PDB-3h8v: Human Ubiquitin-activating Enzyme 5 in Complex with ATP

ID or keywords:

Entry

Database: PDB / ID: 3h8v

Title

Human Ubiquitin-activating Enzyme 5 in Complex with ATP

Components

Ubiquitin-like modifier-activating enzyme 5

Keywords

TRANSFERASE /

ROSSMANN FOLD / ATP-BINDING / UBL CONJUGATION PATHWAY /

STRUCTURAL GENOMICS CONSORTIUM / SGC

Function / homology

Function and homology information

UFM1 activating enzyme activity / protein ufmylation / protein K69-linked ufmylation / megakaryocyte differentiation / regulation of intracellular estrogen receptor signaling pathway / reticulophagy / neuromuscular process / localization / response to endoplasmic reticulum stress /

erythrocyte differentiation ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Walker, J.R. / Bacik, J.P. / Rastgoo, N. / Weigelt, J. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)

Citation

Journal: J.Biol.Chem. / Year: 2010
Title: Crystal structure of the human ubiquitin-activating enzyme 5 (UBA5) bound to ATP: mechanistic insights into a minimalistic E1 enzyme.
Authors: Bacik, J.P. / Walker, J.R. / Ali, M. / Schimmer, A.D. / Dhe-Paganon, S.

History

Deposition	Apr 29, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 26, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Nov 12, 2014	Group: Structure summary
Revision 1.3	Sep 6, 2023	Group: 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_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3h8v.cif.gz	169.7 KB	Display	PDBx/mmCIF format
PDB format	pdb3h8v.ent.gz	131.1 KB	Display	PDB format
PDBx/mmJSON format	3h8v.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/h8/3h8v ftp://data.pdbj.org/pub/pdb/validation_reports/h8/3h8v	HTTPS FTP

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Related structure data

Related structure data	1zfnS 3guc S: Starting model for refinement
Similar structure data	5db1-d 4bt7-1 4xpu-d 5upr-2 4mb2-2 4bt5-1 5yho-d 4o53-1 5ddd-d 3wdk-2 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#203 - Nov 2016 Aminopeptidase 1 and Autophagy similarity (3) #60 - Dec 2004 Ubiquitin similarity (3)

Deposited unit

A: Ubiquitin-like modifier-activating enzyme 5

B: Ubiquitin-like modifier-activating enzyme 5

hetero molecules

65 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	77.999, 77.999, 207.005
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	154
Space group name H-M	P3₂21

#1: Protein	Ubiquitin-like modifier-activating enzyme 5 / Ubiquitin-activating enzyme 5 / Ubiquitin-activating enzyme E1 domain-containing protein 1 / UFM1- ...Ubiquitin-activating enzyme 5 / Ubiquitin-activating enzyme E1 domain-containing protein 1 / UFM1-activating enzyme / ThiFP1 Mass: 32165.947 Da / Num. of mol.: 2 / Fragment: residues 57-329 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBA5, UBE1DC1 / Plasmid: PET28A-LIC / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) References: UniProt: Q9GZZ9, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical	ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₅O₁₃P₃ / Comment: ATP, energy-carrying molecule*YM
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.83 Å³/Da / Density % sol: 56.47 %
Crystal grow	Temperature: 287 K / pH: 6.2 Details: 1 M LITHIUM SULPHATE, 0.3 M AMMONIUM SULPHATE, 0.1 M SODIUM CITRATE, PH 6.2 , VAPOR DIFFUSION, HANGING DROP, temperature 287K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97944
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 8, 2009
Radiation	Monochromator: KOHZU HLD8-24 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97944 Å / Relative weight: 1
Reflection	Resolution: 2→50 Å / Num. obs: 45414 / % possible obs: 90 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / R_sym value: 0.08 / Net I/σ(I): 16.75
Reflection shell	Resolution: 2→2.03 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 1.65 / R_sym value: 0.859 / % possible all: 93.3

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
PHASER		phasing
REFMAC	5.5.0072	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1ZFN

1zfn

Resolution: 2→25.53 Å / Cor.coef. F_o:F_c: 0.957 / Cor.coef. F_o:F_c free: 0.944 / SU B: 7.335 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.224	2372	5.2 %	RANDOM
R_work	0.191	-	-	-
obs	0.193	42909	90.1 %	-
all	-	45281	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 68.49 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.04 Å²	0.02 Å²	0 Å²
2-	-	0.04 Å²	0 Å²
3-	-	-	-0.07 Å²

Refinement step

Cycle: LAST / Resolution: 2→25.53 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3392	0	33	157	3582

