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- EMDB-42949: Microtubule inner proteins in the 48-nm doublet microtubule from ... -

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Basic information

Entry
Database: EMDB / ID: EMD-42949
TitleMicrotubule inner proteins in the 48-nm doublet microtubule from the proximal region of Tetrahymena thermophila strain K40R
Map data
Sample
  • Organelle or cellular component: 48-nm proximal repeat unit of microtubule doublet from Tetrahymena thermophila strain K40R
    • Protein or peptide: CCDC81B
    • Protein or peptide: BMIP1
KeywordsCilia / Axoneme / Doublet Microtubule / Microtubule Inner Protein / STRUCTURAL PROTEIN
Function / homology
Function and homology information


calcium ion binding
Similarity search - Function
CCDC81, HU domain 1 / CCDC81, HU domain 2 / CCDC81 eukaryotic HU domain 1 / CCDC81 eukaryotic HU domain 2 / : / EF hand / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. ...CCDC81, HU domain 1 / CCDC81, HU domain 2 / CCDC81 eukaryotic HU domain 1 / CCDC81 eukaryotic HU domain 2 / : / EF hand / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
EF-hand protein / Uncharacterized protein
Similarity search - Component
Biological speciesTetrahymena thermophila (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsLegal T / Bui KH / Yang SK
Funding support Canada, 2 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT-190195 Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2022-04774 Canada
CitationJournal: To Be Published
Title: 48-nm doublet microtubule from the proximal region of Tetrahymena thermophila strain K40R
Authors: Bui KH
History
DepositionNov 28, 2023-
Header (metadata) releaseMay 1, 2024-
Map releaseMay 1, 2024-
UpdateMay 1, 2024-
Current statusMay 1, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42949.png

Downloads & links

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Map

FileDownload / File: emd_42949.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.37 Å/pix.
x 512 pix.
= 701.44 Å		1.37 Å/pix.
x 512 pix.
= 701.44 Å		1.37 Å/pix.
x 512 pix.
= 701.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.37 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0526
Minimum - Maximum-0.010882882 - 2.2891333
Average (Standard dev.)0.010175973 (±0.06653601)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 701.44 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_42949_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_42949_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_42949_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 : 48-nm proximal repeat unit of microtubule doublet from Tetrahymen...

EntireName: 48-nm proximal repeat unit of microtubule doublet from Tetrahymena thermophila strain K40R
Components
  • Organelle or cellular component: 48-nm proximal repeat unit of microtubule doublet from Tetrahymena thermophila strain K40R
    • Protein or peptide: CCDC81B
    • Protein or peptide: BMIP1

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Supramolecule #1: 48-nm proximal repeat unit of microtubule doublet from Tetrahymen...

SupramoleculeName: 48-nm proximal repeat unit of microtubule doublet from Tetrahymena thermophila strain K40R
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Single Particle Analysis of the proximal 48-nm repeating unit of the axoneme from intact cilia purified from Tetrahymena strain K40R
Source (natural)Organism: Tetrahymena thermophila (eukaryote) / Strain: K40R / Organelle: Cilia
Molecular weightTheoretical: 7.6 MDa

