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- EMDB-42950: Structure of CCP5 class1 -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-42950
TitleStructure of CCP5 class1
Map dataCCP5 class#1 focused map, b-factor sharpened
Sample
  • Complex: CCP5 in complex with beta tubulin tail
    • Protein or peptide: Cytosolic carboxypeptidase-like protein 5
  • Protein or peptide: beta tubulin tail
  • Ligand: ZINC ION
  • Ligand: GLUTAMIC ACID
Keywordscarboxypeptidase / 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 / cytoplasm / cytosol
Similarity search - Function
Cytosolic carboxypeptidase-like protein 5 catalytic domain / Cytosolic carboxypeptidase, N-terminal / Cytosolic carboxypeptidase N-terminal domain / Peptidase family M14 domain profile. / Peptidase M14, carboxypeptidase A / Zinc carboxypeptidase
Similarity search - Domain/homology
Cytosolic carboxypeptidase-like protein 5
Similarity search - Component
Biological speciesHomo sapiens (human) / Sus scrofa (pig)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsChen J / Zehr EA / Gruschus JM / Szyk A / Liu Y / Tanner ME / Tjandra N / Roll-Mecak A
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)1ZIANS003163 United States
CitationJournal: Nature / Year: 2024
Title: Tubulin code eraser CCP5 binds branch glutamates by substrate deformation
Authors: Chen J / Zehr EA / Gruschus JM / Szyk A / Liu Y / Tanner ME / Tjandra N / Roll-Mecak A
History
DepositionNov 28, 2023-
Header (metadata) releaseJul 17, 2024-
Map releaseJul 17, 2024-
UpdateJul 17, 2024-
Current statusJul 17, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42950.png

Downloads & links

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Map

FileDownload / File: emd_42950.map.gz / Format: CCP4 / Size: 381.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCCP5 class#1 focused map, b-factor sharpened
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.25 Å/pix.
x 464 pix.
= 577.68 Å		1.25 Å/pix.
x 464 pix.
= 577.68 Å		1.25 Å/pix.
x 464 pix.
= 577.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.245 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.09203296 - 0.16503958
Average (Standard dev.)0.0000072954863 (±0.0008041619)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions464464464
Spacing464464464
CellA=B=C: 577.68 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_42950_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: CCP5 class#1 focused map, DeepEMhancer processed

Fileemd_42950_additional_1.map
AnnotationCCP5 class#1 focused map, DeepEMhancer processed
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: CCP5 class#1 focused map, raw full map

Fileemd_42950_additional_2.map
AnnotationCCP5 class#1 focused map, raw full map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: CCP5 class#1 focused map, raw half map

Fileemd_42950_half_map_1.map
AnnotationCCP5 class#1 focused map, raw half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: CCP5 class#1 focused map, raw half map

Fileemd_42950_half_map_2.map
AnnotationCCP5 class#1 focused map, raw half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : CCP5 in complex with beta tubulin tail

EntireName: CCP5 in complex with beta tubulin tail
Components
  • Complex: CCP5 in complex with beta tubulin tail
    • Protein or peptide: Cytosolic carboxypeptidase-like protein 5
  • Protein or peptide: beta tubulin tail
  • Ligand: ZINC ION
  • Ligand: GLUTAMIC ACID

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Supramolecule #1: CCP5 in complex with beta tubulin tail

SupramoleculeName: CCP5 in complex with beta tubulin tail / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: Focused refinement of CCP5:microtubule class#1 structure

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Macromolecule #1: Cytosolic carboxypeptidase-like protein 5

MacromoleculeName: Cytosolic carboxypeptidase-like protein 5 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 68.229547 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: 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

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Macromolecule #2: beta tubulin tail

MacromoleculeName: beta tubulin tail / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig) / Organ: brain
Molecular weightTheoretical: 827.967 Da
SequenceString:
(UNK)(UNK)(UNK)(UNK)E(UNK)(UNK)(UNK)(UNK)

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Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #4: GLUTAMIC ACID

MacromoleculeName: GLUTAMIC ACID / type: ligand / ID: 4 / Number of copies: 1 / Formula: GLU
Molecular weightTheoretical: 147.129 Da
Chemical component information

ChemComp-GLU:
GLUTAMIC ACID

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.3 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
150.0 mMKClpotassium chloride
1.0 mMC9H15O6PTCEP
GridModel: 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.
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 303 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average exposure time: 1.651 sec. / Average electron dose: 53.34 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 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 stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 162521
Startup modelType of model: OTHER
Details: Synthetic microtubule references were generated in UCSF Chimera.
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.8) / Number images used: 239249
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: experimental model / Details: crystal structure of apo CCP5
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Cross-correlation coefficient
Output model

PDB-8v3q:
Structure of CCP5 class1

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