PDB-9gli: Crystal Structure of UFC1 T106C

ID or keywords:

Entry

Database: PDB / ID: 9gli

Title

Crystal Structure of UFC1 T106C

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: 1.426 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	9gli.cif.gz	54.6 KB	Display	PDBx/mmCIF format
PDB format	pdb9gli.ent.gz		Display	PDB format
PDBx/mmJSON format	9gli.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9gli_validation.pdf.gz	433.9 KB	Display	wwPDB validaton report
Full document	9gli_full_validation.pdf.gz	434.5 KB	Display
Data in XML	9gli_validation.xml.gz	11.7 KB	Display
Data in CIF	9gli_validation.cif.gz	16 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gl/9gli ftp://data.pdbj.org/pub/pdb/validation_reports/gl/9gli	HTTPS FTP

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Related structure data

Related structure data	9glhC 9gljC 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

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

Unit cell

Length a, b, c (Å)	47.014, 47.014, 142.729
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-320- HOH

#1: Protein	Ubiquitin-fold modifier-conjugating enzyme 1 / Ufm1-conjugating enzyme 1 Mass: 19642.582 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Threonine at 106th position mutated to Cysteine / 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: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 169 / 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: 38.73 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1M Ammonium Citrate tribasic pH 7.0, 0.1M Bis-Tris Propane pH 7.0.

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Data collection

Diffraction	Mean temperature: 298 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.34767 Å
Detector	Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Mar 25, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.34767 Å / Relative weight: 1
Reflection	Resolution: 1.426→44.654 Å / Num. obs: 29760 / % possible obs: 96.5 % / Redundancy: 21.3 % / B_iso Wilson estimate: 15.12 Å² / CC_1/2: 0.999 / R_rim(I) all: 0.02949 / Net I/σ(I): 12.1
Reflection shell	Resolution: 1.426→1.451 Å / Redundancy: 5 % / Mean I/σ(I) obs: 0.7 / Num. unique obs: 1017 / CC_1/2: 0.333 / R_rim(I) all: 0.8167 / % possible all: 68.6

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Processing

Software

Name: REFMAC / Version: 5.8.0267 / Classification: refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.426→44.654 Å / Cor.coef. F_o:F_c: 0.966 / Cor.coef. F_o:F_c free: 0.956 / SU B: 1.312 / SU ML: 0.049 / Cross valid method: FREE R-VALUE / ESU R: 0.068 / ESU R Free: 0.071
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.208	1403	4.734 %
R_work	0.1745	28233	-
all	0.176	-	-
obs	-	29636	96.055 %

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: 16.107 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.333 Å²	0 Å²	0 Å²
2-	-	-0.333 Å²	0 Å²
3-	-	-	0.667 Å²

Refinement step

Cycle: LAST / Resolution: 1.426→44.654 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1358	0	12	169	1539

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.013	1406
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.015	1336
X-RAY DIFFRACTION	r_angle_refined_deg	1.837	1.645	1902
X-RAY DIFFRACTION	r_angle_other_deg	1.51	1.585	3086
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.577	5	165
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.905	22.133	75
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.689	15	244
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.019	15	9
X-RAY DIFFRACTION	r_chiral_restr	0.101	0.2	174
X-RAY DIFFRACTION	r_gen_planes_refined	0.012	0.02	1546
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	320
X-RAY DIFFRACTION	r_nbd_refined	0.216	0.2	275
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.186	0.2	1217
X-RAY DIFFRACTION	r_nbtor_refined	0.178	0.2	688
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.084	0.2	612
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.126	0.2	102
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.301	0.2	24
X-RAY DIFFRACTION	r_nbd_other	0.192	0.2	61
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.197	0.2	31
X-RAY DIFFRACTION	r_mcbond_it	1.501	1.417	663
X-RAY DIFFRACTION	r_mcbond_other	1.385	1.417	662
X-RAY DIFFRACTION	r_mcangle_it	2.124	2.123	827
X-RAY DIFFRACTION	r_mcangle_other	2.153	2.126	828
X-RAY DIFFRACTION	r_scbond_it	2.602	1.713	743
X-RAY DIFFRACTION	r_scbond_other	2.6	1.714	744
X-RAY DIFFRACTION	r_scangle_it	3.895	2.437	1075
X-RAY DIFFRACTION	r_scangle_other	3.893	2.438	1076
X-RAY DIFFRACTION	r_lrange_it	5.061	17.666	1638
X-RAY DIFFRACTION	r_lrange_other	4.853	17.124	1609

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
1.426-1.463	0.358	73	0.348	1398	0.348	2210	0.55	0.585	66.5611	0.347
1.463-1.503	0.322	92	0.305	1770	0.306	2184	0.765	0.759	85.2564	0.302
1.503-1.547	0.318	109	0.25	1863	0.254	2117	0.845	0.86	93.1507	0.244
1.547-1.594	0.269	82	0.202	1952	0.204	2045	0.89	0.916	99.4621	0.19
1.594-1.646	0.202	83	0.181	1905	0.182	1988	0.934	0.944	100	0.164
1.646-1.704	0.184	111	0.165	1839	0.166	1950	0.954	0.954	100	0.149
1.704-1.768	0.203	87	0.154	1787	0.156	1874	0.953	0.962	100	0.136
1.768-1.84	0.198	97	0.158	1717	0.16	1814	0.954	0.96	100	0.141
1.84-1.922	0.194	89	0.151	1638	0.154	1727	0.956	0.962	100	0.138
1.922-2.016	0.233	67	0.159	1609	0.162	1676	0.944	0.959	100	0.145
2.016-2.124	0.185	67	0.158	1517	0.159	1584	0.958	0.964	100	0.148
2.124-2.253	0.197	60	0.141	1458	0.143	1518	0.961	0.97	100	0.135
2.253-2.408	0.177	70	0.16	1352	0.161	1422	0.963	0.966	100	0.157
2.408-2.6	0.222	50	0.164	1291	0.166	1341	0.946	0.959	100	0.165
2.6-2.848	0.243	61	0.172	1178	0.176	1239	0.937	0.957	100	0.178
2.848-3.182	0.174	59	0.177	1073	0.177	1132	0.96	0.957	100	0.189
3.182-3.671	0.207	43	0.163	975	0.165	1018	0.957	0.964	100	0.185
3.671-4.489	0.201	39	0.147	826	0.149	865	0.965	0.975	100	0.18
4.489-6.317	0.172	39	0.202	665	0.2	704	0.977	0.968	100	0.251
6.317-44.654	0.215	25	0.218	420	0.218	445	0.962	0.956	100	0.283

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