PDB-9glt: Crystal Structure of Yeast Ubc13 C87E

ID or keywords:

Entry

Database: PDB / ID: 9glt

Title

Crystal Structure of Yeast Ubc13 C87E

Components

Ubiquitin-conjugating enzyme E2 13

Keywords

LIGASE / Ubiquitin conjugating protein E2 UBC13~UB thioester complex mimic

Function / homology

Function and homology information

protein targeting to vacuolar membrane / PINK1-PRKN Mediated Mitophagy / Interleukin-1 signaling / Aggrephagy / ubiquitin conjugating enzyme complex / free ubiquitin chain polymerization / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / fungal-type vacuole membrane / postreplication repair ...
Similarity search - Function

Biological species

Saccharomyces cerevisiae (brewer's yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.45 Å

Authors

Kumar, M. / Banerjee, S. / Wiener, R.

Funding support

Israel, 1items

Citation

Journal: Nat Commun / Year: 2025
Title: UFC1 reveals the multifactorial and plastic nature of oxyanion holes in E2 conjugating enzymes.
Authors: Kumar, M. / Banerjee, S. / Cohen-Kfir, E. / Mitelberg, M.B. / Tiwari, S. / Isupov, M.N. / Dessau, M. / Wiener, R.

History

Deposition	Aug 28, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 7, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9glt.cif.gz	82 KB	Display	PDBx/mmCIF format
PDB format	pdb9glt.ent.gz		Display	PDB format
PDBx/mmJSON format	9glt.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/gl/9glt ftp://data.pdbj.org/pub/pdb/validation_reports/gl/9glt	HTTPS FTP

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Related structure data

Related structure data	9glhC 9gliC 9gljC 9glkC 9gllC 9glmC 9glnC 9gloC 9glpC 9glrC 9glsC 9gmmC 9gmnC 9gn8C 9i9mC 9i9nC 9i9oC 9i9pC 9ia8C 1jbb C: citing same article (ref.)
Similar structure data	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	#60 - Dec 2004 Ubiquitin similarity (8) #234 - Jun 2019 MDM2 and Cancer similarity (7) #161 - May 2013 Ricin similarity (5) #166 - Oct 2013 Proteasome similarity (1) #203 - Nov 2016 Aminopeptidase 1 and Autophagy similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

Deposited unit

AAA: Ubiquitin-conjugating enzyme E2 13

BBB: Ubiquitin-conjugating enzyme E2 13

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

1

AAA: Ubiquitin-conjugating enzyme E2 13

defined by author
17.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

BBB: Ubiquitin-conjugating enzyme E2 13

defined by author
17.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	25.603, 127.663, 42.330
Angle α, β, γ (deg.)	90.000, 96.210, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Ubiquitin-conjugating enzyme E2 13 / E2 ubiquitin-conjugating enzyme 13 / Ubiquitin carrier protein 13 / Ubiquitin-protein ligase 13 Mass: 17573.008 Da / Num. of mol.: 2 / Mutation: C87E Source method: isolated from a genetically manipulated source Details: UBC13 C87E Chain A Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: UBC13, YDR092W, YD6652.04 / Production host: Escherichia coli (E. coli) References: UniProt: P52490, E2 ubiquitin-conjugating enzyme
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 292 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 1.96 Å³/Da / Density % sol: 37.14 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M sodium cacodylate, pH 6.5, 25% PEG 4000

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Data collection

Diffraction	Mean temperature: 298 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.87313 Å
Detector	Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Feb 21, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.87313 Å / Relative weight: 1
Reflection	Resolution: 1.45→42.08 Å / Num. obs: 46789 / % possible obs: 98.06 % / Redundancy: 2.8 % / B_iso Wilson estimate: 16.26 Å² / CC_1/2: 0.996 / R_rim(I) all: 0.065 / Net I/σ(I): 11.87
Reflection shell	Resolution: 1.45→1.502 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2.6 / Num. unique obs: 4758 / CC_1/2: 0.737 / R_rim(I) all: 0.5799 / % possible all: 99.69

