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

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Basic information

Entry
Database: PDB / ID: 7z6s
TitleMATCAP bound to a human 14 protofilament microtubule
Components
  • Tubulin alpha-1B chain
  • Tubulin beta-3 chain
  • Uncharacterized protein KIAA0895-like
KeywordsPROTEIN BINDING / detyrosination / microtubule-binding / zinc-metalloprotease / tyrosine carboxypeptidase
Function / homology
Function and homology information


tubulinyl-Tyr carboxypeptidase / tubulin-tyrosine carboxypeptidase activity / netrin receptor binding / Post-chaperonin tubulin folding pathway / dorsal root ganglion development / Cilium Assembly / cytoskeleton-dependent intracellular transport / Carboxyterminal post-translational modifications of tubulin / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Intraflagellar transport ...tubulinyl-Tyr carboxypeptidase / tubulin-tyrosine carboxypeptidase activity / netrin receptor binding / Post-chaperonin tubulin folding pathway / dorsal root ganglion development / Cilium Assembly / cytoskeleton-dependent intracellular transport / Carboxyterminal post-translational modifications of tubulin / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / 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 / intercellular bridge / COPI-mediated anterograde transport / Activation of AMPK downstream of NMDARs / cytoplasmic microtubule / metallocarboxypeptidase activity / peptide binding / MHC class II antigen presentation / Mitotic Prometaphase / Recruitment of NuMA to mitotic centrosomes / EML4 and NUDC in mitotic spindle formation / cellular response to interleukin-4 / 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 / ubiquitin protein ligase binding / dendrite / 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 / Helix hairpin bin / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / 60s Ribosomal Protein L30; Chain: A; / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site ...Protein of unknown function DUF1704 / Microtubule-associated tyrosine carboxypeptidase / DUF1704 / Helix hairpin bin / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / 60s Ribosomal Protein L30; Chain: A; / 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 / Helix Hairpins / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Tubulin alpha-1B chain / Tubulin beta-3 chain / Microtubule-associated tyrosine carboxypeptidase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsBak, J. / Perrakis, A.
Funding support Netherlands, 1items
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, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 11, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 16, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_admin / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tubulin alpha-1B chain
B: Tubulin beta-3 chain
H: Tubulin beta-3 chain
K: Tubulin alpha-1B chain
C: Uncharacterized protein KIAA0895-like
E: Uncharacterized protein KIAA0895-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)313,77114
Polymers311,6596
Non-polymers2,1128
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, assay for oligomerization, pelleting assay, microscopy, Colocalization in fluorescently labeled cells
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 3 types, 6 molecules AKBHCE

#1: Protein Tubulin alpha-1B chain / Alpha-tubulin ubiquitous / Tubulin K-alpha-1 / Tubulin alpha-ubiquitous chain


Mass: 51033.324 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Variant: KO MATCAP KO Vash1 KO Vash2 / References: UniProt: P68363
#2: Protein Tubulin beta-3 chain / Tubulin beta-4 chain / Tubulin beta-III


Mass: 51276.367 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TUBB3, TUBB4 / Production host: Homo sapiens (human) / References: UniProt: Q13509
#3: Protein Uncharacterized protein KIAA0895-like


Mass: 53519.848 Da / Num. of mol.: 2 / Mutation: E281Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIAA0895L / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q68EN5

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Non-polymers , 4 types, 8 molecules

#4: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#7: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: MATCAP bound to a human 14 protofilament microtubule / Type: COMPLEX
Details: recombinant MATCAP bound to endogenously obtained tubulin
Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightValue: 0.308 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 6.9
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 303.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 2100 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 2.14 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 8400

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Processing

EM software
IDNameVersionCategory
2EPU2.10.0image acquisition
4cryoSPARCCTF correction
7UCSF ChimeraX3.1model fitting
9cryoSPARCinitial Euler assignment
11cryoSPARCclassification
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 1690210
Details: Templates were created from manually picking 5 micrographs. Particles were then picked with the cryoSPARC filament picker.
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 2221142 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model building

3D fitting-ID: 1 / Source name: PDB / Type: experimental model

IDPDB-IDPdb chain-IDAccession codeInitial refinement model-ID
17SJ7

7sj7

a7SJ71
27SJ7

7sj7

b7SJ71
37SJ7

7sj7

h7SJ71
47SJ7

7sj7

k7SJ71
57Z5H

7z5h

a7Z5H2
67Z5H

7z5h

a7Z5H2

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