PDB-9glh: Crystal Structure of UFC1 T106S

ID or keywords:

Entry

Database: PDB / ID: 9glh

Title

Crystal Structure of UFC1 T106S

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: 1.115 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	9glh.cif.gz	55.8 KB	Display	PDBx/mmCIF format
PDB format	pdb9glh.ent.gz		Display	PDB format
PDBx/mmJSON format	9glh.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9glh_validation.pdf.gz	434.5 KB	Display	wwPDB validaton report
Full document	9glh_full_validation.pdf.gz	435.2 KB	Display
Data in XML	9glh_validation.xml.gz	12.5 KB	Display
Data in CIF	9glh_validation.cif.gz	17.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gl/9glh ftp://data.pdbj.org/pub/pdb/validation_reports/gl/9glh	HTTPS FTP

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Related structure data

Related structure data	9gliC 9gljC 9glkC 9gllC 9glmC 9glnC 9gloC 9glpC 9glrC 9glsC 9gltC 9gmmC 9gmnC 9gn8C 9i9mC 9i9nC 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

19.7 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)	47.160, 47.160, 143.616
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-378- HOH
2	1	AAA-439- HOH
3	1	AAA-518- HOH

#1: Protein	Ubiquitin-fold modifier-conjugating enzyme 1 / Ufm1-conjugating enzyme 1 Mass: 19626.518 Da / Num. of mol.: 1 / Mutation: T106S Source method: isolated from a genetically manipulated source Details: Threonine at position 106 is mutated to Serine / Source: (gene. exp.) Homo sapiens (human) / Gene: UFC1, CGI-126, HSPC155 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y3C8
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 223 / 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: 2.03 Å³/Da / Density % sol: 39.54 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 1.4M Sodium Malonate dibasic monohydrate pH 6.0.

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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 EIGER X 16M / Detector: PIXEL / Date: Nov 9, 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: 1.115→33.35 Å / Num. obs: 63633 / % possible obs: 98.88 % / Redundancy: 2 % / B_iso Wilson estimate: 12.88 Å² / CC_1/2: 1 / R_rim(I) all: 0.02378 / Net I/σ(I): 14.67
Reflection shell	Resolution: 1.115→1.154 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.5 / Num. unique obs: 5823 / CC_1/2: 0.818 / R_rim(I) all: 0.3585 / % possible all: 92.21

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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: 1.115→33.35 Å / Cor.coef. F_o:F_c: 0.972 / Cor.coef. F_o:F_c free: 0.967 / SU B: 0.495 / SU ML: 0.024 / Cross valid method: FREE R-VALUE / ESU R: 0.034 / ESU R Free: 0.035
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.192	3175	4.99 %
R_work	0.174	60458	-
all	0.175	-	-
obs	-	63633	98.887 %

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: 14.251 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.114 Å²	0 Å²	0 Å²
2-	-	-0.114 Å²	0 Å²
3-	-	-	0.228 Å²

Refinement step

Cycle: LAST / Resolution: 1.115→33.35 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1337	0	5	223	1565

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.017	0.013	1398
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.015	1305
X-RAY DIFFRACTION	r_angle_refined_deg	2.002	1.643	1902
X-RAY DIFFRACTION	r_angle_other_deg	1.556	1.583	3011
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.359	5	168
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.69	22.133	75
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	10.393	15	236
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.296	15	9
X-RAY DIFFRACTION	r_chiral_restr	0.128	0.2	175
X-RAY DIFFRACTION	r_gen_planes_refined	0.012	0.02	1567
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	323
X-RAY DIFFRACTION	r_nbd_refined	0.229	0.2	272
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.187	0.2	1133
X-RAY DIFFRACTION	r_nbtor_refined	0.178	0.2	681
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.085	0.2	571
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.115	0.2	105
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.417	0.2	19
X-RAY DIFFRACTION	r_nbd_other	0.263	0.2	41
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.207	0.2	34
X-RAY DIFFRACTION	r_mcbond_it	1.303	1.245	669
X-RAY DIFFRACTION	r_mcbond_other	1.304	1.242	668
X-RAY DIFFRACTION	r_mcangle_it	1.763	1.874	838
X-RAY DIFFRACTION	r_mcangle_other	1.762	1.877	839
X-RAY DIFFRACTION	r_scbond_it	2.549	1.483	729
X-RAY DIFFRACTION	r_scbond_other	2.501	1.481	726
X-RAY DIFFRACTION	r_scangle_it	3.523	2.138	1064
X-RAY DIFFRACTION	r_scangle_other	3.517	2.127	1058
X-RAY DIFFRACTION	r_lrange_it	4.429	15.982	1644
X-RAY DIFFRACTION	r_lrange_other	4.246	15.309	1604

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 (%)
1.115-1.144	0.248	222	0.24	4221	X-RAY DIFFRACTION	95.3229
1.144-1.175	0.248	211	0.23	3860	X-RAY DIFFRACTION	89.12
1.175-1.209	0.219	225	0.211	4241	X-RAY DIFFRACTION	100
1.209-1.246	0.221	191	0.197	4094	X-RAY DIFFRACTION	100
1.246-1.287	0.217	205	0.188	3972	X-RAY DIFFRACTION	100
1.287-1.332	0.18	209	0.18	3838	X-RAY DIFFRACTION	100
1.332-1.382	0.189	189	0.173	3730	X-RAY DIFFRACTION	100
1.382-1.439	0.199	190	0.174	3591	X-RAY DIFFRACTION	100
1.439-1.503	0.204	181	0.167	3430	X-RAY DIFFRACTION	100
1.503-1.576	0.171	193	0.162	3311	X-RAY DIFFRACTION	100
1.576-1.661	0.198	150	0.161	3154	X-RAY DIFFRACTION	100
1.661-1.762	0.194	187	0.164	2966	X-RAY DIFFRACTION	100
1.762-1.883	0.194	144	0.167	2841	X-RAY DIFFRACTION	100
1.883-2.034	0.197	125	0.164	2640	X-RAY DIFFRACTION	100
2.034-2.227	0.175	117	0.158	2475	X-RAY DIFFRACTION	100
2.227-2.489	0.176	111	0.164	2227	X-RAY DIFFRACTION	100
2.489-2.873	0.218	105	0.181	1976	X-RAY DIFFRACTION	100
2.873-3.515	0.216	98	0.17	1703	X-RAY DIFFRACTION	100
3.515-4.956	0.146	73	0.154	1358	X-RAY DIFFRACTION	100

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