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- EMDB-21893: Cryo-EM structure of VASH1-SVBP bound to microtubules -

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Entry
Database: EMDB / ID: EMD-21893
TitleCryo-EM structure of VASH1-SVBP bound to microtubules
Map dataCryo-EM structure of VASH1-SVBP bound to microtubules
Sample
  • Complex: Tenary complex of microtubule with VASH1-SVBP complex
    • Protein or peptide: Tubulin alpha-1A chain
    • Protein or peptide: Tubulin beta-3 chain
    • Protein or peptide: Tubulinyl-Tyr carboxypeptidase 1
    • Protein or peptide: Small vasohibin-binding protein
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
KeywordsMicrotubule / Posttranslational modification / Detyrosination / Vasohibin / PROTEIN BINDING
Function / homology
Function and homology information


regulation of metallopeptidase activity / tubulinyl-Tyr carboxypeptidase / tubulin-tyrosine carboxypeptidase activity / netrin receptor binding / Cargo trafficking to the periciliary membrane / negative regulation of lymphangiogenesis / regulation of cellular senescence / dorsal root ganglion development / Post-chaperonin tubulin folding pathway / axonemal microtubule ...regulation of metallopeptidase activity / tubulinyl-Tyr carboxypeptidase / tubulin-tyrosine carboxypeptidase activity / netrin receptor binding / Cargo trafficking to the periciliary membrane / negative regulation of lymphangiogenesis / regulation of cellular senescence / dorsal root ganglion development / Post-chaperonin tubulin folding pathway / axonemal microtubule / cytoskeleton-dependent intracellular transport / Carboxyterminal post-translational modifications of tubulin / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / organelle transport along microtubule / forebrain morphogenesis / glial cell differentiation / cerebellar cortex morphogenesis / Sealing of the nuclear envelope (NE) by ESCRT-III / Intraflagellar transport / dentate gyrus development / neuron projection arborization / Formation of tubulin folding intermediates by CCT/TriC / Gap junction assembly / labyrinthine layer blood vessel development / pyramidal neuron differentiation / Kinesins / Prefoldin mediated transfer of substrate to CCT/TriC / motor behavior / smoothened signaling pathway / negative regulation of endothelial cell migration / response to L-glutamate / centrosome cycle / Assembly and cell surface presentation of NMDA receptors / COPI-independent Golgi-to-ER retrograde traffic / peptidase activator activity / COPI-dependent Golgi-to-ER retrograde traffic / 'de novo' protein folding / negative regulation of endothelial cell proliferation / axon development / flagellated sperm motility / startle response / intercellular bridge / regulation of synapse organization / Recycling pathway of L1 / microtubule polymerization / protein secretion / negative regulation of blood vessel endothelial cell migration / locomotory exploration behavior / response to tumor necrosis factor / regulation of angiogenesis / response to mechanical stimulus / homeostasis of number of cells within a tissue / sperm flagellum / microtubule-based process / RHO GTPases activate IQGAPs / Hedgehog 'off' state / COPI-mediated anterograde transport / adult locomotory behavior / Activation of AMPK downstream of NMDARs / condensed chromosome / metallocarboxypeptidase activity / ciliary tip / peptide binding / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / negative regulation of protein ubiquitination / MHC class II antigen presentation / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Mitotic Prometaphase / negative regulation of angiogenesis / cellular response to calcium ion / EML4 and NUDC in mitotic spindle formation / axon guidance / AURKA Activation by TPX2 / Resolution of Sister Chromatid Cohesion / cell periphery / sperm end piece / sperm principal piece / Translocation of SLC2A4 (GLUT4) to the plasma membrane / filopodium / neuromuscular junction / RHO GTPases Activate Formins / visual learning / neuron migration / response to wounding / cerebral cortex development / intracellular protein transport / memory / synapse organization / PKR-mediated signaling / microtubule cytoskeleton organization / recycling endosome / mitotic spindle / structural constituent of cytoskeleton / neuron differentiation / apical part of cell / HCMV Early Events
Similarity search - Function
Tubulinyl-Tyr carboxypeptidase / Small vasohibin-binding protein / Vasohibin / Coiled-coil domain-containing protein 23 / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal ...Tubulinyl-Tyr carboxypeptidase / Small vasohibin-binding protein / Vasohibin / Coiled-coil domain-containing protein 23 / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily
Similarity search - Domain/homology
Tubulin beta-3 chain / Tubulin alpha-1A chain / Tubulinyl-Tyr carboxypeptidase 1 / Small vasohibin-binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsLi F / Li Y
Funding support United States, 2 items
OrganizationGrant numberCountry
Cancer Prevention and Research Institute of Texas (CPRIT)RP160667-P2 United States
Welch FoundationI-1441 United States
CitationJournal: Elife / Year: 2020
Title: Cryo-EM structure of VASH1-SVBP bound to microtubules.
Authors: Faxiang Li / Yang Li / Xuecheng Ye / Haishan Gao / Zhubing Shi / Xuelian Luo / Luke M Rice / Hongtao Yu /
Abstract: The dynamic tyrosination-detyrosination cycle of α-tubulin regulates microtubule functions. Perturbation of this cycle impairs mitosis, neural physiology, and cardiomyocyte contraction. The ...The dynamic tyrosination-detyrosination cycle of α-tubulin regulates microtubule functions. Perturbation of this cycle impairs mitosis, neural physiology, and cardiomyocyte contraction. The carboxypeptidases vasohibins 1 and 2 (VASH1 and VASH2), in complex with the small vasohibin-binding protein (SVBP), mediate α-tubulin detyrosination. These enzymes detyrosinate microtubules more efficiently than soluble αβ-tubulin heterodimers. The structural basis for this substrate preference is not understood. Using cryo-electron microscopy (cryo-EM), we have determined the structure of human VASH1-SVBP bound to microtubules. The acidic C-terminal tail of α-tubulin binds to a positively charged groove near the active site of VASH1. VASH1 forms multiple additional contacts with the globular domain of α-tubulin, including contacts with a second α-tubulin in an adjacent protofilament. Simultaneous engagement of two protofilaments by VASH1 can only occur within the microtubule lattice, but not with free αβ heterodimers. These lattice-specific interactions enable preferential detyrosination of microtubules by VASH1.
History
DepositionMay 1, 2020-
Header (metadata) releaseAug 26, 2020-
Map releaseAug 26, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6wsl
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6wsl
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21893.png

