PDB-3ihr: Crystal Structure of Uch37

Basic information

• Entry: Database: PDB / ID: 3ihr
• Title: Crystal Structure of Uch37
• Components: Ubiquitin carboxyl-terminal hydrolase isozyme L5
• Keywords: HYDROLASE / 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:

lateral ventricle development / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / forebrain morphogenesis / cytosolic proteasome complex / Ino80 complex / positive regulation of smoothened signaling pathway / midbrain development / endopeptidase inhibitor activity / proteasome binding / regulation of chromosome organization / regulation of DNA replication / regulation of embryonic development / protein deubiquitination / regulation of DNA repair / regulation of proteasomal protein catabolic process / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / telomere maintenance / positive regulation of DNA repair / 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

Domain/homology:

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

Component:

FORMIC ACID / Ubiquitin carboxyl-terminal hydrolase isozyme L5

• Biological species: Homo sapiens (human)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.95 Å
• Authors: Burgie, E.S. / Bingman, C.A. / Phillips Jr., G.N. / Center for Eukaryotic Structural Genomics (CESG)
• Citation: Journal: Proteins / Year: 2012; Title: Structural characterization of human Uch37.; Authors: Burgie, S.E. / Bingman, C.A. / Soni, A.B. / Phillips Jr., G.N.

History

Deposition	Jul 30, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 11, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Oct 10, 2012	Group: Database references
Revision 1.3	Jan 9, 2013	Group: Database references
Revision 1.4	Jan 23, 2013	Group: Database references
Revision 1.5	Jun 19, 2013	Group: Database references
Revision 1.6	Nov 1, 2017	Group: Refinement description / Category: software
Revision 1.7	Oct 13, 2021	Group: Database references / Derived calculations Category: database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site Item: _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 1.8	Jul 26, 2023	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.name

Assembly

Deposited unit

A: Ubiquitin carboxyl-terminal hydrolase isozyme L5

hetero molecules

Summary:

• 38 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	38,017	4
Polymers	37,902	1
Non-polymers	115	3
Water	180	10

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

Summary:

• defined by author&software
• 152 kDa, 4 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	152,067	16
Polymers	151,607	4
Non-polymers	460	12
Water	72	4

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	2_775	-x+2,-y+2,z	1
crystal symmetry operation	3_755	-x+2,y,-z	1
crystal symmetry operation	4_575	x,-y+2,-z	1

Calculated values:

Buried area	12600 Å2
ΔGint	-90 kcal/mol
Surface area	55120 Å2
Method	PISA

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 number	23
Space group name H-M	I222

• Details: biological 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

Components

#1: Protein

A Ubiquitin carboxyl-terminal hydrolase isozyme L5 / UCH-L5 / Ubiquitin thioesterase L5 / Ubiquitin C-terminal hydrolase UCH37

Details:

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

A-329 A-330 ChemComp-FMT / FORMIC ACID

Details:

Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH₂O₂

#3: Chemical

A-331 ChemComp-NA / SODIUM ION

Details:

Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na

#4: Water

ChemComp-HOH / water

Details:

Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H₂O

• Sequence details: THE PROTEIN SEQUENCE MATCHES UNP ENTRY Q9Y5K5 ISOFORM 3 Q9Y5K5-3, AND DOES NOT MATCH THE ISOFORM 1.

Experimental details

Experiment

• Experiment: Method: X-RAY DIFFRACTION / Number of used crystals: 1

Sample preparation

• Crystal: Density Matthews: 4.52 ų/Da / Density % sol: 72.79 %
• Crystal grow: Temperature: 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

Data collection

• Diffraction: Mean temperature: 100 K
• Diffraction source: Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97949, 0.97973
• Detector: Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 1, 2008
• Radiation: Monochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97949	1
2	0.97973	1

• Reflection: Redundancy: 11.4 % / Av σ(I) over netI: 33.6 / Number: 178965 / R_merge(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 (%)	ID	Rmerge(I) obs	Chi squared	Redundancy
5.92	50	99.7	1	0.056	3.342	11.7
4.7	5.92	100	1	0.069	1.708	12.3
4.11	4.7	100	1	0.066	1.255	12.4
3.73	4.11	100	1	0.081	1.258	12.5
3.46	3.73	99.9	1	0.114	1.121	12.1
3.26	3.46	95.4	1	0.149	1.144	10.9
3.1	3.26	81.6	1	0.217	1.079	10.6
2.96	3.1	69.1	1	0.278	1.015	10.3
2.85	2.96	60.1	1	0.391	0.972	10.1
2.75	2.85	52.7	1	0.47	0.938	8.7

