PDB-9glm: Crystal Structure of UFC1 W145F

ID or keywords:

Entry

Database: PDB / ID: 9glm

Title

Crystal Structure of UFC1 W145F

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: 1.79 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	9glm.cif.gz	53.8 KB	Display	PDBx/mmCIF format
PDB format	pdb9glm.ent.gz		Display	PDB format
PDBx/mmJSON format	9glm.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9glm_validation.pdf.gz	438 KB	Display	wwPDB validaton report
Full document	9glm_full_validation.pdf.gz	439.6 KB	Display
Data in XML	9glm_validation.xml.gz	11.9 KB	Display
Data in CIF	9glm_validation.cif.gz	15.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gl/9glm ftp://data.pdbj.org/pub/pdb/validation_reports/gl/9glm	HTTPS FTP

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Related structure data

Related structure data	9glhC 9gliC 9gljC 9glkC 9gllC 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

19.7 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)	46.950, 46.950, 143.900
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-363- HOH
2	1	AAA-379- HOH

#1: Protein	Ubiquitin-fold modifier-conjugating enzyme 1 / Ufm1-conjugating enzyme 1 Mass: 19601.508 Da / Num. of mol.: 1 / Mutation: W145F Source method: isolated from a genetically manipulated source Details: Tryptophan at position 145 is mutated to Phenyl alanine 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.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.02 Å³/Da / Density % sol: 39.19 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1.5M Ammonium sulfate; 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: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54187 Å
Detector	Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Aug 24, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54187 Å / Relative weight: 1
Reflection	Resolution: 1.79→35.97 Å / Num. obs: 15997 / % possible obs: 99.93 % / Redundancy: 2 % / B_iso Wilson estimate: 18.26 Å² / CC_1/2: 1 / R_rim(I) all: 0.03872 / Net I/σ(I): 18.78
Reflection shell	Resolution: 1.79→1.854 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.62 / Num. unique obs: 1549 / CC_1/2: 0.829 / R_rim(I) all: 0.3525 / % possible all: 99.94

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.79→35.97 Å / Cor.coef. F_o:F_c: 0.952 / Cor.coef. F_o:F_c free: 0.932 / SU B: 3.31 / SU ML: 0.103 / Cross valid method: FREE R-VALUE / ESU R: 0.142 / ESU R Free: 0.137
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.238	787	4.92 %
R_work	0.1924	15210	-
all	0.195	-	-
obs	-	15997	99.931 %

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: 18.932 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.259 Å²	0 Å²	0 Å²
2-	-	-0.259 Å²	0 Å²
3-	-	-	0.517 Å²

Refinement step

Cycle: LAST / Resolution: 1.79→35.97 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1319	0	6	156	1481

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.013	1395
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.015	1315
X-RAY DIFFRACTION	r_angle_refined_deg	1.536	1.647	1897
X-RAY DIFFRACTION	r_angle_other_deg	1.404	1.582	3031
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.407	5	169
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.915	21.538	78
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.597	15	238
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.153	15	11
X-RAY DIFFRACTION	r_chiral_restr	0.08	0.2	175
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	1577
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	333
X-RAY DIFFRACTION	r_nbd_refined	0.216	0.2	294
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.21	0.2	1249
X-RAY DIFFRACTION	r_nbtor_refined	0.172	0.2	684
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.079	0.2	571
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.125	0.2	104
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.342	0.2	11
X-RAY DIFFRACTION	r_nbd_other	0.223	0.2	44
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.174	0.2	20
X-RAY DIFFRACTION	r_mcbond_it	1.452	1.742	667
X-RAY DIFFRACTION	r_mcbond_other	1.408	1.739	666
X-RAY DIFFRACTION	r_mcangle_it	2.077	2.6	839
X-RAY DIFFRACTION	r_mcangle_other	2.078	2.603	840
X-RAY DIFFRACTION	r_scbond_it	2.233	2.057	728
X-RAY DIFFRACTION	r_scbond_other	2.232	2.058	729
X-RAY DIFFRACTION	r_scangle_it	3.582	2.962	1058
X-RAY DIFFRACTION	r_scangle_other	3.58	2.963	1059
X-RAY DIFFRACTION	r_lrange_it	5.07	21.374	1648
X-RAY DIFFRACTION	r_lrange_other	4.985	21.05	1625

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 (%)
1.79-1.836	0.304	53	0.262	1096	X-RAY DIFFRACTION	99.913
1.836-1.887	0.332	72	0.238	1056	X-RAY DIFFRACTION	99.9114
1.887-1.941	0.249	58	0.215	1033	X-RAY DIFFRACTION	100
1.941-2.001	0.249	45	0.206	1010	X-RAY DIFFRACTION	100
2.001-2.066	0.258	46	0.197	981	X-RAY DIFFRACTION	100
2.066-2.139	0.255	41	0.195	976	X-RAY DIFFRACTION	100
2.139-2.219	0.293	43	0.19	917	X-RAY DIFFRACTION	100
2.219-2.31	0.271	56	0.178	858	X-RAY DIFFRACTION	100
2.31-2.412	0.205	45	0.185	863	X-RAY DIFFRACTION	100
2.412-2.529	0.282	38	0.195	822	X-RAY DIFFRACTION	100
2.529-2.666	0.323	35	0.209	795	X-RAY DIFFRACTION	100
2.666-2.827	0.229	37	0.195	743	X-RAY DIFFRACTION	100
2.827-3.021	0.274	32	0.206	719	X-RAY DIFFRACTION	100
3.021-3.262	0.161	35	0.191	648	X-RAY DIFFRACTION	100
3.262-3.571	0.196	34	0.178	615	X-RAY DIFFRACTION	100
3.571-3.99	0.231	35	0.159	560	X-RAY DIFFRACTION	100
3.99-4.601	0.179	27	0.156	498	X-RAY DIFFRACTION	100
4.601-5.62	0.234	21	0.177	443	X-RAY DIFFRACTION	100
5.62-7.886	0.228	26	0.212	351	X-RAY DIFFRACTION	100
7.886-35.97	0.178	8	0.223	221	X-RAY DIFFRACTION	96.2185

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