Downloads & links

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Map

FileDownload / File: emd_21893.map.gz / Format: CCP4 / Size: 101.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of VASH1-SVBP bound to microtubules
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 218 pix.
= 180.94 Å		0.83 Å/pix.
x 467 pix.
= 387.61 Å		0.83 Å/pix.
x 262 pix.
= 217.46 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015 / Movie #1: 0.015
Minimum - Maximum-0.06151651 - 0.13170771
Average (Standard dev.)0.001088013 (±0.010416935)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions467262218
Spacing262467218
CellA: 217.45999 Å / B: 387.61 Å / C: 180.94 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.830.830.83
M x/y/z262467218
origin x/y/z0.0000.0000.000
length x/y/z217.460387.610180.940
α/β/γ90.00090.00090.000
start NX/NY/NZ-64-64-64
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS262467218
D min/max/mean-0.0620.1320.001

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Supplemental data

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Sample components

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Entire : Tenary complex of microtubule with VASH1-SVBP complex

EntireName: Tenary complex of microtubule with VASH1-SVBP complex
Components
  • Complex: Tenary complex of microtubule with VASH1-SVBP complex
    • Protein or peptide: Tubulin alpha-1A chain
    • Protein or peptide: Tubulin beta-3 chain
    • Protein or peptide: Tubulinyl-Tyr carboxypeptidase 1
    • Protein or peptide: Small vasohibin-binding protein
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER

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Supramolecule #1: Tenary complex of microtubule with VASH1-SVBP complex

SupramoleculeName: Tenary complex of microtubule with VASH1-SVBP complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Tubulin alpha-1A chain

MacromoleculeName: Tubulin alpha-1A chain / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 50.188441 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFN TFFSETGAGK HVPRAVFVDL EPTVIDEVRT GTYRQLFHP EQLITGKEDA ANNYARGHYT IGKEIIDLVL DRIRKLADQC TGLQGFLVFH SFGGGTGSGF TSLLMERLSV D YGKKSKLE ...String:
MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFN TFFSETGAGK HVPRAVFVDL EPTVIDEVRT GTYRQLFHP EQLITGKEDA ANNYARGHYT IGKEIIDLVL DRIRKLADQC TGLQGFLVFH SFGGGTGSGF TSLLMERLSV D YGKKSKLE FSIYPAPQVS TAVVEPYNSI LTTHTTLEHS DCAFMVDNEA IYDICRRNLD IERPTYTNLN RLIGQIVSSI TA SLRFDGA LNVDLTEFQT NLVPYPRIHF PLATYAPVIS AEKAYHEQLS VAEITNACFE PANQMVKCDP RHGKYMACCL LYR GDVVPK DVNAAIATIK TKRTIQFVDW CPTGFKVGIN YQPPTVVPGG DLAKVQRAVC MLSNTTAIAE AWARLDHKFD LMYA KRAFV HWYVGEGMEE GEFSEAREDM AALEKDYEEV GVDSVEGEGE EEGEEY

