+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14529 | |||||||||
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Title | MATCAP bound to a human 14 protofilament microtubule | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information tubulinyl-Tyr carboxypeptidase / tubulin-tyrosine carboxypeptidase / netrin receptor binding / Post-chaperonin tubulin folding pathway / Carboxyterminal post-translational modifications of tubulin / dorsal root ganglion development / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / cytoskeleton-dependent intracellular transport / Intraflagellar transport ...tubulinyl-Tyr carboxypeptidase / tubulin-tyrosine carboxypeptidase / netrin receptor binding / Post-chaperonin tubulin folding pathway / Carboxyterminal post-translational modifications of tubulin / dorsal root ganglion development / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / cytoskeleton-dependent intracellular transport / Intraflagellar transport / Sealing of the nuclear envelope (NE) by ESCRT-III / Gap junction assembly / Formation of tubulin folding intermediates by CCT/TriC / COPI-independent Golgi-to-ER retrograde traffic / Prefoldin mediated transfer of substrate to CCT/TriC / Kinesins / Assembly and cell surface presentation of NMDA receptors / COPI-dependent Golgi-to-ER retrograde traffic / intercellular bridge / Recycling pathway of L1 / RHOH GTPase cycle / RHO GTPases activate IQGAPs / Hedgehog 'off' state / cytoplasmic microtubule / metallocarboxypeptidase activity / microtubule-based process / COPI-mediated anterograde transport / Activation of AMPK downstream of NMDARs / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / Recruitment of NuMA to mitotic centrosomes / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / cellular response to interleukin-4 / filopodium / cell periphery / RHO GTPases Activate Formins / Translocation of SLC2A4 (GLUT4) to the plasma membrane / axon guidance / peptide binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / brain development / PKR-mediated signaling / structural constituent of cytoskeleton / mitotic spindle / microtubule cytoskeleton organization / Aggrephagy / HCMV Early Events / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / microtubule cytoskeleton / double-stranded RNA binding / lamellipodium / mitotic cell cycle / growth cone / microtubule / cell division / axon / GTPase activity / dendrite / neuronal cell body / ubiquitin protein ligase binding / structural molecule activity / GTP binding / proteolysis / extracellular exosome / metal ion binding / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / human (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
Authors | Bak J / Perrakis A | |||||||||
Funding support | Netherlands, 1 items
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Citation | Journal: Science / Year: 2022 Title: Posttranslational modification of microtubules by the MATCAP detyrosinase. Authors: Lisa Landskron / Jitske Bak / Athanassios Adamopoulos / Konstantina Kaplani / Maria Moraiti / Lisa G van den Hengel / Ji-Ying Song / Onno B Bleijerveld / Joppe Nieuwenhuis / Tatjana ...Authors: Lisa Landskron / Jitske Bak / Athanassios Adamopoulos / Konstantina Kaplani / Maria Moraiti / Lisa G van den Hengel / Ji-Ying Song / Onno B Bleijerveld / Joppe Nieuwenhuis / Tatjana Heidebrecht / Linda Henneman / Marie-Jo Moutin / Marin Barisic / Stavros Taraviras / Anastassis Perrakis / Thijn R Brummelkamp / Abstract: The detyrosination-tyrosination cycle involves the removal and religation of the C-terminal tyrosine of α-tubulin and is implicated in cognitive, cardiac, and mitotic defects. The vasohibin-small ...The detyrosination-tyrosination cycle involves the removal and religation of the C-terminal tyrosine of α-tubulin and is implicated in cognitive, cardiac, and mitotic defects. The vasohibin-small vasohibin-binding protein (SVBP) complex underlies much, but not all, detyrosination. We used haploid genetic screens to identify an unannotated protein, microtubule associated tyrosine carboxypeptidase (MATCAP), as a remaining detyrosinating enzyme. X-ray crystallography and cryo-electron microscopy structures established MATCAP's cleaving mechanism, substrate specificity, and microtubule recognition. Paradoxically, whereas abrogation of tyrosine religation is lethal in mice, codeletion of MATCAP and SVBP is not. Although viable, defective detyrosination caused microcephaly, associated with proliferative defects during neurogenesis, and abnormal behavior. Thus, MATCAP is a missing component of the detyrosination-tyrosination cycle, revealing the importance of this modification in brain formation. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_14529.map.gz | 138.3 MB | EMDB map data format | |
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Header (meta data) | emd-14529-v30.xml emd-14529.xml | 22.9 KB 22.9 KB | Display Display | EMDB header |
Images | emd_14529.png | 97.7 KB | ||
Masks | emd_14529_msk_1.map | 274.6 MB | Mask map | |
