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- EMDB-37389: cryo-EM structure of native mastigonemes isolated from Chlamydomo... -

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Basic information

Entry
Database: EMDB / ID: EMD-37389
Titlecryo-EM structure of native mastigonemes isolated from Chlamydomonas reinhardtii at 3.0 angstrom resolution
Map data
Sample
  • Organelle or cellular component: mastigoneme
    • Protein or peptide: Mst1
  • Protein or peptide: Mstax
  • Ligand: CALCIUM IONCalcium
  • Ligand: alpha-L-arabinofuranose
  • Ligand: alpha-D-galactopyranose
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsCilia / arabinoglycan / PKD2 / PPII helix / mechanosensation. / MEMBRANE PROTEIN
Function / homologyTyrosine-protein kinase ephrin type A/B receptor-like / Tyrosine-protein kinase ephrin type A/B receptor-like / Putative ephrin-receptor like / Growth factor receptor cysteine-rich domain superfamily / Tyrosine-protein kinase ephrin type A/B receptor-like domain-containing protein
Function and homology information
Biological speciesChlamydomonas reinhardtii (plant) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsHuang J / Tao H / Chen J / Pan J / Yan C / Yan N
Funding support China, 1 items
OrganizationGrant numberCountry
National Basic Research Program of China (973 Program)2020YFA0509301 China
CitationJournal: Cell / Year: 2024
Title: Structure-guided discovery of protein and glycan components in native mastigonemes.
Authors: Junhao Huang / Hui Tao / Jikun Chen / Yang Shen / Jianlin Lei / Junmin Pan / Chuangye Yan / Nieng Yan /
Abstract: Mastigonemes, the hair-like lateral appendages lining cilia or flagella, participate in mechanosensation and cellular motion, but their constituents and structure have remained unclear. Here, we ...Mastigonemes, the hair-like lateral appendages lining cilia or flagella, participate in mechanosensation and cellular motion, but their constituents and structure have remained unclear. Here, we report the cryo-EM structure of native mastigonemes isolated from Chlamydomonas at 3.0 Å resolution. The long stem assembles as a super spiral, with each helical turn comprising four pairs of anti-parallel mastigoneme-like protein 1 (Mst1). A large array of arabinoglycans, which represents a common class of glycosylation in plants and algae, is resolved surrounding the type II poly-hydroxyproline (Hyp) helix in Mst1. The EM map unveils a mastigoneme axial protein (Mstax) that is rich in heavily glycosylated Hyp and contains a PKD2-like transmembrane domain (TMD). Mstax, with nearly 8,000 residues spanning from the intracellular region to the distal end of the mastigoneme, provides the framework for Mst1 assembly. Our study provides insights into the complexity of protein and glycan interactions in native bio-architectures.
History
DepositionSep 6, 2023-
Header (metadata) releaseApr 10, 2024-
Map releaseApr 10, 2024-
UpdateApr 10, 2024-
Current statusApr 10, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37389.png

Downloads & links

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Map

FileDownload / File: emd_37389.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.0825 Å
Density
Contour LevelBy AUTHOR: 0.23
Minimum - Maximum-0.6734782 - 1.5266924
Average (Standard dev.)0.0006518106 (±0.042529024)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 554.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_37389_msk_1.map
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Additional map: #1

Fileemd_37389_additional_1.map
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Additional map: #2

Fileemd_37389_additional_2.map
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Additional map: #3

Fileemd_37389_additional_3.map
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Half map: #1

Fileemd_37389_half_map_1.map
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Half map: #2

Fileemd_37389_half_map_2.map
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Sample components

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Entire : mastigoneme

EntireName: mastigoneme
Components
  • Organelle or cellular component: mastigoneme
    • Protein or peptide: Mst1
  • Protein or peptide: Mstax
  • Ligand: CALCIUM IONCalcium
  • Ligand: alpha-L-arabinofuranose
  • Ligand: alpha-D-galactopyranose
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: mastigoneme

SupramoleculeName: mastigoneme / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Chlamydomonas reinhardtii (plant)