UniProtKB: Tubulin alpha-1A chain

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Macromolecule #2: Tubulin beta-3 chain

MacromoleculeName: Tubulin beta-3 chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 50.48152 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPSGNYVGDS DLQLERISVY YNEASSHKYV PRAILVDLEP GTMDSVRSGA FGHLFRPDN FIFGQSGAGN NWAKGHYTEG AELVDSVLDV VRKECENCDC LQGFQLTHSL GGGTGSGMGT LLISKVREEY P DRIMNTFS ...String:
MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPSGNYVGDS DLQLERISVY YNEASSHKYV PRAILVDLEP GTMDSVRSGA FGHLFRPDN FIFGQSGAGN NWAKGHYTEG AELVDSVLDV VRKECENCDC LQGFQLTHSL GGGTGSGMGT LLISKVREEY P DRIMNTFS VVPSPKVSDT VVEPYNATLS IHQLVENTDE TYCIDNEALY DICFRTLKLA TPTYGDLNHL VSATMSGVTT SL RFPGQLN ADLRKLAVNM VPFPRLHFFM PGFAPLTARG SQQYRALTVP ELTQQMFDAK NMMAACDPRH GRYLTVATVF RGR MSMKEV DEQMLAIQSK NSSYFVEWIP NNVKVAVCDI PPRGLKMSST FIGNSTAIQE LFKRISEQFT AMFRRKAFLH WYTG EGMDE MEFTEAESNM NDLVSEYQQY QDATAEEEGE MYEDDEEESE AQGPK

UniProtKB: Tubulin beta-3 chain

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Macromolecule #3: Tubulinyl-Tyr carboxypeptidase 1

MacromoleculeName: Tubulinyl-Tyr carboxypeptidase 1 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO / EC number: tubulinyl-Tyr carboxypeptidase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 29.780445 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: DLRDGGVPFF VNRGGLPVDE ATWERMWKHV AKIHPDGEKV AQRIRGATDL PKIPIPSVPT FQPSTPVPER LEAVQRYIRE LQYNHTGTQ FFEIKKSRPL TGLMDLAKEM TKEALPIKCL EAVILGIYLT NSMPTLERFP ISFKTYFSGN YFRHIVLGVN F AGRYGALG ...String:
DLRDGGVPFF VNRGGLPVDE ATWERMWKHV AKIHPDGEKV AQRIRGATDL PKIPIPSVPT FQPSTPVPER LEAVQRYIRE LQYNHTGTQ FFEIKKSRPL TGLMDLAKEM TKEALPIKCL EAVILGIYLT NSMPTLERFP ISFKTYFSGN YFRHIVLGVN F AGRYGALG MSRREDLMYK PPAFRTLSEL VLDFEAAYGR CWHVLKKVKL GQSVSHDPHS VEQIEWKHSV LDVERLGRDD FR KELERHA RDMRLKIGKG TG

UniProtKB: Tubulinyl-Tyr carboxypeptidase 1

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Macromolecule #4: Small vasohibin-binding protein

MacromoleculeName: Small vasohibin-binding protein / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.821939 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MDPPARKEKT KVKESVSRVE KAKQKSAQQE LKQRQRAEIY ALNRVMTELE QQQFDEFCKQ MQPPGE

UniProtKB: Small vasohibin-binding protein

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Macromolecule #5: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 2 / Formula: GTP
Molecular weightTheoretical: 523.18 Da
Chemical component information

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM

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Macromolecule #6: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER

MacromoleculeName: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / type: ligand / ID: 6 / Number of copies: 2 / Formula: G2P
Molecular weightTheoretical: 521.208 Da
Chemical component information

ChemComp-G2P:
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / GMP-CPP, energy-carrying molecule analogue*YM

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 86 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 46999
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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