PDB-9gmn: Crystal Structure of UFC1 T106V

ID or keywords:

Entry

Database: PDB / ID: 9gmn

Title

Crystal Structure of UFC1 T106V

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: 2 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 29, 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	9gmn.cif.gz	52 KB	Display	PDBx/mmCIF format
PDB format	pdb9gmn.ent.gz		Display	PDB format
PDBx/mmJSON format	9gmn.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9gmn_validation.pdf.gz	418 KB	Display	wwPDB validaton report
Full document	9gmn_full_validation.pdf.gz	419 KB	Display
Data in XML	9gmn_validation.xml.gz	10.3 KB	Display
Data in CIF	9gmn_validation.cif.gz	13.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gm/9gmn ftp://data.pdbj.org/pub/pdb/validation_reports/gm/9gmn	HTTPS FTP

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Related structure data

Related structure data	9glhC 9gliC 9gljC 9glkC 9gllC 9glmC 9glnC 9gloC 9glpC 9glrC 9glsC 9gltC 9gmmC 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)	46.590, 46.590, 142.540
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-253- HOH
2	1	AAA-264- HOH
3	1	AAA-292- HOH

#1: Protein	Ubiquitin-fold modifier-conjugating enzyme 1 / Ufm1-conjugating enzyme 1 Mass: 19638.570 Da / Num. of mol.: 1 / Mutation: T106V Source method: isolated from a genetically manipulated source Details: Threonine at 106th position is mutated to Valine / 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.: 111 / 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: 1.97 Å³/Da / Density % sol: 37.54 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 1.5M Ammonium sulfate, 0.1M Tris pH 8.0.

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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 22, 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: 2→35.63 Å / Num. obs: 20248 / % possible obs: 100 % / Redundancy: 6.73 % / B_iso Wilson estimate: 27.33 Å² / CC_1/2: 0.999 / R_rim(I) all: 0.098 / Net I/σ(I): 13.77
Reflection shell	Resolution: 2→2.072 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 1.77 / Num. unique obs: 1501 / CC_1/2: 0.73 / R_rim(I) all: 0.73 / % possible all: 99.8

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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: 2→35.63 Å / Cor.coef. F_o:F_c: 0.956 / Cor.coef. F_o:F_c free: 0.921 / SU B: 4.371 / SU ML: 0.12 / Cross valid method: FREE R-VALUE / ESU R: 0.197 / ESU R Free: 0.173
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.231	545	4.817 %
R_work	0.1775	10768	-
all	0.18	-	-
obs	-	11313	100 %

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: 21.919 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.514 Å²	-0 Å²	0 Å²
2-	-	-0.514 Å²	0 Å²
3-	-	-	1.028 Å²

Refinement step

Cycle: LAST / Resolution: 2→35.63 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1319	0	0	111	1430

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.013	1392
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.015	1296
X-RAY DIFFRACTION	r_angle_refined_deg	1.584	1.643	1894
X-RAY DIFFRACTION	r_angle_other_deg	1.344	1.579	2992
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.541	5	168
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.173	22.4	75
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.277	15	234
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.189	15	9
X-RAY DIFFRACTION	r_chiral_restr	0.081	0.2	173
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	1572
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	323
X-RAY DIFFRACTION	r_nbd_refined	0.21	0.2	259
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.189	0.2	1123
X-RAY DIFFRACTION	r_nbtor_refined	0.167	0.2	669
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.081	0.2	530
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.132	0.2	88
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.215	0.2	26
X-RAY DIFFRACTION	r_nbd_other	0.219	0.2	76
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.135	0.2	15
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.009	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	1.665	2.107	666
X-RAY DIFFRACTION	r_mcbond_other	1.626	2.104	665
X-RAY DIFFRACTION	r_mcangle_it	2.353	3.146	836
X-RAY DIFFRACTION	r_mcangle_other	2.352	3.149	837
X-RAY DIFFRACTION	r_scbond_it	2.341	2.406	726
X-RAY DIFFRACTION	r_scbond_other	2.339	2.408	727
X-RAY DIFFRACTION	r_scangle_it	3.645	3.492	1058
X-RAY DIFFRACTION	r_scangle_other	3.644	3.494	1059
X-RAY DIFFRACTION	r_lrange_it	4.783	24.839	1595
X-RAY DIFFRACTION	r_lrange_other	4.733	24.562	1575

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 (%)
2-2.052	0.254	31	0.229	779	X-RAY DIFFRACTION	100
2.052-2.108	0.233	38	0.204	744	X-RAY DIFFRACTION	100
2.108-2.169	0.203	35	0.195	726	X-RAY DIFFRACTION	100
2.169-2.236	0.262	35	0.189	732	X-RAY DIFFRACTION	100
2.236-2.309	0.278	35	0.172	687	X-RAY DIFFRACTION	100
2.309-2.389	0.237	26	0.194	669	X-RAY DIFFRACTION	100
2.389-2.479	0.215	34	0.175	648	X-RAY DIFFRACTION	100
2.479-2.58	0.262	34	0.179	635	X-RAY DIFFRACTION	100
2.58-2.695	0.191	34	0.184	590	X-RAY DIFFRACTION	100
2.695-2.826	0.203	40	0.171	573	X-RAY DIFFRACTION	100
2.826-2.978	0.298	28	0.187	561	X-RAY DIFFRACTION	100
2.978-3.158	0.187	22	0.193	537	X-RAY DIFFRACTION	100
3.158-3.374	0.291	32	0.173	492	X-RAY DIFFRACTION	100
3.374-3.643	0.22	23	0.163	470	X-RAY DIFFRACTION	100
3.643-3.988	0.137	20	0.142	434	X-RAY DIFFRACTION	100
3.988-4.454	0.235	26	0.126	389	X-RAY DIFFRACTION	100
4.454-5.134	0.323	14	0.146	371	X-RAY DIFFRACTION	100
5.134-6.267	0.24	19	0.197	304	X-RAY DIFFRACTION	100
6.267-8.776	0.224	15	0.219	255	X-RAY DIFFRACTION	100
8.776-35.63	0.179	4	0.228	172	X-RAY DIFFRACTION	100

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