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- PDB-3ihr: Crystal Structure of Uch37 -

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Basic information

Entry
Database: PDB / ID: 3ihr
TitleCrystal Structure of Uch37
ComponentsUbiquitin carboxyl-terminal hydrolase isozyme L5
KeywordsHYDROLASE / Center for Eukaryotic Structural Genomics / Uch37 / UCH-L5 / ubiquitin hydrolase / Homo sapiens / ubiquitin / proteasome / ino80 / smad7 / rpn13 / PSI / Protein structure initiative / CESG / structural genomics / Protease / Thiol protease / Ubl conjugation pathway
Function / homology
Function and homology information


lateral ventricle development / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / forebrain morphogenesis / Ino80 complex / cytosolic proteasome complex / positive regulation of smoothened signaling pathway / midbrain development / regulation of chromosome organization / endopeptidase inhibitor activity ...lateral ventricle development / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / forebrain morphogenesis / Ino80 complex / cytosolic proteasome complex / positive regulation of smoothened signaling pathway / midbrain development / regulation of chromosome organization / endopeptidase inhibitor activity / proteasome binding / protein deubiquitination / regulation of DNA replication / regulation of embryonic development / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / regulation of DNA repair / regulation of proteasomal protein catabolic process / positive regulation of DNA repair / telomere maintenance / Downregulation of TGF-beta receptor signaling / UCH proteinases / ubiquitin-dependent protein catabolic process / DNA recombination / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / regulation of cell cycle / chromatin remodeling / DNA repair / nucleolus / positive regulation of DNA-templated transcription / RNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #860 / Ubiquitinyl hydrolase, UCH37 type / Ubiquitinyl hydrolase-L5 / Peptidase C12, C-terminal domain / Ubiquitin carboxyl-terminal hydrolases / 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 ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #860 / Ubiquitinyl hydrolase, UCH37 type / Ubiquitinyl hydrolase-L5 / Peptidase C12, C-terminal domain / Ubiquitin carboxyl-terminal hydrolases / 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 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Papain-like cysteine peptidase superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / Ubiquitin carboxyl-terminal hydrolase isozyme L5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.95 Å
AuthorsBurgie, E.S. / Bingman, C.A. / Phillips Jr., G.N. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: Proteins / Year: 2012
Title: Structural characterization of human Uch37.
Authors: Burgie, S.E. / Bingman, C.A. / Soni, A.B. / Phillips Jr., G.N.
History
DepositionJul 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 10, 2012Group: Database references
Revision 1.3Jan 9, 2013Group: Database references
Revision 1.4Jan 23, 2013Group: Database references
Revision 1.5Jun 19, 2013Group: Database references
Revision 1.6Nov 1, 2017Group: Refinement description / Category: software
Revision 1.7Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.8Jul 26, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.name

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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 L5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0174
Polymers37,9021
Non-polymers1153
Water18010
1
A: Ubiquitin carboxyl-terminal hydrolase isozyme L5
hetero molecules

A: Ubiquitin carboxyl-terminal hydrolase isozyme L5
hetero molecules

A: Ubiquitin carboxyl-terminal hydrolase isozyme L5
hetero molecules

A: Ubiquitin carboxyl-terminal hydrolase isozyme L5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,06716
Polymers151,6074
Non-polymers46012
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_775-x+2,-y+2,z1
crystal symmetry operation3_755-x+2,y,-z1
crystal symmetry operation4_575x,-y+2,-z1
Buried area12600 Å2
ΔGint-90 kcal/mol
Surface area55120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.092, 98.736, 154.061
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Detailsbiological unit is a tetramer generated from the monomer in the asymmetric unit by the operations 1; 2 x,0,0; 2 0,y,0; 2 0,0,z

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Components

#1: Protein Ubiquitin carboxyl-terminal hydrolase isozyme L5 / UCH-L5 / Ubiquitin thioesterase L5 / Ubiquitin C-terminal hydrolase UCH37


Mass: 37901.652 Da / Num. of mol.: 1 / Mutation: M1S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AD-019, CGI-70, UCH37, UCHL5 / Plasmid: pVP 16 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 pRARE2 / References: UniProt: Q9Y5K5, ubiquitinyl hydrolase 1
#2: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE PROTEIN SEQUENCE MATCHES UNP ENTRY Q9Y5K5 ISOFORM 3 Q9Y5K5-3, AND DOES NOT MATCH THE ISOFORM 1.