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.022	3527
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.251	1.962	4786
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.987	5	455
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.463	25.241	145
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.07	15	562
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	24.369	15	12
X-RAY DIFFRACTION	r_chiral_restr	0.083	0.2	557
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	2637
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.701	1.5	722
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.299	2	1164
X-RAY DIFFRACTION	r_scbond_it	2.113	3	403
X-RAY DIFFRACTION	r_scangle_it	3.327	4.5	363
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2→2.05 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.293	193	-
R_work	0.28	3207	-
obs	-	-	93.61 %

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	3.9488	0.8434	-0.5958	3.2839	-0.0682	3.8363	0.042	-0.2376	-0.1487	0.1226	-0.0128	0.0527	0.4322	-0.0877	-0.0291	0.3705	-0.0979	-0.0666	0.0854	-0.0039	0.1636	29.3481	-25.5271	24.9718
2	4.9138	1.0169	-0.4913	1.3428	0.7884	8.9804	-0.0746	-0.0451	-0.1245	0.0603	0.0922	-0.2998	0.3135	0.4107	-0.0175	0.4152	-0.0568	-0.0652	0.041	0.0189	0.2067	33.1762	-28.5942	22.6995
3	8.7666	0.2451	0.1407	2.166	-1.5722	1.1875	0.5507	0.1404	-0.6748	0.0083	-0.7115	-0.3121	0.1279	0.6294	0.1608	0.8127	0.1617	-0.0794	0.5867	-0.0505	0.5667	47.1867	-36.8595	21.2824
4	9.4469	-0.5957	-4.4442	1.4392	0.6632	6.3356	-0.2009	-0.3013	-0.3892	-0.1523	0.2436	-0.3374	0.765	0.5273	-0.0427	0.5555	0.0173	-0.0355	0.1246	0.0512	0.3279	36.0681	-36.1478	24.8296
5	1.3718	0.3145	-1.1577	1.3141	-0.7389	3.7181	-0.0978	0.1253	-0.1332	-0.0177	0.1047	0.0001	0.4378	-0.1149	-0.0069	0.4145	-0.1585	-0.0333	0.0861	-0.0269	0.1794	29.3789	-28.3532	10.8234
6	3.2007	0.6101	0.165	2.113	0.4933	2.7041	-0.1213	0.0819	-0.106	-0.1843	0.2144	-0.0369	0.1625	-0.0568	-0.0932	0.2836	-0.0989	-0.0481	0.0677	0.001	0.1372	31.5739	-17.3939	14.4302
7	1.4234	-0.9186	1.9057	1.3222	-0.4687	4.8445	-0.126	0.0194	-0.0901	-0.1622	0.1991	0.0227	-0.2038	0.0601	-0.0732	0.2788	-0.0757	-0.0301	0.0987	0.0094	0.1841	34.2099	-9.502	19.7821
8	0.4609	-0.9149	1.2898	1.8405	-2.6579	6.5102	0.0532	0.0886	-0.0195	-0.061	-0.1396	-0.0139	0.0883	0.8307	0.0864	0.3568	-0.068	-0.057	0.2524	-0.0296	0.2917	45.2275	-9.3078	23.0537
9	9.7718	0.2834	1.3493	0.6175	0.6517	2.0802	-0.1047	0.1801	-0.0854	-0.016	0.1236	-0.0844	0.187	0.0191	-0.0189	0.2601	-0.0349	-0.025	0.1176	0.0082	0.191	34.5314	-17.095	30.0529
10	0.4655	0.0131	0.8027	0.8623	0.4028	1.6447	-0.0989	-0.0694	0.1069	0.0008	0.0027	0.0852	-0.0347	-0.1769	0.0962	0.301	-0.0521	-0.0609	0.1448	0.0372	0.2647	29.6853	-10.1539	28.8311
11	1.3363	0.2403	0.3172	0.7335	0.2422	2.3809	-0.1992	0.01	0.0873	-0.2011	0.1668	0.0355	-0.2558	-0.1974	0.0324	0.3482	-0.0516	-0.0548	0.085	0.0389	0.1937	31.9927	-4.3531	16.9591
12	3.4646	-3.673	3.949	6.2414	-0.7498	9.5458	0.5539	-0.2619	-0.3836	-1.1406	-0.0398	0.3561	-0.2369	-0.7543	-0.5141	0.4674	0.0357	-0.2087	0.4419	0.0397	0.3944	16.29	-3.7951	10.3281
13	4.0126	-0.9195	0.1984	4.1258	-0.1646	0.7032	0.1333	0.5151	-0.0114	-0.5249	-0.0716	-0.5395	0.3429	0.1908	-0.0617	0.4241	0.2305	0.0109	0.3427	-0.0603	0.3176	60.3053	-21.3194	40.5459
14	2.9195	-0.3299	-0.7265	1.381	-0.7156	6.1271	0.0149	0.1157	-0.0747	-0.1773	0.0813	0.217	0.1198	-0.2309	-0.0962	0.3074	0.123	-0.0547	0.0795	0.0007	0.2069	44.9238	-23.5225	46.5154
15	5.8594	0.4151	-4.1927	2.6933	-2.2284	9.3878	-0.3474	1.0811	-1.0186	-0.4255	0.4968	0.4695	1.5984	-1.7979	-0.1494	0.7421	-0.1231	-0.0792	0.5974	0.0024	0.6478	36.4979	-39.5567	48.5273
16	2.2417	-1.638	-2.4654	2.6442	0.9315	6.1771	-0.2952	0.4676	-0.4582	0.0391	-0.1739	0.36	1.0257	-0.8881	0.4691	0.584	0.0754	0.0007	0.2951	-0.0861	0.2864	46.6392	-34.6435	44.9426
17	0.6944	-0.0678	-0.2462	1.4167	-0.5518	1.6396	-0.174	-0.0161	-0.1884	0.0823	0.1427	-0.148	0.3559	0.2438	0.0313	0.422	0.1887	-0.0349	0.2078	-0.0048	0.2684	50.4824	-25.7915	59.2244
18	0.0986	0.4073	0.0473	2.3837	0.5778	3.1807	-0.052	-0.0165	-0.0475	0.2711	0.1086	-0.1553	0.2513	-0.0023	-0.0566	0.3287	0.1091	-0.0123	0.1225	0.0066	0.207	44.6715	-16.2031	55.9882
19	0.5642	1.0575	0.8099	2.1199	1.7789	3.8207	0.0913	0.0541	-0.1068	0.2635	0.188	-0.089	0.5521	0.0741	-0.2793	0.3952	0.1058	-0.058	0.1859	0.0151	0.2126	39.4715	-9.2362	51.1275
20	8.4457	1.3974	1.6396	1.034	-0.4969	2.9502	-0.06	-0.4356	0.3353	0.0199	0.0513	0.0989	0.0239	-0.0945	0.0088	0.2494	0.0634	-0.0145	0.1078	-0.0051	0.2115	41.712	-13.4883	43.1636
21	1.4744	0.3813	0.1722	1.3233	0.1022	1.717	-0.1965	-0.0594	0.1891	0.0012	0.1091	0.1069	-0.084	-0.0602	0.0874	0.2899	0.0261	-0.0322	0.1562	0.0073	0.2399	36.945	-6.512	40.6484
22	5.7267	-2.2461	1.2546	4.6039	-0.2096	5.0373	-0.2204	-0.6173	0.038	0.7574	0.4219	0.0313	-0.3182	0.2043	-0.2015	0.3824	0.1212	-0.0256	0.1457	-0.063	0.1437	45.0188	-2.4493	63.4839
23	2.6078	5.151	-4.3902	10.2182	-8.7024	7.4592	0.0523	-0.2272	-0.1805	0.2117	-0.3627	-0.4635	-0.1942	0.3505	0.3105	0.3891	0.0402	-0.219	0.4367	-0.1847	0.4272	55.0217	1.1034	61.4117

