PDB-9i9o: Crystal Structure of UFC1 K108M

ID or keywords:

Entry

Database: PDB / ID: 9i9o

Title

Crystal Structure of UFC1 K108M

Components

Ubiquitin-fold modifier-conjugating enzyme 1

Keywords

LIGASE / Ubiquitin fold modifier conjugating enzyme-1 / UFMylation / transthiolation / isopeptide bond / Thioester

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 /

MOLECULAR REPLACEMENT / Resolution: 2.051 Å

Authors

Manoj Kumar, P. / 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	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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PDBx/mmCIF format	9i9o.cif.gz	51.8 KB	Display	PDBx/mmCIF format
PDB format	pdb9i9o.ent.gz		Display	PDB format
PDBx/mmJSON format	9i9o.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9i9o_validation.pdf.gz	428.9 KB	Display	wwPDB validaton report
Full document	9i9o_full_validation.pdf.gz	429.7 KB	Display
Data in XML	9i9o_validation.xml.gz	10.2 KB	Display
Data in CIF	9i9o_validation.cif.gz	13.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/i9/9i9o ftp://data.pdbj.org/pub/pdb/validation_reports/i9/9i9o	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 9i9nC 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

19.6 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)	47.210, 47.210, 143.000
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	92
Space group name H-M	P4₁2₁2

#1: Protein	Ubiquitin-fold modifier-conjugating enzyme 1 / Ufm1-conjugating enzyme 1 Mass: 19642.559 Da / Num. of mol.: 1 / Mutation: K108M Source method: isolated from a genetically manipulated source Details: Lysine at 108th position of UFC1 is mutated to Methionine 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: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.02 Å³/Da / Density % sol: 39.05 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.15M Ammonium sulfate, 0.1M Sodium Hepes pH 7.0, 20%w/v PEG 4000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54187 Å
Detector	Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Aug 24, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54187 Å / Relative weight: 1
Reflection	Resolution: 2.051→19.706 Å / Num. obs: 10757 / % possible obs: 99.47 % / Redundancy: 2 % / B_iso Wilson estimate: 20.85 Å² / CC_1/2: 0.996 / R_rim(I) all: 0.101 / Net I/σ(I): 9.68
Reflection shell	Resolution: 2.051→2.125 Å / Redundancy: 2 % / Mean I/σ(I) obs: 1.38 / Num. unique obs: 999 / CC_1/2: 0.648 / R_rim(I) all: 0.659 / % possible all: 96.52

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
XDS		data reduction
XSCALE		data scaling
Coot	0.9.6	model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.051→19.706 Å / Cor.coef. F_o:F_c: 0.937 / Cor.coef. F_o:F_c free: 0.893 / SU B: 6.509 / SU ML: 0.168 / Cross valid method: FREE R-VALUE / ESU R: 0.257 / ESU R Free: 0.199
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2533	530	4.927 %
R_work	0.2161	10227	-
all	0.218	-	-
obs	-	10757	99.473 %

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: 20.842 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.411 Å²	0 Å²	0 Å²
2-	-	-0.411 Å²	0 Å²
3-	-	-	0.821 Å²

Refinement step

Cycle: LAST / Resolution: 2.051→19.706 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1347	0	0	80	1427

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.013	1404
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.015	1315
X-RAY DIFFRACTION	r_angle_refined_deg	1.331	1.645	1908
X-RAY DIFFRACTION	r_angle_other_deg	1.365	1.581	3037
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.01	5	169
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.116	22.297	74
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.741	15	240
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	22.062	15	9
X-RAY DIFFRACTION	r_chiral_restr	0.076	0.2	177
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	1573
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	322
X-RAY DIFFRACTION	r_nbd_refined	0.201	0.2	295
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.213	0.2	1200
X-RAY DIFFRACTION	r_nbtor_refined	0.172	0.2	682
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.079	0.2	559
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.143	0.2	72
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.325	0.2	13
X-RAY DIFFRACTION	r_nbd_other	0.249	0.2	64
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.312	0.2	12
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.018	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	1.401	2.093	673
X-RAY DIFFRACTION	r_mcbond_other	1.387	2.089	672
X-RAY DIFFRACTION	r_mcangle_it	2.157	3.126	843
X-RAY DIFFRACTION	r_mcangle_other	2.157	3.131	844
X-RAY DIFFRACTION	r_scbond_it	1.855	2.294	731
X-RAY DIFFRACTION	r_scbond_other	1.855	2.294	731
X-RAY DIFFRACTION	r_scangle_it	2.911	3.347	1065
X-RAY DIFFRACTION	r_scangle_other	2.91	3.35	1066
X-RAY DIFFRACTION	r_lrange_it	5.379	38.994	5899
X-RAY DIFFRACTION	r_lrange_other	5.376	38.963	5865

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 (%)
2.051-2.105	0.428	38	0.294	694	X-RAY DIFFRACTION	95.4368
2.105-2.162	0.284	49	0.281	714	X-RAY DIFFRACTION	99.8691
2.162-2.225	0.236	34	0.251	705	X-RAY DIFFRACTION	100
2.225-2.293	0.288	31	0.254	674	X-RAY DIFFRACTION	100
2.293-2.368	0.285	33	0.251	668	X-RAY DIFFRACTION	100
2.368-2.451	0.322	33	0.242	625	X-RAY DIFFRACTION	100
2.451-2.543	0.279	35	0.237	621	X-RAY DIFFRACTION	100
2.543-2.646	0.265	42	0.235	598	X-RAY DIFFRACTION	100
2.646-2.764	0.25	30	0.231	574	X-RAY DIFFRACTION	100
2.764-2.898	0.225	33	0.22	543	X-RAY DIFFRACTION	100
2.898-3.054	0.302	23	0.226	540	X-RAY DIFFRACTION	100
3.054-3.238	0.298	27	0.231	496	X-RAY DIFFRACTION	100
3.238-3.461	0.304	20	0.218	479	X-RAY DIFFRACTION	100
3.461-3.736	0.157	18	0.192	460	X-RAY DIFFRACTION	100
3.736-4.09	0.271	24	0.154	410	X-RAY DIFFRACTION	100
4.09-4.568	0.102	14	0.146	389	X-RAY DIFFRACTION	100
4.568-5.265	0.169	12	0.159	357	X-RAY DIFFRACTION	100
5.265-6.427	0.288	16	0.226	286	X-RAY DIFFRACTION	100
6.427-8.997	0.175	12	0.206	251	X-RAY DIFFRACTION	100
8-19.7	0.156	6	0.196	143	X-RAY DIFFRACTION	88.1657

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