PDB-9glj: Crystal Structure of UFC1 T106A

ID or keywords:

Entry

Database: PDB / ID: 9glj

Title

Crystal Structure of UFC1 T106A

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 /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.213 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	9glj.cif.gz	55.6 KB	Display	PDBx/mmCIF format
PDB format	pdb9glj.ent.gz		Display	PDB format
PDBx/mmJSON format	9glj.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9glj_validation.pdf.gz	420.7 KB	Display	wwPDB validaton report
Full document	9glj_full_validation.pdf.gz	422 KB	Display
Data in XML	9glj_validation.xml.gz	12 KB	Display
Data in CIF	9glj_validation.cif.gz	16.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gl/9glj ftp://data.pdbj.org/pub/pdb/validation_reports/gl/9glj	HTTPS FTP

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Related structure data

Related structure data	9glhC 9gliC 9glkC 9gllC 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

19.6 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)	47.222, 47.222, 142.039
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-296- HOH
2	1	AAA-316- HOH

#1: Protein	Ubiquitin-fold modifier-conjugating enzyme 1 / Ufm1-conjugating enzyme 1 Mass: 19610.518 Da / Num. of mol.: 1 / Mutation: T106A Source method: isolated from a genetically manipulated source Details: Threonine at 106th position is mutated to Alanine / 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.: 207 / 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: 2.02 Å³/Da / Density % sol: 39.08 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M NaCl, 0.1M Bis-Tris pH 6.5, 1.5M Ammonium sulfate.

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Data collection

Diffraction	Mean temperature: 298 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.87313 Å
Detector	Type: DECTRIS EIGER2 XE CdTe 16M / Detector: PIXEL / Date: Nov 10, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.87313 Å / Relative weight: 1
Reflection	Resolution: 1.213→33.43 Å / Num. obs: 49774 / % possible obs: 99.99 % / Redundancy: 2 % / B_iso Wilson estimate: 15.33 Å² / CC_1/2: 1 / R_rim(I) all: 0.022 / Net I/σ(I): 15.16
Reflection shell	Resolution: 1.213→1.256 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.32 / Num. unique obs: 4863 / CC_1/2: 0.836 / R_rim(I) all: 0.3448 / % possible all: 100

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Processing

Software

Name	Version	Classification
autoPROC		data processing
autoPROC		data reduction
autoPROC		data scaling
REFMAC	5.8.0267	refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.213→33.43 Å / Cor.coef. F_o:F_c: 0.972 / Cor.coef. F_o:F_c free: 0.963 / SU B: 0.677 / SU ML: 0.03 / Cross valid method: FREE R-VALUE / ESU R: 0.043 / ESU R Free: 0.045
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1989	2494	5.011 %
R_work	0.1768	47280	-
all	0.178	-	-
obs	-	49774	99.998 %

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: 17.434 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.061 Å²	0 Å²	0 Å²
2-	-	-0.061 Å²	0 Å²
3-	-	-	0.123 Å²

Refinement step

Cycle: LAST / Resolution: 1.213→33.43 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1337	0	0	207	1544

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.013	1434
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.015	1336
X-RAY DIFFRACTION	r_angle_refined_deg	1.916	1.646	1956
X-RAY DIFFRACTION	r_angle_other_deg	1.52	1.583	3080
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.323	5	176
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.122	21.728	81
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.004	15	241
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.406	15	11
X-RAY DIFFRACTION	r_chiral_restr	0.117	0.2	179
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.02	1643
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	343
X-RAY DIFFRACTION	r_nbd_refined	0.232	0.2	271
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.186	0.2	1160
X-RAY DIFFRACTION	r_nbtor_refined	0.178	0.2	687
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.086	0.2	571
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.131	0.2	99
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.015	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.313	0.2	9
X-RAY DIFFRACTION	r_nbd_other	0.26	0.2	43
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.128	0.2	28
X-RAY DIFFRACTION	r_mcbond_it	1.435	1.583	689
X-RAY DIFFRACTION	r_mcbond_other	1.426	1.575	688
X-RAY DIFFRACTION	r_mcangle_it	2.124	2.365	870
X-RAY DIFFRACTION	r_mcangle_other	2.124	2.374	871
X-RAY DIFFRACTION	r_scbond_it	2.798	1.845	745
X-RAY DIFFRACTION	r_scbond_other	2.797	1.852	746
X-RAY DIFFRACTION	r_scangle_it	4.042	2.66	1086
X-RAY DIFFRACTION	r_scangle_other	4.041	2.66	1086
X-RAY DIFFRACTION	r_lrange_it	4.992	19.37	1668
X-RAY DIFFRACTION	r_lrange_other	4.811	18.811	1635

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 (%)
1.213-1.244	0.255	171	0.252	3437	X-RAY DIFFRACTION	100
1.244-1.278	0.215	196	0.215	3311	X-RAY DIFFRACTION	100
1.278-1.315	0.223	160	0.221	3256	X-RAY DIFFRACTION	100
1.315-1.356	0.244	165	0.208	3167	X-RAY DIFFRACTION	100
1.356-1.4	0.212	144	0.197	3084	X-RAY DIFFRACTION	100
1.4-1.449	0.233	171	0.183	2963	X-RAY DIFFRACTION	100
1.449-1.504	0.176	136	0.174	2885	X-RAY DIFFRACTION	100
1.504-1.565	0.198	149	0.165	2783	X-RAY DIFFRACTION	100
1.565-1.635	0.189	140	0.159	2670	X-RAY DIFFRACTION	100
1.635-1.715	0.234	141	0.165	2541	X-RAY DIFFRACTION	100
1.715-1.807	0.189	118	0.168	2460	X-RAY DIFFRACTION	100
1.807-1.917	0.197	126	0.167	2307	X-RAY DIFFRACTION	100
1.917-2.049	0.196	130	0.179	2175	X-RAY DIFFRACTION	100
2.049-2.212	0.173	105	0.161	2049	X-RAY DIFFRACTION	100
2.212-2.423	0.199	101	0.166	1882	X-RAY DIFFRACTION	100
2.423-2.708	0.194	88	0.174	1742	X-RAY DIFFRACTION	100
2.708-3.125	0.202	95	0.177	1525	X-RAY DIFFRACTION	100
3.125-3.823	0.166	74	0.166	1322	X-RAY DIFFRACTION	100
3.823-5.387	0.198	47	0.162	1069	X-RAY DIFFRACTION	100
5.387-33.43	0.248	37	0.23	652	X-RAY DIFFRACTION	99.8551

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