• Reflection: Resolution: 2.75→50 Å / Num. obs: 15698 / % possible obs: 86.1 % / Redundancy: 11.4 % / R_merge(I) obs: 0.078 / Χ²: 1.488 / Net I/σ(I): 13.6
• Reflection shell: Resolution: 2.75→2.85 Å / Redundancy: 8.7 % / R_merge(I) obs: 0.47 / Mean I/σ(I) obs: 3.3 / Num. unique all: 936 / Χ²: 0.938 / % possible all: 52.7

Phasing

• Phasing: Method: MAD

Phasing MAD set

ID	Highest resolution (Å)	Lowest resolution (Å)	Power acentric	Power centric	Reflection acentric	Reflection centric
ISO_1	2.75	45.06	0	0	14003	1693
ISO_2	2.75	45.06	0.97	0.996	13595	1665
ANO_1	2.75	45.06	2.015	0	13508	0
ANO_2	2.75	45.06	0.794	0	13370	0

Phasing MAD set shell

ID	Resolution (Å)	Power acentric	Power centric	Reflection acentric	Reflection centric
ISO_1	11.89-45.06	0	0	165	95
ISO_1	8.55-11.89	0	0	305	99
ISO_1	7.03-8.55	0	0	420	95
ISO_1	6.1-7.03	0	0	497	99
ISO_1	5.47-6.1	0	0	568	103
ISO_1	5-5.47	0	0	629	95
ISO_1	4.63-5	0	0	684	102
ISO_1	4.34-4.63	0	0	753	96
ISO_1	4.09-4.34	0	0	780	97
ISO_1	3.88-4.09	0	0	850	99
ISO_1	3.7-3.88	0	0	887	98
ISO_1	3.55-3.7	0	0	931	96
ISO_1	3.41-3.55	0	0	958	97
ISO_1	3.28-3.41	0	0	973	85
ISO_1	3.17-3.28	0	0	926	76
ISO_1	3.07-3.17	0	0	828	64
ISO_1	2.98-3.07	0	0	790	57
ISO_1	2.9-2.98	0	0	725	53
ISO_1	2.82-2.9	0	0	701	46
ISO_1	2.75-2.82	0	0	633	41
ANO_1	11.89-45.06	4.969	0	164	0
ANO_1	8.55-11.89	4.762	0	305	0
ANO_1	7.03-8.55	5.547	0	420	0
ANO_1	6.1-7.03	5.385	0	497	0
ANO_1	5.47-6.1	4.444	0	568	0
ANO_1	5-5.47	3.71	0	629	0
ANO_1	4.63-5	3.066	0	684	0
ANO_1	4.34-4.63	2.613	0	753	0
ANO_1	4.09-4.34	1.986	0	780	0
ANO_1	3.88-4.09	1.696	0	850	0
ANO_1	3.7-3.88	1.462	0	887	0
ANO_1	3.55-3.7	1.028	0	931	0
ANO_1	3.41-3.55	0.794	0	946	0
ANO_1	3.28-3.41	0.689	0	921	0
ANO_1	3.17-3.28	0.587	0	847	0
ANO_1	3.07-3.17	0.488	0	774	0
ANO_1	2.98-3.07	0.452	0	729	0
ANO_1	2.9-2.98	0.387	0	673	0
ANO_1	2.82-2.9	0.327	0	622	0
ANO_1	2.75-2.82	0.254	0	528	0
ISO_2	11.89-45.06	2.436	1.965	165	95
ISO_2	8.55-11.89	2.364	1.982	305	99
ISO_2	7.03-8.55	2.244	1.738	420	95
ISO_2	6.1-7.03	2.064	1.5	497	99
ISO_2	5.47-6.1	1.803	1.39	568	103
ISO_2	5-5.47	1.467	0.994	629	95
ISO_2	4.63-5	1.209	0.699	684	102
ISO_2	4.34-4.63	1.035	0.664	753	96
ISO_2	4.09-4.34	0.865	0.513	780	97
ISO_2	3.88-4.09	0.761	0.551	850	99
ISO_2	3.7-3.88	0.674	0.391	887	98
ISO_2	3.55-3.7	0.541	0.287	931	96
ISO_2	3.41-3.55	0.427	0.27	953	96
ISO_2	3.28-3.41	0.336	0.213	945	82
ISO_2	3.17-3.28	0.307	0.188	845	70
ISO_2	3.07-3.17	0.26	0.152	768	60
ISO_2	2.98-3.07	0.211	0.097	735	55
ISO_2	2.9-2.98	0.187	0.128	685	46
ISO_2	2.82-2.9	0.163	0.076	644	44
ISO_2	2.75-2.82	0.135	0.104	551	38
ANO_2	11.89-45.06	3.236	0	164	0
ANO_2	8.55-11.89	3.108	0	305	0
ANO_2	7.03-8.55	3.601	0	420	0
ANO_2	6.1-7.03	3.494	0	497	0
ANO_2	5.47-6.1	2.555	0	568	0
ANO_2	5-5.47	2.056	0	629	0
ANO_2	4.63-5	1.564	0	684	0
ANO_2	4.34-4.63	1.322	0	753	0
ANO_2	4.09-4.34	0.932	0	780	0
ANO_2	3.88-4.09	0.672	0	850	0
ANO_2	3.7-3.88	0.549	0	887	0
ANO_2	3.55-3.7	0.388	0	931	0
ANO_2	3.41-3.55	0.305	0	944	0
ANO_2	3.28-3.41	0.246	0	914	0
ANO_2	3.17-3.28	0.212	0	825	0
ANO_2	3.07-3.17	0.168	0	757	0
ANO_2	2.98-3.07	0.147	0	704	0
ANO_2	2.9-2.98	0.136	0	635	0
ANO_2	2.82-2.9	0.112	0	610	0
ANO_2	2.75-2.82	0.098	0	513	0

