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- PDB-4dm9: The Crystal Structure of Ubiquitin Carboxy-terminal hydrolase L1 ... -

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Basic information

Entry
Database: PDB / ID: 4dm9
TitleThe Crystal Structure of Ubiquitin Carboxy-terminal hydrolase L1 (UCHL1) bound to a tripeptide fluoromethyl ketone Z-VAE(OMe)-FMK
Components
  • Tripeptide fluoromethyl ketone inhibitor Z-VAE(OMe)-FMK
  • Ubiquitin carboxyl-terminal hydrolase isozyme L1
KeywordsHYDROLASE / LIGASE/INHIBITOR / Ubiquitin Hydrolase / Ligase / LIGASE-INHIBITOR complex
Function / homology
Function and homology information


axon target recognition / male germ cell proliferation / alpha-2A adrenergic receptor binding / muscle cell development / neuron projection terminus / adult walking behavior / neuromuscular process / eating behavior / axonal transport of mitochondrion / protein deubiquitination ...axon target recognition / male germ cell proliferation / alpha-2A adrenergic receptor binding / muscle cell development / neuron projection terminus / adult walking behavior / neuromuscular process / eating behavior / axonal transport of mitochondrion / protein deubiquitination / regulation of macroautophagy / axon cytoplasm / positive regulation of glycolytic process / negative regulation of MAP kinase activity / ubiquitin binding / response to ischemia / UCH proteinases / cellular response to xenobiotic stimulus / omega peptidase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / cysteine-type endopeptidase activity / neuronal cell body / ubiquitin protein ligase binding / endoplasmic reticulum membrane / nucleoplasm / cytoplasm / cytosol
Similarity search - Function
Ubiquitin carboxyl-terminal hydrolase family 1 cysteine active-site. / Ubiquitin C-terminal Hydrolase UCH-l3 / Peptidase C12, ubiquitin carboxyl-terminal hydrolase / Peptidase C12, ubiquitin carboxyl-terminal hydrolase superfamily / Ubiquitin carboxyl-terminal hydrolase, family 1 / Peptidase C12, ubiquitin carboxyl-terminal hydrolase / Papain-like cysteine peptidase superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Tripeptide fluoromethyl ketone inhibitor Z-VAE(OMe)-FMK / Ubiquitin carboxyl-terminal hydrolase isozyme L1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsDavies, C.W. / Chaney, J. / Korbel, G. / Ringe, D. / Petsko, G.A. / Ploegh, H. / Das, C.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2012
Title: The co-crystal structure of ubiquitin carboxy-terminal hydrolase L1 (UCHL1) with a tripeptide fluoromethyl ketone (Z-VAE(OMe)-FMK).
Authors: Davies, C.W. / Chaney, J. / Korbel, G. / Ringe, D. / Petsko, G.A. / Ploegh, H. / Das, C.
History
DepositionFeb 7, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2012Group: Database references
Revision 1.2Dec 12, 2012Group: Other
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin carboxyl-terminal hydrolase isozyme L1
B: Ubiquitin carboxyl-terminal hydrolase isozyme L1
X: Tripeptide fluoromethyl ketone inhibitor Z-VAE(OMe)-FMK
Y: Tripeptide fluoromethyl ketone inhibitor Z-VAE(OMe)-FMK


Theoretical massNumber of molelcules
Total (without water)51,5344
Polymers51,5344
Non-polymers00
Water75742
1
A: Ubiquitin carboxyl-terminal hydrolase isozyme L1
X: Tripeptide fluoromethyl ketone inhibitor Z-VAE(OMe)-FMK


Theoretical massNumber of molelcules
Total (without water)25,7672
Polymers25,7672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ubiquitin carboxyl-terminal hydrolase isozyme L1
Y: Tripeptide fluoromethyl ketone inhibitor Z-VAE(OMe)-FMK


Theoretical massNumber of molelcules
Total (without water)25,7672
Polymers25,7672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)110.011, 110.011, 78.745
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-308-

HOH

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Components

#1: Protein Ubiquitin carboxyl-terminal hydrolase isozyme L1 / UCH-L1 / Neuron cytoplasmic protein 9.5 / PGP 9.5 / PGP9.5 / Ubiquitin thioesterase L1


Mass: 25266.799 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UCHL1 / Plasmid: pGEX-6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta
References: UniProt: P09936, ubiquitinyl hydrolase 1, Ligases
#2: Protein/peptide Tripeptide fluoromethyl ketone inhibitor Z-VAE(OMe)-FMK


Type: Peptide-like / Class: Inhibitor / Mass: 499.960 Da / Num. of mol.: 2 / Source method: obtained synthetically
References: Tripeptide fluoromethyl ketone inhibitor Z-VAE(OMe)-FMK
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O

