PDB-9glp: Crystal Structure of UFC1 C116E&T106I

ID or keywords:

Entry

Database: PDB / ID: 9glp

Title

Crystal Structure of UFC1 C116E&T106I

Components

Ubiquitin-fold modifier-conjugating enzyme 1

Keywords

LIGASE / UFM1 conjugating enzyme1 / UBC core domain containing protein / UFC1~UFM1 thioester mimic

Function / homology

Function and homology information

UFM1 conjugating enzyme activity / UFM1 transferase activity / protein K69-linked ufmylation / protein ufmylation / regulation of type II interferon production / reticulophagy / response to endoplasmic reticulum stress / brain development / extracellular exosome
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.77 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 27, 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	9glp.cif.gz	53.3 KB	Display	PDBx/mmCIF format
PDB format	pdb9glp.ent.gz		Display	PDB format
PDBx/mmJSON format	9glp.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9glp_validation.pdf.gz	443.6 KB	Display	wwPDB validaton report
Full document	9glp_full_validation.pdf.gz	444 KB	Display
Data in XML	9glp_validation.xml.gz	10.8 KB	Display
Data in CIF	9glp_validation.cif.gz	14.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gl/9glp ftp://data.pdbj.org/pub/pdb/validation_reports/gl/9glp	HTTPS FTP

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Related structure data

Related structure data	9glhC 9gliC 9gljC 9glkC 9gllC 9glmC 9glnC 9gloC 9glrC 9glsC 9gltC 9gmmC 9gmnC 9gn8C 9i9mC 9i9nC 9i9oC 9i9pC 9ia8C 2z6o 7nvj 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	#234 - Jun 2019 MDM2 and Cancer similarity (1) #60 - Dec 2004 Ubiquitin similarity (1)

Deposited unit

AAA: Ubiquitin-fold modifier-conjugating enzyme 1

hetero molecules

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

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	46.837, 46.837, 144.089
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	92
Space group name H-M	P4₁2₁2

Components on special symmetry positions

ID	Model	Components
1	1	AAA-329- HOH
2	1	AAA-335- HOH

#1: Protein	Ubiquitin-fold modifier-conjugating enzyme 1 / Ufm1-conjugating enzyme 1 Mass: 19678.568 Da / Num. of mol.: 1 / Mutation: C116E, T106I Source method: isolated from a genetically manipulated source Details: Threonine and Cysteine at 106th and 116th positions are mutated to Isoleucine and Glutamate respectively Source: (gene. exp.) Homo sapiens (human) / Gene: UFC1, CGI-126, HSPC155 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y3C8
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
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: 2.01 Å³/Da / Density % sol: 38.74 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1 M Bis-Tris, pH 5.5, 2 M ammonium sulfate.

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Data collection

Diffraction	Mean temperature: 298 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87313 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jan 19, 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: 1.7→44.543 Å / Num. obs: 16486 / % possible obs: 99.97 % / Redundancy: 2 % / B_iso Wilson estimate: 20.22 Å² / CC_1/2: 0.999 / R_rim(I) all: 0.04144 / Net I/σ(I): 13.74
Reflection shell	Resolution: 1.77→1.833 Å / Redundancy: 2 % / Mean I/σ(I) obs: 3.44 / Num. unique obs: 1605 / CC_1/2: 0.924 / R_rim(I) all: 0.2425 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
Coot	WinCoot 0.9.6	model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.77→44.543 Å / Cor.coef. F_o:F_c: 0.958 / Cor.coef. F_o:F_c free: 0.958 / SU B: 2.428 / SU ML: 0.076 / Cross valid method: FREE R-VALUE / ESU R: 0.124 / ESU R Free: 0.11
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1996	853	5.174 %
R_work	0.1777	15633	-
all	0.179	-	-
obs	-	16486	99.982 %

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: 19.787 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.042 Å²	-0 Å²	-0 Å²
2-	-	0.042 Å²	-0 Å²
3-	-	-	-0.084 Å²

Refinement step

Cycle: LAST / Resolution: 1.77→44.543 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1329	0	17	119	1465

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.013	1388
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	1302
X-RAY DIFFRACTION	r_angle_refined_deg	1.647	1.642	1884
X-RAY DIFFRACTION	r_angle_other_deg	1.454	1.58	3004
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.234	5	164
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.434	22.466	73
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.472	15	232
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.714	15	8
X-RAY DIFFRACTION	r_chiral_restr	0.095	0.2	173
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	1534
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	314
X-RAY DIFFRACTION	r_nbd_refined	0.211	0.2	269
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.191	0.2	1138
X-RAY DIFFRACTION	r_nbtor_refined	0.17	0.2	668
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.083	0.2	551
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.118	0.2	64
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.24	0.2	16
X-RAY DIFFRACTION	r_nbd_other	0.179	0.2	51
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.132	0.2	20
X-RAY DIFFRACTION	r_mcbond_it	1.713	1.824	656
X-RAY DIFFRACTION	r_mcbond_other	1.684	1.818	655
X-RAY DIFFRACTION	r_mcangle_it	2.444	2.72	820
X-RAY DIFFRACTION	r_mcangle_other	2.443	2.728	821
X-RAY DIFFRACTION	r_scbond_it	2.733	2.189	732
X-RAY DIFFRACTION	r_scbond_other	2.707	2.174	729
X-RAY DIFFRACTION	r_scangle_it	4.055	3.136	1064
X-RAY DIFFRACTION	r_scangle_other	4.006	3.113	1059
X-RAY DIFFRACTION	r_lrange_it	6.854	21.689	1568
X-RAY DIFFRACTION	r_lrange_other	6.846	21.51	1556

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.77-1.816	0.288	46	0.218	1144	0.22	1190	0.902	0.933	100	0.204
1.816-1.866	0.208	57	0.21	1098	0.21	1155	0.944	0.931	100	0.196
1.866-1.92	0.243	70	0.217	1047	0.219	1117	0.923	0.926	100	0.199
1.92-1.979	0.26	57	0.201	1047	0.204	1104	0.9	0.93	100	0.186
1.979-2.043	0.255	56	0.191	1001	0.194	1057	0.916	0.942	100	0.172
2.043-2.115	0.209	47	0.178	992	0.18	1039	0.938	0.951	100	0.165
2.115-2.194	0.261	56	0.175	932	0.179	988	0.918	0.957	100	0.164
2.194-2.284	0.193	57	0.173	905	0.174	962	0.957	0.957	100	0.16
2.284-2.385	0.22	49	0.177	880	0.179	929	0.947	0.958	100	0.164
2.385-2.501	0.145	42	0.161	837	0.161	880	0.974	0.963	99.8864	0.151
2.501-2.636	0.231	46	0.168	809	0.171	855	0.951	0.963	100	0.158
2.636-2.795	0.225	33	0.164	773	0.166	806	0.947	0.966	100	0.158
2.795-2.987	0.159	35	0.181	724	0.18	759	0.966	0.962	100	0.176
2.987-3.226	0.176	45	0.182	670	0.182	715	0.964	0.961	100	0.178
3.226-3.532	0.245	36	0.165	631	0.17	667	0.952	0.969	100	0.168
3.532-3.945	0.145	38	0.163	569	0.161	607	0.98	0.973	100	0.172
3.945-4.55	0.193	20	0.142	527	0.144	547	0.985	0.979	100	0.156
4.55-5.558	0.153	27	0.18	449	0.179	476	0.984	0.975	100	0.204
5.558-7.8	0.25	21	0.198	362	0.201	383	0.957	0.971	100	0.214
7.8-44.543	0.149	14	0.232	231	0.228	247	0.967	0.938	99.1903	0.294

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