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
Coot	WinCoot 0.9.6 EL	model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.45→42.08 Å / Cor.coef. F_o:F_c: 0.96 / Cor.coef. F_o:F_c free: 0.946 / SU B: 1.511 / SU ML: 0.059 / Cross valid method: FREE R-VALUE / ESU R: 0.08 / ESU R Free: 0.083
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.228	2339	5.004 %
R_work	0.1913	44406	-
all	0.193	-	-
obs	-	46745	98.074 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 17.453 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.128 Å²	-0 Å²	0.148 Å²
2-	-	-0.103 Å²	-0 Å²
3-	-	-	-0.056 Å²

Refinement step

Cycle: LAST / Resolution: 1.45→42.08 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2366	0	0	292	2658

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.013	2450
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.015	2329
X-RAY DIFFRACTION	r_angle_refined_deg	1.758	1.654	3349
X-RAY DIFFRACTION	r_angle_other_deg	1.49	1.576	5391
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.402	5	300
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.148	23.226	124
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.662	15	414
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.746	15	14
X-RAY DIFFRACTION	r_chiral_restr	0.092	0.2	326
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.02	2737
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	507
X-RAY DIFFRACTION	r_nbd_refined	0.231	0.2	524
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.214	0.2	2199
X-RAY DIFFRACTION	r_nbtor_refined	0.177	0.2	1217
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.088	0.2	1099
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.145	0.2	179
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.361	0.2	19
X-RAY DIFFRACTION	r_nbd_other	0.274	0.2	87
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.219	0.2	30
X-RAY DIFFRACTION	r_mcbond_it	1.672	1.578	1200
X-RAY DIFFRACTION	r_mcbond_other	1.671	1.576	1199
X-RAY DIFFRACTION	r_mcangle_it	2.416	2.363	1500
X-RAY DIFFRACTION	r_mcangle_other	2.415	2.364	1501
X-RAY DIFFRACTION	r_scbond_it	2.772	1.894	1250
X-RAY DIFFRACTION	r_scbond_other	2.771	1.895	1251
X-RAY DIFFRACTION	r_scangle_it	4.077	2.725	1849
X-RAY DIFFRACTION	r_scangle_other	4.076	2.727	1850
X-RAY DIFFRACTION	r_lrange_it	5.475	20.447	2853
X-RAY DIFFRACTION	r_lrange_other	5.341	19.856	2787

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.45-1.488	0.282	177	0.253	3341	X-RAY DIFFRACTION	99.7448
1.488-1.528	0.261	178	0.24	3242	X-RAY DIFFRACTION	99.5923
1.528-1.573	0.256	176	0.229	3138	X-RAY DIFFRACTION	99.4299
1.573-1.621	0.275	155	0.216	3089	X-RAY DIFFRACTION	99.4177
1.621-1.674	0.253	162	0.205	2909	X-RAY DIFFRACTION	98.8095
1.674-1.733	0.252	156	0.203	2852	X-RAY DIFFRACTION	99.5038
1.733-1.798	0.246	144	0.197	2773	X-RAY DIFFRACTION	99.3529
1.798-1.872	0.271	140	0.201	2633	X-RAY DIFFRACTION	98.8944
1.872-1.955	0.259	117	0.202	2569	X-RAY DIFFRACTION	98.2084
1.955-2.05	0.215	120	0.195	2408	X-RAY DIFFRACTION	98.6344
2.05-2.161	0.247	127	0.191	2307	X-RAY DIFFRACTION	97.6334
2.161-2.292	0.215	98	0.185	2139	X-RAY DIFFRACTION	97.1764
2.292-2.45	0.226	95	0.182	2055	X-RAY DIFFRACTION	97.5942
2.45-2.646	0.217	108	0.173	1854	X-RAY DIFFRACTION	96.1293
2.646-2.898	0.22	94	0.198	1717	X-RAY DIFFRACTION	96.5867
2.898-3.239	0.232	81	0.184	1535	X-RAY DIFFRACTION	93.7899
3.239-3.738	0.204	74	0.176	1352	X-RAY DIFFRACTION	95.7047
3.738-4.575	0.2	60	0.152	1124	X-RAY DIFFRACTION	94.4179
4.575-6.453	0.184	50	0.199	890	X-RAY DIFFRACTION	93.1615
6.453-42.08	0.227	27	0.21	478	X-RAY DIFFRACTION	92.6606

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