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Macromolecule #1: Mst1

MacromoleculeName: Mst1 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 206.316203 KDa
SequenceString: MAMPRHGRRP ARCSSNRASQ WLLLVLGVAL AASPRFLLLV EAATYTLTLD KLGPTVNPTT SDAVTFTATV ASPDSTTAVF FTLDYGDGV TAETTRTTTG ALSTTPTANL VSAGTYTVTY ASIGTKFVTL RLYDSAVAPG VLLASKTVPI YVEDSTLTAT L LQSGVPRL ...String:
MAMPRHGRRP ARCSSNRASQ WLLLVLGVAL AASPRFLLLV EAATYTLTLD KLGPTVNPTT SDAVTFTATV ASPDSTTAVF FTLDYGDGV TAETTRTTTG ALSTTPTANL VSAGTYTVTY ASIGTKFVTL RLYDSAVAPG VLLASKTVPI YVEDSTLTAT L LQSGVPRL NLAFSGFKGR VSSSTANRAD MWATIQLDTA PGVFESSRIF IGIAPTASTN YDFVIPDQVY NLEGAKTTVL RI YDAPVGG TLLRTFTPAA ANAVYVVDPS KYVLTLTVGP TSVTTADQVT FTQTTTEVSY SASATSPILQ WRFNWDDPSV VET PLAYPD ALTAASNFPT TATAVSSAAA STFRYTSTGS KNARLRLYDG ANNVIAEKIV VITVSNAGYT LALAKTTADP VTTD DTIAF SAGAKHLSST SQVWWTIDYG AGESSPRTAL TMTNVGAAAP NAIASLSNQY TSGGTKLATL RIYDRDGVGA NTGLL LAST TVTFTVTPVL YALESAVEPF SPIATVAAKW SFRIQRSKAT PAGVTESIKC AFFGADTGTA PADLAAWLTA ANGAGG LTA TILPSSIPSD IISFTRTYAA AAASLQGKLQ CFIGSTPLWD PYYPTPVFQV LAAAPTYTLS ASVTPAVVPV DTATLWT YN IIRSVPVPAG GPSLPILCSF WDGKTGAAPT TDAGWAALAG SANGKGTSMA PGSTTATCSF TPSYSTTGTA TPTLQLIQ N SFALDAATTV GFLSPVYTAP AFATVTAASY TISSYLNPVT PVAGGAAAVW RIVITRNAAV TASAKTLTCQ MPDNGQGGS PADVTADIAV GGTTTVCVFS IAGYTTATPG PYFATVNVVD GAVTTSHITK NFTVLASGTT APTYAVTSVV SPATPVKVST PVTYTFTIT RTTAVPAGGI PQPIICEFFN GEGTAPASAA AYWRVSTTIP DADTVVAVMA PGETTTTCTF TTYYTTVSAG G FTAKLMVF GESATAAPLL TSLSVTPSQL LAAVHSFATP MVVAAAVVAV ESTTISPNYN PTTPYTNIPT YFTFTLLRDP PV PPSASSG VQFACALYTG QNVNPASAPS AITDAVYKTF TDVTTAVATD ANYFADQQLR VVTMAPGTGR VSCTFPTLYA AAG PFSPKF FVFEYASSTV GANALAVADT VTSLTSFTTQ AAPTFITGPT NVPQRVPLPK GFRTTCFDGY ELIFSNDNYT NGVR VAVDA YPYPVGQCRK CPGGTATMDG YRCIPCPSGY WSNEGARECT ACPAGTIAKP AALTARAKYS IDPTTYHFVT HLAMG PESC KKCPKGYFQP NIAGTVCLPC PSGFVSTSGA TGCTACSEGT YHTDGVGTTT PGEATSLDTT DTFGSIYPII PNTCRQ CPA NTYLPLRGQA AIASMNLAAV SSATPCRPCE DGTWSKAGAA GCQKCPPGTY RNTWFSGQLG SPFITADGVP VATTLTE LG SGCSQCPPGT YAPTFGMSVC LPCPAGTFAS APGATACQQC KPGTNSLMGD RTQQMALVVT NAANDFPALR AYTISGMV A GPAYAKPIVT GPDTNFFMAG KSETCSTNLP GYYTDVDGLP IQLPCKPGTF MPFDTATANL LDTGLTVDGT QCYTCQTGT FNDEFSQPVC KACWSGSFAS KRGLPTCEIA QPGTFTNVAA AANATFNTAT LIPTGLVKGA QAPTPCGMGY FQSSAETTTC TACAVGTYA DQAGLAACKP CQPGRYQNSI GQRVCKPCDM GTYSRYGGEL CTKCPAGTVA SKTGSSQCTP CAAGFYANAP D SATSCRAC PRGYYGPYSG AYADNLGDEF EGPRGCYKCP YDFFADRPGV RQCTACPPLD LGGGNLVEQC TEDLGSQRCK PC SLLSKPK TARTEQS(HYP)(HYP)(HYP) (HYP)S(HYP)S(HYP)(HYP)(HYP)(HYP)(HYP)(HYP) (HYP)S (HYP)R(HYP)(HYP)S(HYP)N (HYP)(HYP)S(HYP)R(HYP)(HYP)S(HYP)A (HYP)(HYP)S(HYP)N(HYP) (HYP)(HYP)T S(HYP)(HYP)(HYP)S(HYP)(HYP)(HYP)S(HYP) (HYP)(HYP)(HYP)R(HYP)(HYP)(HYP) (HYP)(HYP) (HYP)(HYP)(HYP)(HYP)S(HYP)(HYP)(HYP)(HYP)N RS(HYP)(HYP)(HYP)(HYP)(HYP) (HYP)A SSAINPGGGV NQNGDPVGHR RAILSLMEDE DAEAAQEEQA IVDVDAEMQP QDDE

