+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-42972 | |||||||||
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Title | CCP5 in complex with microtubules class2 | |||||||||
Map data | Composite map of CCP5 class2 in complex with two microtubule protofilaments, stitched from deepEMhancer processed focused CCP5 map and two protofilament maps. | |||||||||
Sample |
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Keywords | carboxypeptidase deglutamylation branch glutamate removal microtubule / HYDROLASE / HYDROLASE-SUBSTRATE complex / HYDROLASE-SUBSTRATE / STRUCTURAL PROTEIN complex | |||||||||
Function / homology | Function and homology information tubulin-glutamate carboxypeptidase / protein deglutamylation / protein side chain deglutamylation / protein branching point deglutamylation / C-terminal protein deglutamylation / Carboxyterminal post-translational modifications of tubulin / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Hedgehog 'off' state / Cilium Assembly / Intraflagellar transport ...tubulin-glutamate carboxypeptidase / protein deglutamylation / protein side chain deglutamylation / protein branching point deglutamylation / C-terminal protein deglutamylation / Carboxyterminal post-translational modifications of tubulin / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Hedgehog 'off' state / Cilium Assembly / Intraflagellar transport / COPI-dependent Golgi-to-ER retrograde traffic / Carboxyterminal post-translational modifications of tubulin / RHOH GTPase cycle / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins / PKR-mediated signaling / The role of GTSE1 in G2/M progression after G2 checkpoint / Aggrephagy / Resolution of Sister Chromatid Cohesion / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Separation of Sister Chromatids / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / Recruitment of NuMA to mitotic centrosomes / COPI-mediated anterograde transport / intercellular bridge / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / metallocarboxypeptidase activity / tubulin binding / mitotic spindle / structural constituent of cytoskeleton / microtubule cytoskeleton organization / microtubule cytoskeleton / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / mitotic cell cycle / midbody / defense response to virus / microtubule / GTPase activity / GTP binding / proteolysis / zinc ion binding / nucleus / metal ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Sus scrofa (pig) / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
Authors | Chen J / Zehr EA / Gruschus JM / Szyk A / Liu Y / Tanner ME / Tjandra N / Roll-Mecak A | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nature / Year: 2024 Title: Tubulin code eraser CCP5 binds branch glutamates by substrate deformation. Authors: Jiayi Chen / Elena A Zehr / James M Gruschus / Agnieszka Szyk / Yanjie Liu / Martin E Tanner / Nico Tjandra / Antonina Roll-Mecak / Abstract: Microtubule function is modulated by the tubulin code, diverse posttranslational modifications that are altered dynamically by writer and eraser enzymes. Glutamylation-the addition of branched ...Microtubule function is modulated by the tubulin code, diverse posttranslational modifications that are altered dynamically by writer and eraser enzymes. Glutamylation-the addition of branched (isopeptide-linked) glutamate chains-is the most evolutionarily widespread tubulin modification. It is introduced by tubulin tyrosine ligase-like enzymes and erased by carboxypeptidases of the cytosolic carboxypeptidase (CCP) family. Glutamylation homeostasis, achieved through the balance of writers and erasers, is critical for normal cell function, and mutations in CCPs lead to human disease. Here we report cryo-electron microscopy structures of the glutamylation eraser CCP5 in complex with the microtubule, and X-ray structures in complex with transition-state analogues. Combined with NMR