8c0d

UFL1/DDRGK1 bound to UFC1

Method: X-RAY DIFFRACTION D_max: 183.4 Å Quality: REASONABLE

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1. Protein Identity and Related Structures Protein Identity & Related Structures

E3 UFM1-protein ligase 1

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 1–179	Not recorded	DDRGK domain-containing protein 1 × 1 （Q96HY6） Ubiquitin-fold modifier-conjugating enzyme 1 × 1 （Q9Y3C8）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.2；292 K；0.1M HEPES, 1.03M Li2SO4	Resolution 2.56 Å R-free 0.286
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain D； UniProt 1–179	Not recorded	DDRGK domain-containing protein 1 × 1 （Q96HY6） Ubiquitin-fold modifier-conjugating enzyme 1 × 1 （Q9Y3C8）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.2；292 K；0.1M HEPES, 1.03M Li2SO4	Resolution 2.56 Å R-free 0.286

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 8C0D	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8B9X Chimeric protein of human UFM1 E3 ligase, UFL1, and DDRGK1 Deposited 2022-10-10	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 27–200（174 aa）	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；Sodium acetate trihydrate Ammonium tartrate dibasic	Resolution 3.07 Å R-free 0.272
8B9X Chimeric protein of human UFM1 E3 ligase, UFL1, and DDRGK1 Deposited 2022-10-10	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 27–200（174 aa）	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；Sodium acetate trihydrate Ammonium tartrate dibasic	Resolution 3.07 Å R-free 0.272
8OHD 60S ribosomal subunit bound to the E3-UFM1 complex - state 3 (native) Deposited 2023-03-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 50-meric	Chain A 1–794（794 aa）	Not recorded	MG MAGNESIUM ION × 220 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
8OJ0 60S ribosomal subunit bound to the E3-UFM1 complex - state 2 (native) Deposited 2023-03-23	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 53-meric	Chain A 1–794（794 aa）	Not recorded	MG MAGNESIUM ION × 220 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
8OJ5 60S ribosomal subunit bound to the E3-UFM1 complex - state 3 (in-vitro reconstitution) Deposited 2023-03-23	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric	Chain A 1–794（794 aa）	Not recorded	MG MAGNESIUM ION × 220 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
8OJ8 60S ribosomal subunit bound to the E3-UFM1 complex - state 1 (native) Deposited 2023-03-24	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 50-meric	Chain A 1–794（794 aa）	Not recorded	MG MAGNESIUM ION × 220 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
8QFC UFL1 E3 ligase bound 60S ribosome Deposited 2023-09-04	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain B 1–794（794 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；25 mM HEPES pH 7.5, 50 mM KCl, 5 mM MgCl2, 2 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
8QFD UFL1 E3 ligase bound 60S ribosome Deposited 2023-09-04	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 42 PDB declaration: 45-meric	Chain s 1–794（794 aa）	Not recorded	MG MAGNESIUM ION × 161 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；25 mM HEPES pH 7.5, 50 mM KCl, 5 mM MgCl2, 2 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.20 Å
9GY4 60S ribosomal subunit in complex with E3-UFM1 ligase and RQC machinery components NEMF and LTN1 (Composite map) Deposited 2024-10-01	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 55-meric	Chain E 1–794（794 aa）	Not recorded	MG MAGNESIUM ION × 219 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å

8 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	UFL1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 16–194； UniProt 1–179 Author chain D； PDBConstruct 16–194； UniProt 1–179

DDRGK domain-containing protein 1

Homo sapiens

UniProt Q96HY6

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain B； UniProt 205–314	Not recorded	E3 UFM1-protein ligase 1 × 1 （O94874） Ubiquitin-fold modifier-conjugating enzyme 1 × 1 （Q9Y3C8）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.2；292 K；0.1M HEPES, 1.03M Li2SO4	Resolution 2.56 Å R-free 0.286
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain E； UniProt 205–314	Not recorded	E3 UFM1-protein ligase 1 × 1 （O94874） Ubiquitin-fold modifier-conjugating enzyme 1 × 1 （Q9Y3C8）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.2；292 K；0.1M HEPES, 1.03M Li2SO4	Resolution 2.56 Å R-free 0.286

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 8C0D	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7W3N Crystal structure of Ufm1 fused to UFBP1 UFIM Deposited 2021-11-25	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 194–202（9 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；28% 2-propanol, 3% PEG 200, 0.1M MES at pH 6.0	Resolution 1.60 Å R-free 0.200
8B9X Chimeric protein of human UFM1 E3 ligase, UFL1, and DDRGK1 Deposited 2022-10-10	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 207–305（99 aa）	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；Sodium acetate trihydrate Ammonium tartrate dibasic	Resolution 3.07 Å R-free 0.272
8B9X Chimeric protein of human UFM1 E3 ligase, UFL1, and DDRGK1 Deposited 2022-10-10	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 207–305（99 aa）	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；Sodium acetate trihydrate Ammonium tartrate dibasic	Resolution 3.07 Å R-free 0.272
8OHD 60S ribosomal subunit bound to the E3-UFM1 complex - state 3 (native) Deposited 2023-03-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 50-meric	Chain C 1–314（314 aa）	Not recorded	MG MAGNESIUM ION × 220 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
8OJ0 60S ribosomal subunit bound to the E3-UFM1 complex - state 2 (native) Deposited 2023-03-23	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 53-meric	Chain C 1–314（314 aa）	Not recorded	MG MAGNESIUM ION × 220 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
8OJ5 60S ribosomal subunit bound to the E3-UFM1 complex - state 3 (in-vitro reconstitution) Deposited 2023-03-23	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric	Chain C 1–314（314 aa）	Not recorded	MG MAGNESIUM ION × 220 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
8QFC UFL1 E3 ligase bound 60S ribosome Deposited 2023-09-04	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain D 29–314（286 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；25 mM HEPES pH 7.5, 50 mM KCl, 5 mM MgCl2, 2 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
9GY4 60S ribosomal subunit in complex with E3-UFM1 ligase and RQC machinery components NEMF and LTN1 (Composite map) Deposited 2024-10-01	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 55-meric	Chain C 1–314（314 aa）	Not recorded	MG MAGNESIUM ION × 219 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å