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	69 - 89
2	X-RAY DIFFRACTION	2	A	90 - 107
3	X-RAY DIFFRACTION	3	A	108 - 126
4	X-RAY DIFFRACTION	4	A	127 - 140
5	X-RAY DIFFRACTION	5	A	141 - 170
6	X-RAY DIFFRACTION	6	A	171 - 208
7	X-RAY DIFFRACTION	7	A	209 - 228
8	X-RAY DIFFRACTION	8	A	229 - 253
9	X-RAY DIFFRACTION	9	A	254 - 272
10	X-RAY DIFFRACTION	10	A	273 - 286
11	X-RAY DIFFRACTION	11	A	287 - 311
12	X-RAY DIFFRACTION	12	A	312 - 318
13	X-RAY DIFFRACTION	13	B	70 - 89
14	X-RAY DIFFRACTION	14	B	90 - 106
15	X-RAY DIFFRACTION	15	B	125 - 140
16	X-RAY DIFFRACTION	16	B	141 - 170
17	X-RAY DIFFRACTION	17	B	171 - 208
18	X-RAY DIFFRACTION	18	B	209 - 228
19	X-RAY DIFFRACTION	19	B	229 - 253
20	X-RAY DIFFRACTION	20	B	254 - 272
21	X-RAY DIFFRACTION	21	B	273 - 295
22	X-RAY DIFFRACTION	22	B	296 - 311
23	X-RAY DIFFRACTION	23	B	312 - 318

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