+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-42952 | |||||||||
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Title | Structure of CCP5 class3 | |||||||||
Map data | CCP5 class#3 focused map, b-factor sharpened | |||||||||
Sample |
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Keywords | carboxypeptidase deglutamylation branch glutamate removal microtubule / HYDROLASE / HYDROLASE-SUBSTRATE 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 / intercellular bridge / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / metallocarboxypeptidase activity / tubulin binding ...tubulin-glutamate carboxypeptidase / protein deglutamylation / protein side chain deglutamylation / protein branching point deglutamylation / C-terminal protein deglutamylation / Carboxyterminal post-translational modifications of tubulin / intercellular bridge / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / metallocarboxypeptidase activity / tubulin binding / mitotic spindle / microtubule cytoskeleton / midbody / defense response to virus / proteolysis / zinc ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Sus scrofa (pig) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 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_42952.map.gz | 8.7 MB | EMDB map data format | |
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Header (meta data) | emd-42952-v30.xml emd-42952.xml | 23.4 KB 23.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_42952_fsc.xml | 21 KB | Display | FSC data file |
Images | emd_42952.png | 89.7 KB | ||
Masks | emd_42952_msk_1.map | 381.1 MB | Mask map | |
Filedesc metadata | emd-42952.cif.gz | 6.8 KB | ||
Others | emd_42952_additional_1.map.gz emd_42952_additional_2.map.gz emd_42952_half_map_1.map.gz emd_42952_half_map_2.map.gz | 300 MB 334.9 MB 302.1 MB 302.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-42952 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-42952 | HTTPS FTP |
-Validation report
Summary document | emd_42952_validation.pdf.gz | 697.9 KB | Display | EMDB validaton report |
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Full document | emd_42952_full_validation.pdf.gz | 697.5 KB | Display | |
Data in XML | emd_42952_validation.xml.gz | 24.2 KB | Display | |
Data in CIF | emd_42952_validation.cif.gz | 32.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-42952 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-42952 | HTTPS FTP |
-Related structure data
Related structure data | 8v3sMC 8v3mC 8v3nC 8v3oC 8v3pC 8v3qC 8v3rC 8v4kC 8v4lC 8v4mC 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_42952.map.gz / Format: CCP4 / Size: 381.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | CCP5 class#3 focused map, b-factor sharpened | ||||||||||||||||||||||||||||||||||||
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
-Mask #1
File | emd_42952_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: CCP5 class#3 focused map, raw full map
File | emd_42952_additional_1.map | ||||||||||||
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Annotation | CCP5 class#3 focused map, raw full map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: CCP5 class#3 focused map, DeepEMhancer processed
File | emd_42952_additional_2.map | ||||||||||||
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Annotation | CCP5 class#3 focused map, DeepEMhancer processed | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: CCP5 class#3 focused map, raw half map
File | emd_42952_half_map_1.map | ||||||||||||
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Annotation | CCP5 class#3 focused map, raw half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: CCP5 class#3 focused map, raw half map
File | emd_42952_half_map_2.map | ||||||||||||
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Annotation | CCP5 class#3 focused map, raw half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : CCP5 in complex with beta tubulin tail
Entire | Name: CCP5 in complex with beta tubulin tail |
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Components |
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-Supramolecule #1: CCP5 in complex with beta tubulin tail
Supramolecule | Name: CCP5 in complex with beta tubulin tail / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 Details: Focused refinement of CCP5:microtubule class#3 structure |
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-Macromolecule #1: Cytosolic carboxypeptidase-like protein 5
Macromolecule | Name: Cytosolic carboxypeptidase-like protein 5 / type: protein_or_peptide / ID: 1 / 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 #2: beta tubulin tail
Macromolecule | Name: beta tubulin tail / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Sus scrofa (pig) / Organ: brain |
Molecular weight | Theoretical: 487.548 Da |
Sequence | String: (UNK)(UNK)E(UNK)(UNK) |
-Macromolecule #3: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Macromolecule #4: GLUTAMIC ACID
Macromolecule | Name: GLUTAMIC ACID / type: ligand / ID: 4 / Number of copies: 1 / Formula: GLU |
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Molecular weight | Theoretical: 147.129 Da |
Chemical component information | ChemComp-GLU: |
-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 / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 45 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. | ||||||||||||
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 | Chain - Source name: Other / Chain - Initial model type: experimental model / Details: crystal structure of apo CCP5 |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: Cross-correlation coefficient |
Output model | PDB-8v3s: |