analysis, these analyses show that CCP5 deforms the tubulin main chain into a unique turn that enables lock-and-key recognition of the branch glutamate in a cationic pocket that is unique to CCP family proteins. CCP5 binding of the sequences flanking the branch point primarily through peptide backbone atoms enables processing of diverse tubulin isotypes and non-tubulin substrates. Unexpectedly, CCP5 exhibits inefficient processing of an abundant β-tubulin isotype in the brain. This work provides an atomistic view into glutamate branch recognition and resolution, and sheds light on homeostasis of the tubulin glutamylation syntax. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_42972.map.gz | 258 MB | EMDB map data format | |
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Header (meta data) | emd-42972-v30.xml emd-42972.xml | 21 KB 21 KB | Display Display | EMDB header |
Images | emd_42972.png | 164.1 KB | ||
Filedesc metadata | emd-42972.cif.gz | 7.7 KB | ||
Others | emd_42972_additional_1.map.gz | 281.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-42972 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-42972 | HTTPS FTP |
-Validation report
Summary document | emd_42972_validation.pdf.gz | 441.5 KB | Display | EMDB validaton report |
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Full document | emd_42972_full_validation.pdf.gz | 441.1 KB | Display | |
Data in XML | emd_42972_validation.xml.gz | 7.6 KB | Display | |
Data in CIF | emd_42972_validation.cif.gz | 8.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-42972 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-42972 | HTTPS FTP |
-Related structure data
Related structure data | 8v4lMC 8v3mC 8v3nC 8v3oC 8v3pC 8v3qC 8v3rC 8v3sC 8v4kC 8v4mC C: citing same article (ref.) M: atomic model generated by this map |
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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_42972.map.gz / Format: CCP4 / Size: 381.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Composite map of CCP5 class2 in complex with two microtubule protofilaments, stitched from deepEMhancer processed focused CCP5 map and two protofilament maps. | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.245 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Composite map of CCP5 class2 in complex with...
File | emd_42972_additional_1.map | ||||||||||||
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Annotation | Composite map of CCP5 class2 in complex with two microtubule protofilaments, stitched from CCP5 focused and two protofilament raw full maps. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : CCP5 in complex with microtubules
Entire | Name: CCP5 in complex with microtubules |
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Components |
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-Supramolecule #1: CCP5 in complex with microtubules
Supramolecule | Name: CCP5 in complex with microtubules / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 / Details: Composite structure of CCP5:microtubule class#2 |
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-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: Sus scrofa (pig) / Organ: brain |
Molecular weight | Theoretical: 50.204445 KDa |
Sequence | String: 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 RLISQIVSSI TA SLRFDGA LNVDLTEFQT NLVPYPRIHF PLATYAPVIS AEKAYHEQLS VAEITNACFE PANQMVKCDP RHGKYMACCL LYR GDVVPK DVNAAIATIK TKRSIQFVDW CPTGFKVGIN YQPPTVVPGG DLAKVQRAVC MLSNTTAIAE AWARLDHKFD LMYA KRAFV HWYVGEGMEE GEFSEAREDM AALEKDYEEV GVDSVEGEGE EEGEEY UniProtKB: Tubulin alpha-1B chain |
-Macromolecule #2: Tubulin beta chain
Macromolecule | Name: Tubulin beta chain / type: protein_or_peptide / ID: 2 Details: Beta tubulin from porcine brain microtubules, heterogeneous in tail sequence Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Sus scrofa (pig) / Organ: brain |