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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: 4.52 Å3/Da / Density % sol: 72.79 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Total volume 4 ul; 5 mg/ml Uch37, 1.3 M sodium formate, 100 mM Tris, 2.5 mM BisTris, 0.15 mM TCEP, pH 8.5, hanging drop, batch, temperature 277K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97949, 0.97973
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 1, 2008
RadiationMonochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979491
20.979731
ReflectionRedundancy: 11.4 % / Av σ(I) over netI: 33.6 / Number: 178965 / Rmerge(I) obs: 0.078 / Χ2: 1.49 / D res high: 2.75 Å / D res low: 50 Å / Num. obs: 15698 / % possible obs: 86.1
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.925099.710.0563.34211.7
4.75.9210010.0691.70812.3
4.114.710010.0661.25512.4
3.734.1110010.0811.25812.5
3.463.7399.910.1141.12112.1
3.263.4695.410.1491.14410.9
3.13.2681.610.2171.07910.6
2.963.169.110.2781.01510.3
2.852.9660.110.3910.97210.1
2.752.8552.710.470.9388.7
ReflectionResolution: 2.75→50 Å / Num. obs: 15698 / % possible obs: 86.1 % / Redundancy: 11.4 % / Rmerge(I) obs: 0.078 / Χ2: 1.488 / Net I/σ(I): 13.6
Reflection shellResolution: 2.75→2.85 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 3.3 / Num. unique all: 936 / Χ2: 0.938 / % possible all: 52.7

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Phasing

PhasingMethod: MAD
Phasing MAD set
IDHighest resolution (Å)Lowest resolution (Å)Power acentricPower centricReflection acentricReflection centric
ISO_12.7545.0600140031693
ISO_22.7545.060.970.996135951665
ANO_12.7545.062.0150135080
ANO_22.7545.060.7940133700
Phasing MAD set shell
IDResolution (Å)Power acentricPower centricReflection acentricReflection centric
ISO_111.89-45.060016595
ISO_18.55-11.890030599
ISO_17.03-8.550042095
ISO_16.1-7.030049799
ISO_15.47-6.100568103
ISO_15-5.470062995
ISO_14.63-500684102
ISO_14.34-4.630075396
ISO_14.09-4.340078097
ISO_13.88-4.090085099
ISO_13.7-3.880088798
ISO_13.55-3.70093196
ISO_13.41-3.550095897
ISO_13.28-3.410097385
ISO_13.17-3.280092676
ISO_13.07-3.170082864
ISO_12.98-3.070079057
ISO_12.9-2.980072553
ISO_12.82-2.90070146
ISO_12.75-2.820063341
ANO_111.89-45.064.96901640
ANO_18.55-11.894.76203050
ANO_17.03-8.555.54704200
ANO_16.1-7.035.38504970
ANO_15.47-6.14.44405680
ANO_15-5.473.7106290
ANO_14.63-53.06606840
ANO_14.34-4.632.61307530
ANO_14.09-4.341.98607800
ANO_13.88-4.091.69608500
ANO_13.7-3.881.46208870
ANO_13.55-3.71.02809310
ANO_13.41-3.550.79409460
ANO_13.28-3.410.68909210
ANO_13.17-3.280.58708470
ANO_13.07-3.170.48807740
ANO_12.98-3.070.45207290
ANO_12.9-2.980.38706730
ANO_12.82-2.90.32706220
ANO_12.75-2.820.25405280
ISO_211.89-45.062.4361.96516595
ISO_28.55-11.892.3641.98230599
ISO_27.03-8.552.2441.73842095
ISO_26.1-7.032.0641.549799
ISO_25.47-6.11.8031.39568103
ISO_25-5.471.4670.99462995
ISO_24.63-51.2090.699684102
ISO_24.34-4.631.0350.66475396
ISO_24.09-4.340.8650.51378097
ISO_23.88-4.090.7610.55185099
ISO_23.7-3.880.6740.39188798
ISO_23.55-3.70.5410.28793196
ISO_23.41-3.550.4270.2795396
ISO_23.28-3.410.3360.21394582
ISO_23.17-3.280.3070.18884570
ISO_23.07-3.170.260.15276860
ISO_22.98-3.070.2110.09773555
ISO_22.9-2.980.1870.12868546
ISO_22.82-2.90.1630.07664444
ISO_22.75-2.820.1350.10455138
ANO_211.89-45.063.23601640
ANO_28.55-11.893.10803050
ANO_27.03-8.553.60104200
ANO_26.1-7.033.49404970
ANO_25.47-6.12.55505680
ANO_25-5.472.05606290
ANO_24.63-51.56406840
ANO_24.34-4.631.32207530
ANO_24.09-4.340.93207800
ANO_23.88-4.090.67208500
ANO_23.7-3.880.54908870
ANO_23.55-3.70.38809310
ANO_23.41-3.550.30509440
ANO_23.28-3.410.24609140
ANO_23.17-3.280.21208250
ANO_23.07-3.170.16807570
ANO_22.98-3.070.14707040
ANO_22.9-2.980.13606350
ANO_22.82-2.90.11206100
ANO_22.75-2.820.09805130
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
120.7361.04-38.76SE95.291.45
23.76710.176-33.344SE76.671.07
33.965-11.156-42.506SE82.191.08
48.40513.682-24.407SE1011.09
537.467-44.047-68.382SE206.741.72
626.465-14.079-50.777SE94.730.79
713.272-14.598-60.73SE244.870.94
8-8.815-5.983-146.931SE284.671.65
9-26.65-23.542-24.61SE155.50.61
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 15695
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
9.43-100520.851507
7.4-9.4348.20.925503
6.44-7.449.80.9504
5.83-6.4452.40.898506
5.4-5.8349.20.902503
5.07-5.452.40.903520
4.8-5.0752.20.907517
4.57-4.855.10.907557
4.37-4.5756.30.918588
4.19-4.3761.70.888593
4.04-4.1964.10.875628
3.89-4.0464.40.874634
3.77-3.89670.851662
3.65-3.7772.20.84694
3.55-3.6579.40.82705
3.45-3.5575.90.808740
3.36-3.4581.40.757732
3.28-3.3681.50.787703
3.2-3.2881.50.757659
3.13-3.280.20.778666
3.07-3.13840.779620
3-3.0786.40.775578
2.94-382.80.774541
2.89-2.9487.90.75516
2.84-2.8985.30.714505
2.75-2.8489.50.696814

