PDB-9i9m: Crystal structure of chimeric UFC1, TAK MotiF replaced with HPN m...

ID or keywords:

Entry

Database: PDB / ID: 9i9m

Title

Crystal structure of chimeric UFC1, TAK MotiF replaced with HPN motif of other E2 proteins

Components

Ubiquitin-fold modifier-conjugating enzyme 1

Keywords

LIGASE / Ubiquitin fold modifier conjugating enzyme-1 / UFMylation / Chimeric UFC1 / HPN motif / Isopeptide / oxyanion hole

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: 1.543 Å

Authors

Manoj Kumar, P. / 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	Feb 6, 2025	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	9i9m.cif.gz	53.4 KB	Display	PDBx/mmCIF format
PDB format	pdb9i9m.ent.gz		Display	PDB format
PDBx/mmJSON format	9i9m.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/i9/9i9m ftp://data.pdbj.org/pub/pdb/validation_reports/i9/9i9m	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 9gmnC 9gn8C 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

19.9 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)	47.163, 47.163, 144.632
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-341- HOH

#1: Protein	Ubiquitin-fold modifier-conjugating enzyme 1 / Ufm1-conjugating enzyme 1 Mass: 19688.547 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: chimeric UFC1 TAK (106-108) is changed to HPN motif present in other E2 proteins Source: (gene. exp.) Homo sapiens (human) / Gene: UFC1, CGI-126, HSPC155 / Production host: Escherichia coli (E. coli) / Strain (production host): T7-Express / 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.: 109 / 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: 2.32 Å³/Da / Density % sol: 47 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.1M sodium citrate tribasic dihydrate pH 5.5, 20% w/v 2-propanol, 20% w/v PEG 4000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.87313 Å
Detector	Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Jan 26, 2025
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.87313 Å / Relative weight: 1
Reflection	Resolution: 1.543→44.84 Å / Num. obs: 24971 / % possible obs: 99.86 % / Redundancy: 2 % / B_iso Wilson estimate: 20.41 Å² / CC_1/2: 0.999 / R_rim(I) all: 0.03874 / Net I/σ(I): 12.8
Reflection shell	Resolution: 1.543→1.598 Å / Redundancy: 2 % / Mean I/σ(I) obs: 0.81 / Num. unique obs: 2414 / CC_1/2: 0.525 / R_rim(I) all: 0.9574 / % possible all: 98.65

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
autoPROC		data reduction
autoPROC		data scaling
Coot	0.9.6	model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.543→44.839 Å / Cor.coef. F_o:F_c: 0.962 / Cor.coef. F_o:F_c free: 0.958 / SU B: 1.879 / SU ML: 0.065 / Cross valid method: FREE R-VALUE / ESU R: 0.087 / ESU R Free: 0.082
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2088	1259	5.042 %
R_work	0.1902	23712	-
all	0.191	-	-
obs	-	24971	99.868 %

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: 21.516 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.067 Å²	0 Å²	0 Å²
2-	-	-0.067 Å²	0 Å²
3-	-	-	0.135 Å²

Refinement step

Cycle: LAST / Resolution: 1.543→44.839 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1362	0	12	109	1483

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.013	1424
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.015	1348
X-RAY DIFFRACTION	r_angle_refined_deg	1.583	1.649	1930
X-RAY DIFFRACTION	r_angle_other_deg	1.431	1.586	3110
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.564	5	166
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.57	21.605	81
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.5	15	246
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.497	15	11
X-RAY DIFFRACTION	r_chiral_restr	0.096	0.2	174
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	1584
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	334
X-RAY DIFFRACTION	r_nbd_refined	0.213	0.2	281
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.19	0.2	1160
X-RAY DIFFRACTION	r_nbtor_refined	0.171	0.2	686
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.08	0.2	579
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.123	0.2	56
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.243	0.2	14
X-RAY DIFFRACTION	r_nbd_other	0.182	0.2	51
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.133	0.2	21
X-RAY DIFFRACTION	r_mcbond_it	1.914	1.904	664
X-RAY DIFFRACTION	r_mcbond_other	1.914	1.896	663
X-RAY DIFFRACTION	r_mcangle_it	2.866	2.842	830
X-RAY DIFFRACTION	r_mcangle_other	2.864	2.852	831
X-RAY DIFFRACTION	r_scbond_it	3.454	2.368	760
X-RAY DIFFRACTION	r_scbond_other	3.452	2.369	761
X-RAY DIFFRACTION	r_scangle_it	5.138	3.364	1100
X-RAY DIFFRACTION	r_scangle_other	5.135	3.366	1101
X-RAY DIFFRACTION	r_lrange_it	6.25	23.069	1613
X-RAY DIFFRACTION	r_lrange_other	6.177	22.806	1597

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
1.543-1.583	0.373	88	0.373	1691	0.373	1810	0.695	0.65	98.2873	0.371
1.583-1.626	0.348	99	0.319	1669	0.32	1769	0.79	0.801	99.9435	0.316
1.626-1.673	0.291	75	0.27	1632	0.271	1707	0.869	0.859	100	0.266
1.673-1.725	0.267	81	0.236	1558	0.238	1639	0.899	0.903	100	0.224
1.725-1.781	0.238	65	0.203	1541	0.205	1606	0.903	0.925	100	0.186
1.781-1.844	0.234	65	0.196	1524	0.198	1589	0.923	0.931	100	0.174
1.844-1.913	0.208	87	0.195	1420	0.196	1507	0.94	0.938	100	0.168
1.913-1.991	0.23	78	0.175	1393	0.178	1471	0.916	0.951	100	0.154
1.991-2.079	0.213	76	0.173	1333	0.175	1410	0.945	0.959	99.9291	0.152
2.079-2.181	0.21	68	0.172	1268	0.174	1336	0.939	0.961	100	0.155
2.181-2.298	0.172	72	0.163	1227	0.163	1299	0.964	0.967	100	0.146
2.298-2.437	0.168	65	0.169	1157	0.169	1222	0.969	0.968	100	0.152
2.437-2.605	0.18	57	0.177	1098	0.177	1155	0.965	0.959	100	0.16
2.605-2.813	0.234	47	0.175	1038	0.178	1085	0.932	0.957	100	0.158
2.813-3.08	0.214	49	0.189	957	0.19	1006	0.949	0.953	100	0.175
3.08-3.442	0.169	51	0.176	866	0.176	917	0.965	0.964	100	0.171
3.442-3.97	0.172	54	0.15	773	0.152	827	0.969	0.973	100	0.154
3.97-4.853	0.167	32	0.162	682	0.162	714	0.977	0.971	100	0.174
4.853-6.823	0.297	30	0.235	542	0.238	572	0.942	0.962	100	0.255
6.823-44.839	0.249	20	0.248	342	0.248	362	0.949	0.957	100	0.274

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