PDB-9ia8: Crystal Structure of UFC1 K108R

ID or keywords:

Entry

Database: PDB / ID: 9ia8

Title

Crystal Structure of UFC1 K108R

Components

Ubiquitin-fold modifier-conjugating enzyme 1

Keywords

LIGASE / Ubiquitin-fold modifier-conjugating enzyme 1 / UFM1 conjugating enzyme / UFC1 / UFMylation / UFM1 transferring enzyme / Aminoacyl transferase activity / Ligase activity / Transthiolation

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: 1.9 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 8, 2025	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 7, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	9ia8.cif.gz	53.3 KB	Display	PDBx/mmCIF format
PDB format	pdb9ia8.ent.gz		Display	PDB format
PDBx/mmJSON format	9ia8.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ia/9ia8 ftp://data.pdbj.org/pub/pdb/validation_reports/ia/9ia8	HTTPS FTP

-
Related structure data

Related structure data	9glhC 9gliC 9gljC 9glkC 9gllC 9glmC 9glnC 9gloC 9glpC 9glrC 9glsC 9gltC 9gmmC 9gmnC 9gn8C 9i9mC 9i9nC 9i9oC 9i9pC 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

-
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

19.7 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)	47.010, 47.010, 142.150
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-288- HOH
2	1	AAA-318- HOH

#1: Protein	Ubiquitin-fold modifier-conjugating enzyme 1 / Ufm1-conjugating enzyme 1 Mass: 19668.559 Da / Num. of mol.: 1 / Mutation: K08R Source method: isolated from a genetically manipulated source Details: Lysine at 108th position is mutated to Arginine / 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: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	N

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 1.96 Å³/Da / Density % sol: 37.39 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1M Bis-Tris pH 5.5, 2M Ammonium Sulfate

-
Data collection

Diffraction	Mean temperature: 100 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 11, 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: 1.9→44.63 Å / Num. obs: 13433 / % possible obs: 96.78 % / Redundancy: 1.2 % / B_iso Wilson estimate: 11.33 Å² / CC_1/2: 0.99 / Net I/σ(I): 8.52
Reflection shell	Resolution: 1.9→1.95 Å / Num. unique obs: 971 / CC_1/2: 0.474 / % possible all: 100

-
Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.9→44.63 Å / Cor.coef. F_o:F_c: 0.941 / Cor.coef. F_o:F_c free: 0.902 / SU B: 5.526 / SU ML: 0.151 / Cross valid method: FREE R-VALUE / ESU R: 0.19 / ESU R Free: 0.166
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2475	669	5.042 %
R_work	0.205	12599	-
all	0.207	-	-
obs	-	13268	99.527 %

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: 17.341 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.211 Å²	0 Å²	0 Å²
2-	-	-0.211 Å²	0 Å²
3-	-	-	0.421 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→44.63 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1335	0	0	159	1494

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.013	1385
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.015	1296
X-RAY DIFFRACTION	r_angle_refined_deg	1.483	1.646	1884
X-RAY DIFFRACTION	r_angle_other_deg	1.368	1.582	2982
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.928	5	166
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	29.279	21.711	76
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.685	15	230
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	22.048	15	10
X-RAY DIFFRACTION	r_chiral_restr	0.079	0.2	175
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	1554
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	326
X-RAY DIFFRACTION	r_nbd_refined	0.202	0.2	280
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.188	0.2	1187
X-RAY DIFFRACTION	r_nbtor_refined	0.167	0.2	666
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.082	0.2	559
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.16	0.2	100
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.242	0.2	17
X-RAY DIFFRACTION	r_nbd_other	0.212	0.2	66
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.152	0.2	19
X-RAY DIFFRACTION	r_mcbond_it	1.126	1.701	664
X-RAY DIFFRACTION	r_mcbond_other	1.125	1.695	663
X-RAY DIFFRACTION	r_mcangle_it	1.743	2.537	830
X-RAY DIFFRACTION	r_mcangle_other	1.742	2.543	831
X-RAY DIFFRACTION	r_scbond_it	1.696	1.866	721
X-RAY DIFFRACTION	r_scbond_other	1.696	1.87	722
X-RAY DIFFRACTION	r_scangle_it	2.72	2.718	1054
X-RAY DIFFRACTION	r_scangle_other	2.718	2.718	1054
X-RAY DIFFRACTION	r_lrange_it	4.514	20.127	1622
X-RAY DIFFRACTION	r_lrange_other	4.358	19.855	1596

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 (%)
1.9-1.949	0.326	44	0.279	925	X-RAY DIFFRACTION	100
1.949-2.002	0.297	37	0.297	876	X-RAY DIFFRACTION	99.5638
2.002-2.06	0.336	41	0.255	878	X-RAY DIFFRACTION	99.8913
2.06-2.124	0.256	53	0.225	818	X-RAY DIFFRACTION	99.8853
2.124-2.193	0.292	44	0.211	805	X-RAY DIFFRACTION	100
2.193-2.27	0.277	31	0.23	811	X-RAY DIFFRACTION	99.763
2.27-2.355	0.303	32	0.277	763	X-RAY DIFFRACTION	97.546
2.355-2.451	0.258	46	0.221	731	X-RAY DIFFRACTION	100
2.451-2.56	0.437	38	0.224	691	X-RAY DIFFRACTION	98.3806
2.56-2.684	0.264	39	0.205	668	X-RAY DIFFRACTION	100
2.684-2.829	0.214	33	0.193	650	X-RAY DIFFRACTION	99.5627
2.829-3	0.24	33	0.196	632	X-RAY DIFFRACTION	100
3-3.206	0.216	33	0.194	578	X-RAY DIFFRACTION	99.8366
3.206-3.461	0.199	30	0.189	536	X-RAY DIFFRACTION	97.9239
3.461-3.79	0.234	29	0.155	505	X-RAY DIFFRACTION	100
3.79-4.233	0.164	37	0.14	467	X-RAY DIFFRACTION	100
4.233-4.881	0.132	19	0.132	418	X-RAY DIFFRACTION	99.5444
4.881-5.96	0.303	19	0.186	366	X-RAY DIFFRACTION	99.7409
5.96-8.354	0.237	21	0.216	291	X-RAY DIFFRACTION	99.3631
8-44.63	0.327	10	0.211	190	X-RAY DIFFRACTION	99.0099

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi