year. Among the most ...Female mosquitoes inject saliva into vertebrate hosts during blood feeding. This process transmits mosquito-borne human pathogens that collectively cause ~1,000,000 deaths/year. Among the most abundant and conserved proteins secreted by female salivary glands is a high-molecular weight protein called salivary gland surface protein 1 (SGS1) that facilitates pathogen transmission, but its mechanism remains elusive. Here, we determine the native structure of SGS1 by the cryoID approach, showing that the 3364 amino-acid protein has a Tc toxin-like Rhs/YD shell, four receptor domains, and a set of C-terminal daisy-chained helices. These helices are partially shielded inside the Rhs/YD shell and poised to transform into predicted transmembrane helices. This transformation, and the numerous receptor domains on the surface of SGS1, are likely key in facilitating sporozoite/arbovirus invasion into the salivary glands and manipulating the host's immune response.
History
DepositionDec 20, 2022-
Header (metadata) releaseMar 1, 2023-
Map releaseMar 1, 2023-
UpdateMar 1, 2023-
Current statusMar 1, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29245.png

Downloads & links

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Map

FileDownload / File: emd_29245.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.36 Å
Density
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.099575296 - 0.18934736
Average (Standard dev.)-1.0288636e-05 (±0.004426146)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 408.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_29245_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_29245_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 : salivary gland surface protein 1 (SGS1)

EntireName: salivary gland surface protein 1 (SGS1)
Components
  • Complex: salivary gland surface protein 1 (SGS1)
    • Protein or peptide: salivary gland surface protein 1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: salivary gland surface protein 1 (SGS1)

SupramoleculeName: salivary gland surface protein 1 (SGS1) / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Aedes aegypti (yellow fever mosquito)

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Macromolecule #1: salivary gland surface protein 1

