PDB-9gll: Crystal Structure of UFC1 T106L

ID or keywords:

Entry

Database: PDB / ID: 9gll

Title

Crystal Structure of UFC1 T106L

Components

Ubiquitin-fold modifier-conjugating enzyme 1

Keywords

LIGASE / UFM1 conjugating enzyme1 / UBC core domain containing protein / Brain development / Infantile encephalopathy

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: 1.65 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	9gll.cif.gz	55.2 KB	Display	PDBx/mmCIF format
PDB format	pdb9gll.ent.gz		Display	PDB format
PDBx/mmJSON format	9gll.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/9gll ftp://data.pdbj.org/pub/pdb/validation_reports/gl/9gll	HTTPS FTP

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Related structure data

Related structure data	9glhC 9gliC 9gljC 9glkC 9glmC 9glnC 9gloC 9glpC 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

19.7 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)	47.200, 47.200, 142.800
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-257- HOH
2	1	AAA-297- HOH

#1: Protein	Ubiquitin-fold modifier-conjugating enzyme 1 / Ufm1-conjugating enzyme 1 Mass: 19652.598 Da / Num. of mol.: 1 / Mutation: T106L Source method: isolated from a genetically manipulated source Details: Threonine at 106th position is mutated to Leucine / Source: (gene. exp.) Homo sapiens (human) / Gene: UFC1, CGI-126, HSPC155 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y3C8
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 152 / 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: 39.21 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 1.4M Sodium potassium monobasic monohydrate/Potassium phosphate dibasic pH 9.0

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Data collection

Diffraction	Mean temperature: 298 K / Serial crystal experiment: N
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54187 Å
Detector	Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Dec 20, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54187 Å / Relative weight: 1
Reflection	Resolution: 1.65→44.82 Å / Num. obs: 20255 / % possible obs: 99.58 % / Redundancy: 2 % / B_iso Wilson estimate: 11.53 Å² / CC_1/2: 0.998 / R_rim(I) all: 0.06703 / Net I/σ(I): 12.61
Reflection shell	Resolution: 1.65→1.709 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 1.61 / Num. unique obs: 1959 / CC_1/2: 0.664 / R_rim(I) all: 0.594 / % possible all: 98.49

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
XDS		data reduction
XSCALE		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.65→44.815 Å / Cor.coef. F_o:F_c: 0.945 / Cor.coef. F_o:F_c free: 0.926 / SU B: 2.569 / SU ML: 0.084 / Cross valid method: FREE R-VALUE / ESU R: 0.119 / ESU R Free: 0.111
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.231	1031	5.091 %
R_work	0.203	19221	-
all	0.204	-	-
obs	-	20252	99.577 %

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: 13.882 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.423 Å²	0 Å²	0 Å²
2-	-	-0.423 Å²	0 Å²
3-	-	-	0.845 Å²

Refinement step

Cycle: LAST / Resolution: 1.65→44.815 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1352	0	0	152	1504

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.013	1469
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.015	1373
X-RAY DIFFRACTION	r_angle_refined_deg	1.68	1.646	2003
X-RAY DIFFRACTION	r_angle_other_deg	1.429	1.584	3174
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.789	5	180
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.205	22.024	84
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.132	15	253
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.691	15	11
X-RAY DIFFRACTION	r_chiral_restr	0.086	0.2	182
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	1687
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	351
X-RAY DIFFRACTION	r_nbd_refined	0.207	0.2	292
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.184	0.2	1202
X-RAY DIFFRACTION	r_nbtor_refined	0.171	0.2	696
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.079	0.2	615
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.156	0.2	93
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.121	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.295	0.2	25
X-RAY DIFFRACTION	r_nbd_other	0.254	0.2	70
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.342	0.2	23
X-RAY DIFFRACTION	r_mcbond_it	1.325	1.266	702
X-RAY DIFFRACTION	r_mcbond_other	1.245	1.261	701
X-RAY DIFFRACTION	r_mcangle_it	2.058	1.885	888
X-RAY DIFFRACTION	r_mcangle_other	2.063	1.889	889
X-RAY DIFFRACTION	r_scbond_it	2.085	1.493	767
X-RAY DIFFRACTION	r_scbond_other	2.074	1.493	767
X-RAY DIFFRACTION	r_scangle_it	3.235	2.137	1114
X-RAY DIFFRACTION	r_scangle_other	3.238	2.138	1115
X-RAY DIFFRACTION	r_lrange_it	5.331	23.907	6130
X-RAY DIFFRACTION	r_lrange_other	4.991	23.363	5998

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 (%)
1.65-1.693	0.29	71	0.286	1389	X-RAY DIFFRACTION	98.582
1.693-1.739	0.259	62	0.259	1330	X-RAY DIFFRACTION	98.5836
1.739-1.789	0.256	85	0.245	1299	X-RAY DIFFRACTION	99.2115
1.789-1.844	0.313	72	0.232	1269	X-RAY DIFFRACTION	99.407
1.844-1.905	0.226	73	0.226	1235	X-RAY DIFFRACTION	99.4677
1.905-1.972	0.259	61	0.22	1218	X-RAY DIFFRACTION	99.766
1.972-2.046	0.278	64	0.209	1160	X-RAY DIFFRACTION	99.8369
2.046-2.129	0.251	68	0.189	1113	X-RAY DIFFRACTION	99.9154
2.129-2.224	0.196	62	0.172	1091	X-RAY DIFFRACTION	100
2.224-2.332	0.222	61	0.187	1022	X-RAY DIFFRACTION	100
2.332-2.458	0.18	56	0.18	998	X-RAY DIFFRACTION	100
2.458-2.606	0.23	41	0.181	949	X-RAY DIFFRACTION	100
2.606-2.786	0.274	44	0.198	915	X-RAY DIFFRACTION	99.8958
2.786-3.008	0.231	36	0.207	834	X-RAY DIFFRACTION	100
3.008-3.293	0.225	37	0.205	776	X-RAY DIFFRACTION	100
3.293-3.68	0.215	37	0.195	714	X-RAY DIFFRACTION	99.7344
3.68-4.244	0.223	33	0.168	642	X-RAY DIFFRACTION	99.7046
4.244-5.186	0.172	36	0.166	538	X-RAY DIFFRACTION	99.8261
5.186-7.286	0.238	16	0.201	445	X-RAY DIFFRACTION	99.3534
7.286-44.815	0.194	16	0.222	284	X-RAY DIFFRACTION	98.6842

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