Molecular weight | Theoretical: 50.377309 KDa |
Sequence | String: MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGSYHGDS DLQLERINVY YNEAAGNKYV PRAILVDLEP GTMDSVRSGP FGQIFRPDN FVFGQSGAGN NWAKGHYTEG AELVDSVLDV VRKESESCDC LQGFQLTHSL GGGTGSGMGT LLISKIREEY P DRIMNTFS ...String: MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGSYHGDS DLQLERINVY YNEAAGNKYV PRAILVDLEP GTMDSVRSGP FGQIFRPDN FVFGQSGAGN NWAKGHYTEG AELVDSVLDV VRKESESCDC LQGFQLTHSL GGGTGSGMGT LLISKIREEY P DRIMNTFS VVPSPKVSDT VVEPYNATLS VHQLVENTDE TYCIDNEALY DICFRTLKLT TPTYGDLNHL VSATMSGVTT CL RFPGQLN ADLRKLAVNM VPFPRLHFFM PGFAPLTSRG SQQYRALTVP ELTQQMFDAK NMMAACDPRH GRYLTVAAVF RGR MSMKEV DEQMLNVQNK NSSYFVEWIP NNVKTAVCDI PPRGLKMSAT FIGNSTAIQE LFKRISEQFT AMFRRKAFLH WYTG EGMDE MEFTEAESNM NDLVSEYQQY QDATADEQGE FEEEGEEDEA (UNK)(UNK)E(UNK)(UNK) UniProtKB: Tubulin beta chain |
-Macromolecule #3: Cytosolic carboxypeptidase-like protein 5
Macromolecule | Name: Cytosolic carboxypeptidase-like protein 5 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 68.229547 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: NELRCGGLLF SSRFDSGNLA HVEKVESLSS DGEGVGGGAS ALTSGIASSP DYEFNVWTRP DCAETEFENG NRSWFYFSVR GGMPGKLIK INIMNMNKQS KLYSQGMAPF VRTLPTRPRW ERIRDRPTFE MTETQFVLSF VHRFVEGRGA TTFFAFCYPF S YSDCQELL ...String: NELRCGGLLF SSRFDSGNLA HVEKVESLSS DGEGVGGGAS ALTSGIASSP DYEFNVWTRP DCAETEFENG NRSWFYFSVR GGMPGKLIK INIMNMNKQS KLYSQGMAPF VRTLPTRPRW ERIRDRPTFE MTETQFVLSF VHRFVEGRGA TTFFAFCYPF S YSDCQELL NQLDQRFPEN HPTHSSPLDT IYYHRELLCY SLDGLRVDLL TITSCHGLRE DREPRLEQLF PDTSTPRPFR FA GKRIFFL SSRVHPGETP SSFVFNGFLD FILRPDDPRA QTLRRLFVFK LIPMLNPDGV VRGHYRTDSR GVNLNRQYLK PDA VLHPAI YGAKAVLLYH HVHSRLNSQS SSEHQPSSCL PPDAPVSDLE KANNLQNEAQ CGHSADRHNA EAWKQTEPAE QKLN SVWIM PQQSAGLEES APDTIPPKES GVAYYVDLHG HASKRGCFMY GNSFSDESTQ VENMLYPKLI SLNSAHFDFQ GCNFS EKNM YARDRRDGQS KEGSGRVAIY KASGIIHSYT LACNYNTGRS VNSIPAACHD NGRASPPPPP AFPSRYTVEL FEQVGR AMA IAALDMAECN PWPRIVLSEH SSLTNLRAWM LKHVRNSRGL SS UniProtKB: Cytosolic carboxypeptidase-like protein 5 |
-Macromolecule #4: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 4 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #5: GUANOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 2 / Formula: GTP |
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Molecular weight | Theoretical: 523.18 Da |
Chemical component information | ChemComp-GTP: |
-Macromolecule #6: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
Macromolecule | Name: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / type: ligand / ID: 6 / Number of copies: 2 / Formula: G2P |
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Molecular weight | Theoretical: 521.208 Da |
Chemical component information | ChemComp-G2P: |
-Macromolecule #7: GLUTAMIC ACID
Macromolecule | Name: GLUTAMIC ACID / type: ligand / ID: 7 Details: enzymatically linked to the side chain of GLU B 503 of beta-tubulin Number of copies: 1 / Formula: GLU |
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Molecular weight | Theoretical: 147.129 Da |
Chemical component information | ChemComp-GLU: |
-Macromolecule #8: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 8 / Number of copies: 1 / 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 | particle |
-Sample preparation
Concentration | 0.3 mg/mL | ||||||||||||
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Buffer | pH: 7.4 Component:
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Grid | Model: Au-flat 1.2/1.3 / Material: GOLD / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 45 | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 303 K / Instrument: LEICA EM GP |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average exposure time: 1.651 sec. / Average electron dose: 53.34 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 135000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: Cross-correlation coefficient | |||||||||
Output model | PDB-8v4l: |