MacromoleculeName: salivary gland surface protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: yellow fever mosquito (yellow fever mosquito)
Molecular weightTheoretical: 380.453688 KDa
SequenceString: MLRIKEVKKY NNRLGFPAGK EVRIRPLLEA GGFARGPIYV KYGRELSKHD PSSRSMAWNA TVFDTALNHP TRPWTVTVVG GKKMVLGVR KEGLGFSEDD PPRSLNVKGG DDMADENYGG GNSTIVLVKS GGKDFAIGLD DLKELNSFGI GAGNGKLSLA L GNPVNVLT ...String:
MLRIKEVKKY NNRLGFPAGK EVRIRPLLEA GGFARGPIYV KYGRELSKHD PSSRSMAWNA TVFDTALNHP TRPWTVTVVG GKKMVLGVR KEGLGFSEDD PPRSLNVKGG DDMADENYGG GNSTIVLVKS GGKDFAIGLD DLKELNSFGI GAGNGKLSLA L GNPVNVLT GVVLPVEQRD GSVAYVAVNS DTKSVIYKVD AKGLQKNQKI DVNVRASAEK ILLTKNNELL HISPQGLNVY SV QGSASTF KYFCPYFSSF GGWSRRFVDT VTLMDEGGNQ EALIGTGPKG IEYMPVDEKC KNYVVEGVQD AKHAVVAPGA TKE GNDIKV LGVYNGELCL LTLEVVDAVE PKLDQGSPAK PSAERVKATK SSKVTVRSGA LSKPVSWLRD SLDEASFKNI VDKL SGKIR FSFPLVDLQG RMGLPIKLVV YYDESDGEDM SVLGRHWTLG RDCIVLDHGN TVFEDKQDYY LVKDQMKIRL ERDWT KPSA NGKVLFNMVG NKDATFEYTA REEKWEVSDG KIRYVYGMNN QGVVSVPGWA DWYGPSANYD SKKIHSVQWN LVEISS VAH RDVKLKYTYT PLDPSTHTMH LLSITDDSNK TTIKFSYKTI EGLGKQVSSG LVKEHKFINN KLLEKVEIDS PSTAQVL KL TSTKIDSLYY LESIKQDDDP DPVLGFEYNK DDKLKPRVQQ IRLPSKSVVD FKYTKQAIAT QQFEQEIAKM ADLYTGNE Y SLEIEKTVGE TDLYVRLKDS AGKNDFIKNQ SIRIESYRGF KIKSYSPFMM HSYIAILVRY AEEKEKLHNK IYILNKGED DSWKLDTTNN NSRVSEDKKF KYDFQEDSFV YYHSKKVHFE YKKSGTKVWS YTSKDIGDVD AFTLMNRGAV YCKNDLVLIR WDALGKLQQ ETLSDAKSKP SISDVDTFFE YIDVQGTFPE DEAEAKKEVD DYKRDLKESL SDYGLILYNN VVALRTIKLS F TGRITVKV LLYLLKHDYT VSSRSSIELQ GGDLAKFNLT LDVFDEHKTK NTNDLDKYRF EFKKQGSKFK LTYIEATDKD NK PTKPSSQ NEKLIGQYER RMKIPLDFEK YMMQVNQEGI IVNDHQIIHD NGNFIAKQLD RDTLKLTKFK IPLGAFSNFK KDS DGDEIK LCTKTEQERT ESCVSLQTNS ARNVSIKYPY YLVTQKKNDI KVLPLKINSR GWEDSVDYRG EILHGSSSHA AMVT TRMSD QKTIVRPLKA LNKINKIYAQ VISEEKLTTP YDSYVIKYEY EDPVVSMNQV AFKTTIVVPG GGKSATGYYR ETNDL QDNQ QIVQVMTADN QVFDPEYVKR MNEMQQEEDK QRDGAQLDAE QTITDKSGYH PILKTTPYSA NQELVQFLGF EDYEDM TGW TVNKRPIQES NIRRNEFSAT GRNFLLLKKG EELIAEFPNT AYYDNFIAST WIRTAQEATV GSTTDMLLLY VDNKPMK GT IKQSIDEWIY VEADSREIVV SESTTVKRVL FKIIVKSTGA DDVHVDHVRL SPVNFNFEGS VYDARIGQRT ATIQTNGF V SRRLYDAYNR RIAEVDETGN IKYLASYSKR VGNTKDEKKR EGGYSSRIQM RAKHSWVESF SPYTMEKRWQ IGGTATVEP NQAILQGQII SKEKFSSESI CIRLVYSMSG SSQLSLTIGK TTVVVKPNAV QYKGHTATTP SNAELVIFAT PKLTSIWVDG HLRIEAPET HAKFNNEAVS LQTSGPVGIK DVIVMEDAEI QVSYLNRDSK PLQEILLLDS SNVLIRQMMY DVIGRRVAET V WVQKSLID GRSTAFKAFQ YHDDFVSNDN PTDRNYFLNT GPMQGYVATA TNTIYEGYPY SQTVYYNNPL EIRHKVGHPG VK NSIKGAF VHQYAIASDL AFIQRNYPKN EGYRQEEEKS PNGKKHVVVY NRRNKKVAEY TQVKDYNNIL TTYIYDQHGN QIQ MLPPSY YHEKSRSGDY QPEKQVVASP WAVTSKYDST GEFITSKETP DGGRVEFIYN EYNQLRYQIH YKEDKQADKI VYFL YNIFG RMCEAGQVPA NPTTLQQVRE TTKSHQAIPN RDQAVYFDYG ETESEPSLRG RIQRTVKKNK EVLFSEVMFF DEESN IIRK SYISPTTNET LSLVYLQEND KVSGIQYPFG VDGKQLILKY KHNLRGEIVE VARVEQKTSG QTEFIPIAGI DHDAEG KVT KISHNYGDSK FDQTYKYVAP GYLVEIANNF LTEKLYYTEK GYGCEPTGDG SILRTEFKAS WHDKCDQNLI PLTARAF VS GGIDFTTAET CFDALLNLGY IDTTGRPVKT FYPDLETGLP MKCATPSNWR YISEKMLEQG YPEHYGHAYD YGSHGELI A AKSFVGKEKD SLTAPLSKAS FANAGMKSHE LDRFWDSLSR SINKVEGTKA IFEGTQQLTT GLVGSVIHKP KLESLLEGK GGDSSICTPW SSGDRTEEAK CKREYQQAFD KLKLKQVIQS LQEPVRKNVL RILKNTLASM LGNSPGDVES FSIDPNGNHG VFYTGFKRF ELKYKHQKNQ IATIKEGTKQ QEKMIVHDDE GNVIKALHKK IDKIEYDPLT QRVSRIEMSD RSRTLEFGYD F RGERTFKR VRNKDNDIIS VNYYVRDNKG NVLVEYKQEY PNPKDTNKPI NTVTAYIHGP LGLLGFFRNN KYYNVLLDHE GS TRLVIHQ GKVVAAYDYL PYGQMIRKYG SNPEAHIAFR YTGQEFDEET GLYNYHARLY DPDIGRFFQM DPMEQYASPY KYA GNSPVS QIDPDGQIAV TLVLMIIGAI VGAYLGAASA NNSWNPAKWA WGDKKTWIGL FAGAIMGAFA VYGGAATFSY FTAM FGGSM IAGALATGVI SVAGAFLGAA AASNQWNPAK WDWTSPAVWN GLLSGASIAV SFPSGFVGIT RSFMSISSNL VKMIY ASLM VGGFLLFVYL GGGMANNFNF QISQWDWKSP RTWFGMIEGA STIFMGTAGT AKHGAAKVYN VVKPNGLKMI WHKVNI PSK AFTMRRVKDT IILTWYKNGQ SISKQILKTT VKADLAKIPK DFIMIHRGFF MPYQRIGYAA IAMPSMAGLM FKKNQYF FT NHPNGTLTKH VRKKRSAPMS SSAASPSVSN FLNDFFENMS ELFDSFFSQT EHSHQDSQSS LSIGASYGRP SNESYHKS F QKLCYSPDSD GNQIICPQRE STVNIFSKGE TFAPEAFGQD LFSRCLPLTW HDRPSIACDG EQTTFIYTPN QNIRVFDMV DGWLMLARIA PAALRNLKAG FSFLRDVVFS DEREQTVQVN DLSRCKQDLE VELLDLKRVM LKKQPNEVKW AQPILNDLED DIGEFLSER KPSEKEFELL QERLSALREE IMENSSVATE LNLSTLIGDM LKKMDGVNVG LNGDVRDMIS TLSGMVPFSS S NLLA

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Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 1 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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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: 7.4
Details: 137 mM NaCl, 2.7 mM KCl, 4.3 mM Na2HPO4, and 1.4 mM KH2PO4, pH 7.4
GridModel: PELCO Ultrathin Carbon with Lacey Carbon / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: LACEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 105000
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 30.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL / In silico model: Ab-Initio Reconstruction via CryoSPARC
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION
Final 3D classificationSoftware - Name: RELION
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 161092
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Overall B value: 109.4
Output model

PDB-8fjp:
Cryo-EM structure of native mosquito salivary gland surface protein 1 (SGS1)

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