PDB-9i9n: Crystal Structure of UFC1 C116E & K108A

ID or keywords:

Entry

Database: PDB / ID: 9i9n

Title

Crystal Structure of UFC1 C116E & K108A

Components

Ubiquitin-fold modifier-conjugating enzyme 1

Keywords

LIGASE / Ubiquitin fold modifier conjugation enzyme 1 / UFC1 / UFMylation / transthiolation activity / Ligase activity / aminoacyl transferase activity / Thioester mimetic

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: 1.88 Å

Authors

Manoj Kumar, P. / Banerjee, S. / Weiner, 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	Feb 6, 2025	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	9i9n.cif.gz	52.6 KB	Display	PDBx/mmCIF format
PDB format	pdb9i9n.ent.gz		Display	PDB format
PDBx/mmJSON format	9i9n.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9i9n_validation.pdf.gz	442.4 KB	Display	wwPDB validaton report
Full document	9i9n_full_validation.pdf.gz	442.7 KB	Display
Data in XML	9i9n_validation.xml.gz	10.8 KB	Display
Data in CIF	9i9n_validation.cif.gz	13.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/i9/9i9n ftp://data.pdbj.org/pub/pdb/validation_reports/i9/9i9n	HTTPS FTP

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Related structure data

Related structure data	9glhC 9gliC 9gljC 9glkC 9gllC 9glmC 9glnC 9gloC 9glpC 9glrC 9glsC 9gltC 9gmmC 9gmnC 9gn8C 9i9mC 9i9oC 9i9pC 9ia8C 2z6o 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

19.8 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, monomeric assembly

Unit cell

Length a, b, c (Å)	46.458, 46.458, 143.776
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-379- HOH

#1: Protein	Ubiquitin-fold modifier-conjugating enzyme 1 / Ufm1-conjugating enzyme 1 Mass: 19608.412 Da / Num. of mol.: 1 / Mutation: C116E, K108A Source method: isolated from a genetically manipulated source Details: UFC1 C116E & K108A / Source: (gene. exp.) Homo sapiens (human) / Gene: UFC1, CGI-126, HSPC155 / Production host: Escherichia coli (E. coli) / Strain (production host): T7-Express / References: UniProt: Q9Y3C8
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / 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.: 107 / 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: 1.96 Å³/Da / Density % sol: 37.4 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.1M Tris pH 8.0, 2M Ammonium sulfate

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Data collection

Diffraction	Mean temperature: 100 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: 1.88→44.21 Å / Num. obs: 12610 / % possible obs: 92.84 % / Redundancy: 2 % / B_iso Wilson estimate: 23.02 Å² / CC_1/2: 0.999 / R_rim(I) all: 0.03682 / Net I/σ(I): 15.5
Reflection shell	Resolution: 1.88→1.947 Å / Mean I/σ(I) obs: 2.07 / Num. unique obs: 841 / CC_1/2: 0.806 / R_rim(I) all: 0.3467

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
EDNA		data collection
autoPROC		data scaling
Coot	0.9.6	model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.88→44.208 Å / Cor.coef. F_o:F_c: 0.958 / Cor.coef. F_o:F_c free: 0.934 / SU B: 3.394 / SU ML: 0.1 / Cross valid method: FREE R-VALUE / ESU R: 0.169 / ESU R Free: 0.155
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2288	601	4.766 %
R_work	0.1793	12009	-
all	0.182	-	-
obs	-	12610	92.83 %

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: 21.539 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.014 Å²	-0 Å²	-0 Å²
2-	-	0.014 Å²	-0 Å²
3-	-	-	-0.028 Å²

Refinement step

Cycle: LAST / Resolution: 1.88→44.208 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1317	0	11	107	1435

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.013	1371
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.015	1277
X-RAY DIFFRACTION	r_angle_refined_deg	1.525	1.643	1865
X-RAY DIFFRACTION	r_angle_other_deg	1.394	1.579	2943
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.607	5	163
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.307	22.027	74
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.138	15	227
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.338	15	9
X-RAY DIFFRACTION	r_chiral_restr	0.086	0.2	172
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	1526
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	316
X-RAY DIFFRACTION	r_nbd_refined	0.209	0.2	275
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.193	0.2	1134
X-RAY DIFFRACTION	r_nbtor_refined	0.168	0.2	671
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.081	0.2	541
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.155	0.2	72
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.207	0.2	9
X-RAY DIFFRACTION	r_nbd_other	0.169	0.2	49
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.172	0.2	21
X-RAY DIFFRACTION	r_mcbond_it	1.634	2.021	652
X-RAY DIFFRACTION	r_mcbond_other	1.599	2.02	651
X-RAY DIFFRACTION	r_mcangle_it	2.218	3.019	815
X-RAY DIFFRACTION	r_mcangle_other	2.217	3.02	816
X-RAY DIFFRACTION	r_scbond_it	2.668	2.382	719
X-RAY DIFFRACTION	r_scbond_other	2.642	2.365	716
X-RAY DIFFRACTION	r_scangle_it	4.053	3.444	1050
X-RAY DIFFRACTION	r_scangle_other	4.009	3.418	1045
X-RAY DIFFRACTION	r_lrange_it	5.361	24.365	1575
X-RAY DIFFRACTION	r_lrange_other	5.319	24.13	1561

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
1.88-1.929	0.3	29	0.229	579	0.232	984	0.884	0.879	61.7886	0.233
1.929-1.981	0.26	37	0.212	659	0.215	924	0.883	0.912	75.3247	0.211
1.981-2.039	0.25	40	0.192	712	0.195	944	0.914	0.934	79.661	0.185
2.039-2.101	0.214	35	0.184	778	0.185	893	0.934	0.938	91.0414	0.179
2.101-2.17	0.261	42	0.178	770	0.183	869	0.923	0.945	93.4407	0.17
2.17-2.246	0.183	37	0.168	781	0.169	838	0.956	0.956	97.6134	0.164
2.246-2.331	0.234	30	0.178	805	0.18	841	0.939	0.951	99.2866	0.169
2.331-2.426	0.268	37	0.196	749	0.2	787	0.918	0.938	99.8729	0.187
2.426-2.533	0.251	47	0.183	720	0.187	767	0.938	0.946	100	0.173
2.533-2.656	0.284	28	0.172	697	0.176	725	0.922	0.95	100	0.164
2.656-2.799	0.292	33	0.174	672	0.179	705	0.926	0.951	100	0.164
2.799-2.969	0.209	27	0.183	636	0.184	663	0.931	0.951	100	0.176
2.969-3.172	0.192	30	0.179	600	0.18	631	0.963	0.955	99.8415	0.174
3.172-3.425	0.26	32	0.177	554	0.181	587	0.925	0.96	99.8296	0.174
3.425-3.75	0.211	39	0.165	502	0.168	542	0.961	0.967	99.8155	0.168
3.75-4.189	0.292	22	0.161	490	0.165	513	0.924	0.97	99.8051	0.171
4.189-4.829	0.171	10	0.143	432	0.143	443	0.973	0.977	99.7743	0.156
4.829-5.897	0.138	19	0.187	381	0.184	401	0.985	0.975	99.7506	0.199
5.897-8.267	0.19	17	0.229	298	0.227	318	0.972	0.965	99.0566	0.238
8.267-44.208	0.217	10	0.22	192	0.22	206	0.972	0.964	98.0583	0.276

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