Others | emd_14529_half_map_1.map.gz emd_14529_half_map_2.map.gz | 255 MB 255.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14529 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14529 | HTTPS FTP |
-Related structure data
Related structure data | 7z6sMC 7z5gC 7z5hC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_14529.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.3 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_14529_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_14529_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_14529_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : MATCAP bound to a human 14 protofilament microtubule
Entire | Name: MATCAP bound to a human 14 protofilament microtubule |
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Components |
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-Supramolecule #1: MATCAP bound to a human 14 protofilament microtubule
Supramolecule | Name: MATCAP bound to a human 14 protofilament microtubule / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 Details: recombinant MATCAP bound to endogenously obtained tubulin |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Molecular weight | Theoretical: 308 KDa |
-Macromolecule #1: Tubulin alpha-1B chain
Macromolecule | Name: Tubulin alpha-1B chain / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: human (human) |
Molecular weight | Theoretical: 51.033324 KDa |
Sequence | String: MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIHHHHHHGG GDDSFNTFFS ETGAGKHVPR AVFVDLEPTV IDEVRTGTY RQLFHPEQLI TGKEDAANNY ARGHYTIGKE IIDLVLDRIR KLADQCTGLQ GFLVFHSFGG GTGSGFTSLL M ERLSVDYG ...String: MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIHHHHHHGG GDDSFNTFFS ETGAGKHVPR AVFVDLEPTV IDEVRTGTY RQLFHPEQLI TGKEDAANNY ARGHYTIGKE IIDLVLDRIR KLADQCTGLQ GFLVFHSFGG GTGSGFTSLL M ERLSVDYG KKSKLEFSIY PAPQVSTAVV EPYNSILTTH TTLEHSDCAF MVDNEAIYDI CRRNLDIERP TYTNLNRLIS QI VSSITAS LRFDGALNVD LTEFQTNLVP YPRIHFPLAT YAPVISAEKA YHEQLSVAEI TNACFEPANQ MVKCDPRHGK YMA CCLLYR GDVVPKDVNA AIATIKTKRS IQFVDWCPTG FKVGINYQPP TVVPGGDLAK VQRAVCMLSN TTAIAEAWAR LDHK FDLMY AKRAFVHWYV GEGMEEGEFS EAREDMAALE KDYEEVGVDS VEGEGEEEGE EY |
-Macromolecule #2: Tubulin beta-3 chain
Macromolecule | Name: Tubulin beta-3 chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 51.276367 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 AQGPKENLYF Q |
-Macromolecule #3: Uncharacterized protein KIAA0895-like
Macromolecule | Name: Uncharacterized protein KIAA0895-like / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 53.519848 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MVLDSGAQAY DQAPPSPPTS PPSLRHRLKP SDRDGPPLYP WSQSLALPLA LAVPPALQPQ PEQQPFSQML LGHRGHMRRS ESTYSVNST GRRGRGTLGR PPPGRGRNPG GGTLRPAASL PHIAKTQRDA GHIASKSPCM LVALRPTNMD RERDKFFQSH Y TYNPQFEY ...String: MVLDSGAQAY DQAPPSPPTS PPSLRHRLKP SDRDGPPLYP WSQSLALPLA LAVPPALQPQ PEQQPFSQML LGHRGHMRRS ESTYSVNST GRRGRGTLGR PPPGRGRNPG GGTLRPAASL PHIAKTQRDA GHIASKSPCM LVALRPTNMD RERDKFFQSH Y TYNPQFEY QEPMPTAVLE KYCEASGQFI HQAVGIIEAV LEKFGTYEHF EAATGGQLLT KCQIWSIVRK YMQKEGCAGE VV VQLSEDL LSQAVMMVEN SRPTLAINLT GARQYWLEGM LRHQIGTHYL RGVNNARQPW HNAEGRLRYG LRPANPTEEG LAS LHSVLF RKQPFLWRAA LLYYTIHRAA RMSFRQLFQD LERYVQDADV RWEYCVRAKR GQTDTSLPGC FSKDQVYLDG IVRI LRHRQ TIDFPLLTSL GKVSYEDVDH LRPHGVLDNT RVPHFMQDLA RYRQQLEHIM ATNRLDEAEL GRLLPD |
-Macromolecule #4: GUANOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 2 / Formula: GTP |
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Molecular weight | Theoretical: 523.18 Da |
Chemical component information | ChemComp-GTP: |
-Macromolecule #5: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #6: GUANOSINE-5'-DIPHOSPHATE
Macromolecule | Name: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 2 / Formula: GDP |
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Molecular weight | Theoretical: 443.201 Da |
Chemical component information | ChemComp-GDP: |
-Macromolecule #7: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 7 / Number of copies: 2 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | helical array |
-Sample preparation
Buffer | pH: 6.9 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 303.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 81000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 8400 / Average exposure time: 2.14 sec. / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 1690210 Details: Templates were created from manually picking 5 micrographs. Particles were then picked with the cryoSPARC filament picker. |
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CTF correction | Software - Name: cryoSPARC |
Startup model | Type of model: NONE Details: The start-up model was created using the helical refinement job in cryoSPARC |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC / Details: branch-and-bound |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Details: branch-and-bound |
Final reconstruction | Number classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 2221142 |