Phasing MAD set site

ID	Cartn x (Å)	Cartn y (Å)	Cartn z (Å)	Atom type symbol	B iso	Occupancy
1	20.736	1.04	-38.76	SE	95.29	1.45
2	3.767	10.176	-33.344	SE	76.67	1.07
3	3.965	-11.156	-42.506	SE	82.19	1.08
4	8.405	13.682	-24.407	SE	101	1.09
5	37.467	-44.047	-68.382	SE	206.74	1.72
6	26.465	-14.079	-50.777	SE	94.73	0.79
7	13.272	-14.598	-60.73	SE	244.87	0.94
8	-8.815	-5.983	-146.931	SE	284.67	1.65
9	-26.65	-23.542	-24.61	SE	155.5	0.61

• Phasing dm: Method: Solvent flattening and Histogram matching / Reflection: 15695

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
9.43-100	52	0.851	507
7.4-9.43	48.2	0.925	503
6.44-7.4	49.8	0.9	504
5.83-6.44	52.4	0.898	506
5.4-5.83	49.2	0.902	503
5.07-5.4	52.4	0.903	520
4.8-5.07	52.2	0.907	517
4.57-4.8	55.1	0.907	557
4.37-4.57	56.3	0.918	588
4.19-4.37	61.7	0.888	593
4.04-4.19	64.1	0.875	628
3.89-4.04	64.4	0.874	634
3.77-3.89	67	0.851	662
3.65-3.77	72.2	0.84	694
3.55-3.65	79.4	0.82	705
3.45-3.55	75.9	0.808	740
3.36-3.45	81.4	0.757	732
3.28-3.36	81.5	0.787	703
3.2-3.28	81.5	0.757	659
3.13-3.2	80.2	0.778	666
3.07-3.13	84	0.779	620
3-3.07	86.4	0.775	578
2.94-3	82.8	0.774	541
2.89-2.94	87.9	0.75	516
2.84-2.89	85.3	0.714	505
2.75-2.84	89.5	0.696	814

Processing

Software

Name	Version	Classification	NB
DENZO		data reduction
SCALEPACK		data scaling
SHARP		phasing
DM	5	phasing
PHENIX		refinement
PDB_EXTRACT	3.005	data extraction
HKL-2000		data collection
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method 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

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.242	682	4.94 %	RANDOM
Rwork	0.199	-	-	-
obs	0.201	13796	92.88 %	-

