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- PDB-8v3n: CCP5 in complex with Glu-P-Glu transition state analog -

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Basic information

Entry
Database: PDB / ID: 8v3n
TitleCCP5 in complex with Glu-P-Glu transition state analog
ComponentsCytosolic carboxypeptidase-like protein 5
KeywordsHYDROLASE/INHIBITOR / carboxypeptidase deglutamylation branch glutamate removal microtubule / HYDROLASE / HYDROLASE-INHIBITOR 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
: / D-MALATE / Cytosolic carboxypeptidase-like protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsChen, J. / Zehr, E.A. / Gruschus, J.M. / Szyk, A. / Liu, Y. / Tanner, M.E. / Tjandra, N. / Roll-Mecak, A.
Funding support United States, 1items
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, E.A. / Gruschus, J.M. / Szyk, A. / Liu, Y. / Tanner, M.E. / Tjandra, N. / Roll-Mecak, A.
History
DepositionNov 28, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytosolic carboxypeptidase-like protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8855
Polymers59,1711
Non-polymers7144
Water3,063170
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.114, 80.414, 103.229
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Cytosolic carboxypeptidase-like protein 5 / ATP/GTP-binding protein-like 5 / Protein deglutamylase CCP5


Mass: 59170.668 Da / Num. of mol.: 1 / Mutation: E516A,residues 339-424 replaced with a SGSGG loop
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AGBL5, CCP5 / Plasmid: pFastBac / Details (production host): His_MBP_Asn10_TEV / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): IPLB-Sf-21-AE
References: UniProt: Q8NDL9, Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases, tubulin-glutamate carboxypeptidase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O5
#4: Chemical ChemComp-A1AAG / (2S)-2-{[(S)-[(3S)-3-acetamido-4-(ethylamino)-4-oxobutyl](hydroxy)phosphoryl]methyl}pentanedioic acid


Mass: 380.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H25N2O8P / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.14 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 0.15 M DL-Malic acid, pH7.0, 0.1 M imidazole, pH7.0, 16% PEG MME 550

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.27→103.23 Å / Num. obs: 25523 / % possible obs: 99.4 % / Redundancy: 12.9 % / CC1/2: 0.961 / Rmerge(I) obs: 0.306 / Rrim(I) all: 0.334 / Net I/σ(I): 11.1
Reflection shellResolution: 2.27→2.35 Å / Redundancy: 12.5 % / Rmerge(I) obs: 1.869 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2238 / CC1/2: 0.613 / Rrim(I) all: 1.992 / % possible all: 95.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→65.11 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2218 1230 4.99 %
Rwork0.193 --
obs0.1945 24673 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→65.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3855 0 44 170 4069
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.003
X-RAY DIFFRACTIONf_angle_d0.556
X-RAY DIFFRACTIONf_dihedral_angle_d13.915
X-RAY DIFFRACTIONf_chiral_restr0.038
X-RAY DIFFRACTIONf_plane_restr0.005
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.390.26551260.24352566X-RAY DIFFRACTION100
2.39-2.50.28131330.23032578X-RAY DIFFRACTION100
2.5-2.630.23841120.23442569X-RAY DIFFRACTION100
2.63-2.80.2751360.22982580X-RAY DIFFRACTION100
2.8-3.010.2591310.21122580X-RAY DIFFRACTION100
3.01-3.320.21761380.20172606X-RAY DIFFRACTION100
3.32-3.80.20781490.17992597X-RAY DIFFRACTION100
3.8-4.780.18821630.162590X-RAY DIFFRACTION99
4.78-65.110.21841420.18272777X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.112-0.0881-0.03511.80440.1250.3079-0.02120.03240.047-0.08140.117-0.4223-0.06120.1825-0.0940.3177-0.02430.0220.3641-0.06130.3091-11.30082.343336.483
22.0951-0.32710.49911.24130.11411.7841-0.0003-0.0954-0.11790.06020.01190.24040.1154-0.2172-0.00640.2561-0.00160.04010.2108-0.00730.2582-39.0064-10.902437.1938
32.21090.79690.2952.62631.02832.732-0.09710.13340.0443-0.20860.10740.0476-0.14540.1734-0.00680.2707-0.00240.00760.26040.01270.2301-31.9874-14.015418.1546
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 174 )
2X-RAY DIFFRACTION2chain 'A' and (resid 175 through 338 )
3X-RAY DIFFRACTION3chain 'A' and (resid 339 through 601 )

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