UniProtKB: Tyrosine-protein kinase ephrin type A/B receptor-like domain-containing protein

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Macromolecule #2: Mstax

MacromoleculeName: Mstax / type: protein_or_peptide / ID: 2
Details: Our Mstax sequence in the structure (chain G, H and I) represents the average sequence resulting from the statistical analysis of a segment of 34 repeated sequences in Mstax.
Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 6.239464 KDa
SequenceString: (HYP)(HYP)(HYP)(HYP)(HYP)(HYP)(HYP)(HYP)(HYP)(HYP) (HYP)GT(HYP)DQ(HYP)AA(HYP) AA (HYP)AA(HYP)AA(HYP) AA(HYP)(HYP)(HYP)AL(HYP)GA (HYP)(HYP)(HYP)(HYP)(HYP)(HYP)(HYP) (HYP)(HYP) (HYP)(HYP)(HYP) ...String:
(HYP)(HYP)(HYP)(HYP)(HYP)(HYP)(HYP)(HYP)(HYP)(HYP) (HYP)GT(HYP)DQ(HYP)AA(HYP) AA (HYP)AA(HYP)AA(HYP) AA(HYP)(HYP)(HYP)AL(HYP)GA (HYP)(HYP)(HYP)(HYP)(HYP)(HYP)(HYP) (HYP)(HYP) (HYP)(HYP)(HYP)(HYP)GV(HYP)(HYP)AA AAAAAA

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Macromolecule #25: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 25 / Number of copies: 6 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #26: alpha-L-arabinofuranose

MacromoleculeName: alpha-L-arabinofuranose / type: ligand / ID: 26 / Number of copies: 20 / Formula: AHR
Molecular weightTheoretical: 150.13 Da
Chemical component information

ChemComp-AHR:
alpha-L-arabinofuranose / Arabinose

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Macromolecule #27: alpha-D-galactopyranose

MacromoleculeName: alpha-D-galactopyranose / type: ligand / ID: 27 / Number of copies: 62 / Formula: GLA
Molecular weightTheoretical: 180.156 Da
Chemical component information

ChemComp-GLA:
alpha-D-galactopyranose / Galactose

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Macromolecule #28: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 28 / Number of copies: 7 / 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 statefilament

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Sample preparation

Concentration5 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 69065
FSC plot (resolution estimation)

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