• Solvent computation: Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 68.343 Ų / k_sol: 0.309 e/ų

Displacement parameters

B_iso max: 344.77 Ų / B_iso mean: 107.038 Ų / B_iso min: 41.39 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	-16.611 Å2	-0 Å2	0 Å2
2-	-	-14.279 Å2	-0 Å2
3-	-	-	26.329 Å2

Refinement step

Cycle: LAST / Resolution: 2.95→45.56 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2273	0	7	10	2290

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	2331
X-RAY DIFFRACTION	f_angle_d	1.092	3141
X-RAY DIFFRACTION	f_chiral_restr	0.067	344
X-RAY DIFFRACTION	f_plane_restr	0.004	409
X-RAY DIFFRACTION	f_dihedral_angle_d	17.634	874

LS refinement shell

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

Resolution (Å)	Rfactor Rfree	Num. reflection Rfree	Rfactor Rwork	Num. reflection Rwork	Num. reflection all	% reflection obs (%)
2.95-3.178	0.278	127	0.248	1959	2086	71
3.178-3.497	0.267	141	0.215	2575	2716	93
3.497-4.003	0.199	134	0.177	2796	2930	100
4.003-5.043	0.213	137	0.154	2837	2974	100
5.043-45.565	0.25	143	0.219	2947	3090	100

Refinement TLS params.

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

ID	L11 (°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)
1	1.7883	2.0547	0.5806	1.186	-0.5771	2.3298	-0.6939	0.2496	0.249	-0.5229	0.5125	-0.1195	-0.6224	0.3153	0.2284	0.7121	0.0051	0.0191	0.4488	0.0338	0.6875	82.3178	88.5944	35.0592
2	3.9588	-1.6068	7.9351	2.3802	0.0442	6.2208	2.6093	-1.331	1.2359	0.0851	1.2132	-2.2198	1.5497	0.0178	-3.9575	1.1326	0.0701	-0.0053	1.4816	-0.1505	1.6309	94.9038	70.2357	34.4067
3	2.9147	2.4722	-1.6635	2.5999	1.4648	4.5624	-0.499	0.1507	-0.631	-0.1434	0.268	0.5074	0.6608	-0.2054	0.2198	0.6674	-0.0217	0.0506	0.5093	0.0441	0.8691	73.6033	75.9128	31.4822
4	5.0393	2.3673	3.1857	5.7594	-0.541	1.6106	0.0389	-0.186	-1.0785	0.7222	-0.3258	-0.5724	0.3164	-0.0464	0.2451	0.7211	0.0919	-0.0207	0.622	0.0577	0.7618	86.587	77.3443	43.3157
5	1.5159	-2.0645	-0.4583	2.5912	2.2745	1.9874	-0.2026	0.1313	-0.5199	-0.4262	-0.0332	0.233	-0.3663	-0.2436	0.1737	0.4267	0.0488	-0.034	0.2971	0.1315	0.7031	78.1351	104.8118	42.3369
6	1.2854	-1.0548	-8.4898	3.6024	2.1726	7.3023	-0.3666	-1.9274	0.5806	1.5058	1.2902	0.6195	1.2685	2.6499	-0.7093	1.8681	0.4128	-0.1732	1.2575	0.0539	0.6433	91.9406	94.3099	7.2298
7	8.0942	1.4977	-3.7673	5.0016	-1.3714	-2.5461	1.5581	1.4668	0.0368	-1.6392	-2.0605	-0.1713	1.9378	3.6264	0.5745	1.1739	0.4765	0.0125	2.5179	-0.239	0.6795	104.645	96.9035	-6.962

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	(chain A and resid 7:56)	A	7 - 56
2	X-RAY DIFFRACTION	2	(chain A and resid 57:65)	A	57 - 65
3	X-RAY DIFFRACTION	3	(chain A and resid 66:163)	A	66 - 163
4	X-RAY DIFFRACTION	4	(chain A and resid 164:216)	A	164 - 216
5	X-RAY DIFFRACTION	5	(chain A and resid 217:284)	A	217 - 284
6	X-RAY DIFFRACTION	6	(chain A and resid 285:302)	A	285 - 302
7	X-RAY DIFFRACTION	7	(chain A and resid 303:311)	A	303 - 311