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
DM5phasing
PHENIXrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.95→45.56 Å / Occupancy max: 1 / Occupancy min: 0.49 / SU ML: -0 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Stereochemistry target values: ML / Details: TLS refinement was included
RfactorNum. reflection% reflectionSelection details
Rfree0.242 682 4.94 %RANDOM
Rwork0.199 ---
obs0.201 13796 92.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 68.343 Å2 / ksol: 0.309 e/Å3
Displacement parametersBiso max: 344.77 Å2 / Biso mean: 107.038 Å2 / Biso min: 41.39 Å2
Baniso -1Baniso -2Baniso -3
1--16.611 Å2-0 Å20 Å2
2---14.279 Å2-0 Å2
3---26.329 Å2
Refinement stepCycle: LAST / Resolution: 2.95→45.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2273 0 7 10 2290
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072331
X-RAY DIFFRACTIONf_angle_d1.0923141
X-RAY DIFFRACTIONf_chiral_restr0.067344
X-RAY DIFFRACTIONf_plane_restr0.004409
X-RAY DIFFRACTIONf_dihedral_angle_d17.634874
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.95-3.1780.2781270.2481959208671
3.178-3.4970.2671410.2152575271693
3.497-4.0030.1991340.17727962930100
4.003-5.0430.2131370.15428372974100
5.043-45.5650.251430.21929473090100
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)
11.78832.05470.58061.186-0.57712.3298-0.69390.24960.249-0.52290.5125-0.1195-0.62240.31530.22840.71210.00510.01910.44880.03380.687582.317888.594435.0592
23.9588-1.60687.93512.38020.04426.22082.6093-1.3311.23590.08511.2132-2.21981.54970.0178-3.95751.13260.0701-0.00531.4816-0.15051.630994.903870.235734.4067
32.91472.4722-1.66352.59991.46484.5624-0.4990.1507-0.631-0.14340.2680.50740.6608-0.20540.21980.6674-0.02170.05060.50930.04410.869173.603375.912831.4822
45.03932.36733.18575.7594-0.5411.61060.0389-0.186-1.07850.7222-0.3258-0.57240.3164-0.04640.24510.72110.0919-0.02070.6220.05770.761886.58777.344343.3157
51.5159-2.0645-0.45832.59122.27451.9874-0.20260.1313-0.5199-0.4262-0.03320.233-0.3663-0.24360.17370.42670.0488-0.0340.29710.13150.703178.1351104.811842.3369
61.2854-1.0548-8.48983.60242.17267.3023-0.3666-1.92740.58061.50581.29020.61951.26852.6499-0.70931.86810.4128-0.17321.25750.05390.643391.940694.30997.2298
78.09421.4977-3.76735.0016-1.3714-2.54611.55811.46680.0368-1.6392-2.0605-0.17131.93783.62640.57451.17390.47650.01252.5179-0.2390.6795104.64596.9035-6.962
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 7:56)A7 - 56
2X-RAY DIFFRACTION2(chain A and resid 57:65)A57 - 65
3X-RAY DIFFRACTION3(chain A and resid 66:163)A66 - 163
4X-RAY DIFFRACTION4(chain A and resid 164:216)A164 - 216
5X-RAY DIFFRACTION5(chain A and resid 217:284)A217 - 284
6X-RAY DIFFRACTION6(chain A and resid 285:302)A285 - 302
7X-RAY DIFFRACTION7(chain A and resid 303:311)A303 - 311

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