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Macromolecule #1: CCDC81B

MacromoleculeName: CCDC81B / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tetrahymena thermophila (eukaryote) / Strain: K40R
Molecular weightTheoretical: 179.311766 KDa
SequenceString: MRSVISEQSL ASTKTQKLFN NLISKGQSKI PLLEGQLDEE SLTKTWGAFG LYLSRQLRMG RGTNIPHFGT FTFSAPECNL TGVTNPIER DKQFRVPVFL VSKEFVLGQP IKTGIFIDKH IRPYNVQTSG SISVTKINFT EIAQYADQNK EAVKISFERI I RQLADQTR ...String:
MRSVISEQSL ASTKTQKLFN NLISKGQSKI PLLEGQLDEE SLTKTWGAFG LYLSRQLRMG RGTNIPHFGT FTFSAPECNL TGVTNPIER DKQFRVPVFL VSKEFVLGQP IKTGIFIDKH IRPYNVQTSG SISVTKINFT EIAQYADQNK EAVKISFERI I RQLADQTR QKRVVDMEIP GIGVFQVRNN IAAVHFDEYL IQNIKGVPKR PLSERKQKGD MNLTADRLSM LENTSRIGAD AE QYLKTKL GIDIDNISTK SRPLTAVRNA STSNLLQPNN KTLQRPATST TLRQSAINLK QPELGPLEFG LKRLKFWIRQ NCF NAQDAF LEMCNCALGR TRAQRVKVDY KQFFEAINKM ELDLNEEQIQ ELFKQLDANK DGYINYTDWR NTIKDDNDHL QYIK DVIYK RQLHTDDVLK TMGLDREHPP INKYQLKDAL KKLDLTLTDI KAIRVAQTLL GHEEYISMYD LARSFETIEE DDKIF DPSW FKDILYKIKQ KIMALENPNE IRESFENYDE HNEGILDTAN FKTCLMRSQL KLTVKEINRI VRYLPKVKVN NIDYYN FLK LVERVDINAS APDAVSDISE FAVKLGKFIK DKKFTIPSFL KTVRRFSFVL DSSNNQDYFV TLTQMSEFLH RNVFKGN DR LDIDFYVNEL DIDCDGYIKE NDVQSFLNRY TYFDQTQYTP LSMTRSLTLK SLDPRTVSMN TKTLYPFKAL SEAKVDTI L RDLRKKMELK KMKAAELFST LDADQDGFLT INEFSENIRK IIELSQPAID GFFAYMDKLH TGMVDLSSFL KVMRKSIVT KDQPIKEDNF DWENEMVFRI RQWFKKEGIT VEDSFRAIDQ NFKREINVDD LEIFLKDCLK VKSEELNKAK LDRLFKLIDQ YKRGKVNFV DWKRFIMEDF GYGMNQTIMG GKKIDNISSF DWKINARQQL GLVLTRRFST LSHSFDVISG YRKKLLFSHF K KWVQDTDA LRGFDLTESL MQELFSDLDS HNKGYLSESD WEIAFGGFDW EHQMHEEIKE YVKQNFKSIE KAFEFFCQGN QN KIIEQAD FNKAINSILP KRFIDSDLKD LWVYVSSGQP QVDFHRFKIA FQKYIPHYER TIEYDQENMR PKTAGPLSSL SKS TSWNNI YGASQLNGNS QNPFGTSSIV DGNEDDVFEE KLLSKIRRLL RPTIKSVKKV LEQLDVNNIG YITNLEFRNA IKTL NLGLA QNEVDLLLNI CEIDGRVNIK QFLKFIDFSE SDKKIVQRSI LKLREITNQV YTFLLSPKDA FRMFDVDSNG YLDFD QFSQ FIGKLSQLSG HDMLPYSIIK DLFEYIDSKK DGVIDQAEWM DIFNKFEYVP QASINKQPLS KATVYNLQKR PQTSFN KST LNELPHNKFN LEYISSNYPL TVKNEKIHQI SDKEKYGTMN KFFDEVERQP ESKPVQDNHF NQILGEWGKT KEFDKII IS IGKNRRFLLD MFGSLQQRNI PITFERAKAI IGQMLRNSGQ SLKEESWPII LKFAERNGLI DYKFLLEVYK ERIKRIDS H PIMSRNRSLQ KFTS

UniProtKB: EF-hand protein

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Macromolecule #2: BMIP1

MacromoleculeName: BMIP1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Tetrahymena thermophila (eukaryote) / Strain: K40R
Molecular weightTheoretical: 28.564789 KDa
SequenceString: MQSTITSTTS LTPQQILNQI IKPEYIKYYS DWIHTANEKE ARGLQLLGAI YKHKGSKKFR AKPPSVQLQQ LHAQQEFDFQ KAEEMYRKS QITSSYGQEF GYLQKDLKPT QNVFKYKKCS DLPFAKPLSD LAKLFIDNWI ELNDELEFQE LVLACLRSLH S RCIAQEVP ...String:
MQSTITSTTS LTPQQILNQI IKPEYIKYYS DWIHTANEKE ARGLQLLGAI YKHKGSKKFR AKPPSVQLQQ LHAQQEFDFQ KAEEMYRKS QITSSYGQEF GYLQKDLKPT QNVFKYKKCS DLPFAKPLSD LAKLFIDNWI ELNDELEFQE LVLACLRSLH S RCIAQEVP KTEMKTKYEW KEDWNLSKPI RIDKAGSDLK AYKTNYNAIF KQRLKQEHIN EQLKQLDNSD FAKQLKIFKP FK IN

UniProtKB: Uncharacterized protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statecell

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Sample preparation

Concentration2.2 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

8537

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 45618
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software: (Name: RELION (ver. 3.1), cryoSPARC (ver. 2.3))
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

mb72

chain_id: A1, source_name: AlphaFold, initial_model_type: in silico model

m688

chain_id: A, source_name: AlphaFold, initial_model_type: in silico model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8v3l:
Microtubule inner proteins in the 48-nm doublet microtubule from the proximal region of Tetrahymena thermophila strain K40R

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