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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: 2.31 Å3/Da / Density % sol: 46.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.4M ammonium sulfate, 0.1M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 6, 2006 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. all: 20719 / Num. obs: 20326 / % possible obs: 98.1 % / Observed criterion σ(F): 2.1 / Observed criterion σ(I): 2.1 / Redundancy: 12.9 % / Rsym value: 0.051 / Net I/σ(I): 48.5
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsRsym valueDiffraction-ID% possible all
2.35-2.437.82.10.499189.6
2.43-2.538.93.80.355192.8
2.53-2.6511.35.20.419199.6
2.65-2.7913.98.20.3681100
2.79-2.9614.713.70.2471100
2.96-3.1914.726.40.131100
3.19-3.5114.639.20.0781100
3.51-4.0214.555.60.0451100
4.02-5.0614.493.30.031100
5.06-5013.490.20.022198.5

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ETL

2etl


Resolution: 2.35→34.873 Å / SU ML: 0.38 / σ(F): 1.34 / Phase error: 27.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2502 1037 5.12 %
Rwork0.197 --
obs0.1995 20267 97.89 %
all-20703 -
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.657 Å2 / ksol: 0.357 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-8.915 Å20 Å2-0 Å2
2--8.915 Å20 Å2
3----17.8301 Å2
Refinement stepCycle: LAST / Resolution: 2.35→34.873 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3547 0 0 42 3589
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053611
X-RAY DIFFRACTIONf_angle_d1.0484856
X-RAY DIFFRACTIONf_dihedral_angle_d16.5361361
X-RAY DIFFRACTIONf_chiral_restr0.088530
X-RAY DIFFRACTIONf_plane_restr0.004643
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3503-2.47420.38321340.33692437X-RAY DIFFRACTION89
2.4742-2.62910.33711380.28012696X-RAY DIFFRACTION98
2.6291-2.83210.30771650.25862747X-RAY DIFFRACTION100
2.8321-3.11690.35031620.24032753X-RAY DIFFRACTION100
3.1169-3.56750.24581680.21392777X-RAY DIFFRACTION100
3.5675-4.49320.18031320.15172842X-RAY DIFFRACTION100
4.4932-34.87660.23681380.17882978X-RAY DIFFRACTION99
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)
13.5907-0.44240.85715.67191.2133.8446-0.1107-0.0529-0.04540.00490.27310.2469-0.156-0.4633-0.13970.21310.02590.02120.35250.08420.24236.175116.639914.5648
26.59153.0473-6.63021.588-3.52849.0049-0.8111-0.5419-0.8537-0.07510.4172-0.27540.87970.66850.32670.5280.13970.00350.5180.02670.421847.484211.040223.1044
39.0015-1.47495.41238.0962-2.04897.42480.0420.5642-0.2451-0.74430.18740.4170.1659-0.2229-0.21590.38220.02360.00590.44720.03830.261933.001713.35563.4491
43.5202-5.2664-2.74728.14774.954.8391-0.18620.27160.0443-0.19990.5389-0.23620.0577-0.1825-0.28750.435-0.13470.0280.51380.03460.550137.90143.87569.5624
58.573-0.94652.98286.44322.42687.8430.15440.25240.482-0.4520.201-0.986-0.8570.6289-0.32690.43880.02880.15670.45280.00540.453654.874422.082444.8497
66.26541.4365-0.48418.2477-0.26354.14220.2031-0.5834-0.40851.0916-0.13530.3504-0.0759-1.3217-0.03680.4745-0.05560.01210.7314-0.05870.320144.499215.669461.6965
75.0121-0.2953-0.78974.82742.93754.99710.13640.28420.528-0.5247-0.17660.4168-1.245-1.01330.01760.60490.2618-0.08080.6702-0.03060.473638.573326.763147.3766
85.16413.9454-4.60783.0443-3.47814.1343-0.09840.1664-0.8112-0.6641-0.5297-0.03650.34410.20360.52820.65670.24280.10020.5312-0.01720.489846.757510.617940.4082
98.1196-4.536-0.61933.58962.46158.0553-0.0316-0.19220.76770.6923-0.18190.0167-0.7578-0.59680.1190.52410.0657-0.05640.4365-0.01750.394145.106425.560458.7128
103.86762.32231.69342.959-0.73247.46280.3846-0.96210.30421.6720.2097-0.2050.1403-0.0337-0.47780.52650.03-0.05940.6773-0.11170.627355.265924.743262.7919
119.5371-5.71013.91454.1077-1.06379.01010.002-0.5052-0.08650.52190.3936-0.5478-0.60310.3883-0.35030.3839-0.0803-0.07380.5043-0.030.446756.602417.725553.7477
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:136)
2X-RAY DIFFRACTION2chain 'A' and (resseq 137:159)
3X-RAY DIFFRACTION3chain 'A' and (resseq 160:207)
4X-RAY DIFFRACTION4chain 'A' and (resseq 208:223)
5X-RAY DIFFRACTION5chain 'B' and (resseq 1:45)
6X-RAY DIFFRACTION6chain 'B' and (resseq 46:69)
7X-RAY DIFFRACTION7chain 'B' and (resseq 70:136)
8X-RAY DIFFRACTION8chain 'B' and (resseq 137:159)
9X-RAY DIFFRACTION9chain 'B' and (resseq 160:189)
10X-RAY DIFFRACTION10chain 'B' and (resseq 190:207)
11X-RAY DIFFRACTION11chain 'B' and (resseq 208:223)

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