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- EMDB-14529: MATCAP bound to a human 14 protofilament microtubule -

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Basic information

Entry
Database: EMDB / ID: EMD-14529
TitleMATCAP bound to a human 14 protofilament microtubule
Map data
Sample
  • Complex: MATCAP bound to a human 14 protofilament microtubule
    • Protein or peptide: Tubulin alpha-1B chain
    • Protein or peptide: Tubulin beta-3 chain
    • Protein or peptide: Uncharacterized protein KIAA0895-like
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: ZINC ION
Keywordsdetyrosination / microtubule-binding / zinc-metalloprotease / tyrosine carboxypeptidase / PROTEIN BINDING
Function / homology
Function and homology information


tubulinyl-Tyr carboxypeptidase / tubulin-tyrosine carboxypeptidase / netrin receptor binding / Post-chaperonin tubulin folding pathway / dorsal root ganglion development / Cilium Assembly / cytoskeleton-dependent intracellular transport / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Carboxyterminal post-translational modifications of tubulin / Intraflagellar transport ...tubulinyl-Tyr carboxypeptidase / tubulin-tyrosine carboxypeptidase / netrin receptor binding / Post-chaperonin tubulin folding pathway / dorsal root ganglion development / Cilium Assembly / cytoskeleton-dependent intracellular transport / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Carboxyterminal post-translational modifications of tubulin / Intraflagellar transport / Sealing of the nuclear envelope (NE) by ESCRT-III / Formation of tubulin folding intermediates by CCT/TriC / Gap junction assembly / Prefoldin mediated transfer of substrate to CCT/TriC / Kinesins / COPI-independent Golgi-to-ER retrograde traffic / Assembly and cell surface presentation of NMDA receptors / COPI-dependent Golgi-to-ER retrograde traffic / Recycling pathway of L1 / RHOH GTPase cycle / RHO GTPases activate IQGAPs / microtubule-based process / Hedgehog 'off' state / COPI-mediated anterograde transport / Activation of AMPK downstream of NMDARs / intercellular bridge / cytoplasmic microtubule / metallocarboxypeptidase activity / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / peptide binding / MHC class II antigen presentation / cellular response to interleukin-4 / Recruitment of NuMA to mitotic centrosomes / axon guidance / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Resolution of Sister Chromatid Cohesion / cell periphery / Translocation of SLC2A4 (GLUT4) to the plasma membrane / filopodium / RHO GTPases Activate Formins / brain development / PKR-mediated signaling / structural constituent of cytoskeleton / microtubule cytoskeleton organization / HCMV Early Events / Aggrephagy / The role of GTSE1 in G2/M progression after G2 checkpoint / mitotic spindle / Separation of Sister Chromatids / mitotic cell cycle / lamellipodium / double-stranded RNA binding / microtubule cytoskeleton / growth cone / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / cilium / axon / cell division / neuronal cell body / GTPase activity / dendrite / ubiquitin protein ligase binding / GTP binding / structural molecule activity / proteolysis / extracellular exosome / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Protein of unknown function DUF1704 / Microtubule-associated tyrosine carboxypeptidase / DUF1704 / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain ...Protein of unknown function DUF1704 / Microtubule-associated tyrosine carboxypeptidase / DUF1704 / 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 alpha-1B chain / Tubulin beta-3 chain / Microtubule-associated tyrosine carboxypeptidase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsBak J / Perrakis A
Funding support Netherlands, 1 items
OrganizationGrant numberCountry
Oncode Institute Netherlands
CitationJournal: 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
DepositionMar 14, 2022-
Header (metadata) releaseMay 11, 2022-
Map releaseMay 11, 2022-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14529.png

Downloads & links

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Map

FileDownload / File: emd_14529.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.3 Å/pix.
x 416 pix.
= 540.8 Å		1.3 Å/pix.
x 416 pix.
= 540.8 Å		1.3 Å/pix.
x 416 pix.
= 540.8 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.7125788 - 1.3639016
Average (Standard dev.)0.0026608456 (±0.03257488)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions416416416
Spacing416416416
CellA=B=C: 540.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_14529_msk_1.map
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Half map: #2

Fileemd_14529_half_map_1.map
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Half map: #1

Fileemd_14529_half_map_2.map
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Sample components

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Entire : MATCAP bound to a human 14 protofilament microtubule

EntireName: MATCAP bound to a human 14 protofilament microtubule
Components
  • Complex: MATCAP bound to a human 14 protofilament microtubule
    • Protein or peptide: Tubulin alpha-1B chain
    • Protein or peptide: Tubulin beta-3 chain
    • Protein or peptide: Uncharacterized protein KIAA0895-like
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: ZINC ION

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Supramolecule #1: MATCAP bound to a human 14 protofilament microtubule

SupramoleculeName: MATCAP bound to a human 14 protofilament microtubule / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Details: recombinant MATCAP bound to endogenously obtained tubulin
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 308 KDa

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Macromolecule #1: Tubulin alpha-1B chain

MacromoleculeName: Tubulin alpha-1B chain / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 51.033324 KDa
SequenceString: 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

UniProtKB: Tubulin alpha-1B 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: 51.276367 KDa
Recombinant expressionOrganism: Homo sapiens (human)
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 AQGPKENLYF Q

UniProtKB: Tubulin beta-3 chain

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Macromolecule #3: Uncharacterized protein KIAA0895-like

MacromoleculeName: Uncharacterized protein KIAA0895-like / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 53.519848 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: 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

UniProtKB: Microtubule-associated tyrosine carboxypeptidase 1

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Macromolecule #4: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / 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 #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #6: GUANOSINE-5'-DIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 2 / Formula: GDP
Molecular weightTheoretical: 443.201 Da
Chemical component information

ChemComp-GDP:
GUANOSINE-5'-DIPHOSPHATE / GDP, energy-carrying molecule*YM

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Macromolecule #7: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 7 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 6.9
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 303.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm 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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 81000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1690210
Details: Templates were created from manually picking 5 micrographs. Particles were then picked with the cryoSPARC filament picker.
Startup modelType of model: NONE
Details: The start-up model was created using the helical refinement job in cryoSPARC
Final reconstructionNumber 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
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC / Details: branch-and-bound
Final angle assignmentType: MAXIMUM LIKELIHOOD / Details: branch-and-bound

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Atomic model buiding 1

Initial model
PDB IDChain

7sj7

chain_id: a, source_name: PDB, initial_model_type: experimental model

7sj7

chain_id: b, source_name: PDB, initial_model_type: experimental model

7sj7

chain_id: h, source_name: PDB, initial_model_type: experimental model

7sj7

chain_id: k, source_name: PDB, initial_model_type: experimental model

7z5h

chain_id: a, source_name: PDB, initial_model_type: experimental model

7z5h

chain_id: a, source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-7z6s:
MATCAP bound to a human 14 protofilament microtubule

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