7 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DDRGK_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–110； UniProt 205–314 Author chain E； PDBConstruct 1–110； UniProt 205–314

Ubiquitin-fold modifier-conjugating enzyme 1

Homo sapiens

UniProt Q9Y3C8

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain C； UniProt 1–167	Not recorded	E3 UFM1-protein ligase 1 × 1 （O94874） DDRGK domain-containing protein 1 × 1 （Q96HY6）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.2；292 K；0.1M HEPES, 1.03M Li2SO4	Resolution 2.56 Å R-free 0.286
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain F； UniProt 1–167	Not recorded	E3 UFM1-protein ligase 1 × 1 （O94874） DDRGK domain-containing protein 1 × 1 （Q96HY6）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.2；292 K；0.1M HEPES, 1.03M Li2SO4	Resolution 2.56 Å R-free 0.286

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 8C0D	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2K07 Solution NMR structure of human E2-like ubiquitin-fold modifier conjugating enzyme 1 (UFC1). Northeast Structural Genomics Consortium target HR41 Deposited 2008-01-25	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–167（167 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) na；Pressure ambient NMR sample composition 1.1 mM [U-100% 13C; U-100% 15N] protein UFC1, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
2Z6O Crystal Structure of the Ufc1, Ufm1 conjugating enzyme 1 Deposited 2007-08-06	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–167（167 aa）	Not recorded	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；28% (w/v) PEG 4000, 0.1M Tris-HCl pH 8.5, 0.2M MgCl2 , VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.60 Å R-free 0.221
2Z6P Crystal Structure of the Ufc1, Ufm1 conjugating enzyme 1 Deposited 2007-08-06	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–167（167 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；1.5M ammonium sulfate, 0.1M MES pH 7.0, 10%(w/v) dioxan, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.80 Å R-free 0.243
3EVX Crystal structure of the human E2-like ubiquitin-fold modifier conjugating enzyme 1 (Ufc1). Northeast Structural Genomics Consortium target HR41 Deposited 2008-10-13	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–167（167 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	SCN THIOCYANATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；291 K；Protein solution: 10 mM Tris (pH 7.5), 100 mM sodium chloride, and 5 mM DTT. Reservoir solution:100mM Sodium acetate, 18% PEG8000, 100mM (NH4)SCN, 50mM LiSCN, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.54 Å R-free 0.279
3EVX Crystal structure of the human E2-like ubiquitin-fold modifier conjugating enzyme 1 (Ufc1). Northeast Structural Genomics Consortium target HR41 Deposited 2008-10-13	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–167（167 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	SCN THIOCYANATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；291 K；Protein solution: 10 mM Tris (pH 7.5), 100 mM sodium chloride, and 5 mM DTT. Reservoir solution:100mM Sodium acetate, 18% PEG8000, 100mM (NH4)SCN, 50mM LiSCN, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.54 Å R-free 0.279
3EVX Crystal structure of the human E2-like ubiquitin-fold modifier conjugating enzyme 1 (Ufc1). Northeast Structural Genomics Consortium target HR41 Deposited 2008-10-13	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–167（167 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	SCN THIOCYANATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；291 K；Protein solution: 10 mM Tris (pH 7.5), 100 mM sodium chloride, and 5 mM DTT. Reservoir solution:100mM Sodium acetate, 18% PEG8000, 100mM (NH4)SCN, 50mM LiSCN, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.54 Å R-free 0.279
3EVX Crystal structure of the human E2-like ubiquitin-fold modifier conjugating enzyme 1 (Ufc1). Northeast Structural Genomics Consortium target HR41 Deposited 2008-10-13	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 1–167（167 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	SCN THIOCYANATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；291 K；Protein solution: 10 mM Tris (pH 7.5), 100 mM sodium chloride, and 5 mM DTT. Reservoir solution:100mM Sodium acetate, 18% PEG8000, 100mM (NH4)SCN, 50mM LiSCN, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.54 Å R-free 0.279
7NVJ Crystal structure of UFC1 Y110A & F121A Deposited 2021-03-15	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain AAA 1–167（167 aa）	Mutation：Y110A, F121A	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1M HEPES pH 7.5, 2M Ammonium sulfate	Resolution 2.20 Å R-free 0.246
7NVK Crystal structure of UBA5 fragment fused to the N-terminus of UFC1 Deposited 2021-03-15	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain AAA 1–167（167 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；2% (v/v) Tacsimate pH 7.0, 20% PEG 3350, 0.1M HEPES pH 7.5, 6mM zinc sulfate	Resolution 2.65 Å R-free 0.264
7NW1 Crystal structure of UFC1 in complex with UBA5 Deposited 2021-03-16	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain AAA 1–167（167 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 9 PEG DI(HYDROXYETHYL)ETHER × 2 PGE TRIETHYLENE GLYCOL × 1 GOL GLYCEROL × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；35 mM citric acid, 65 mM bis-tris propane, 19% PEG3350, 100 mM lithium chloride	Resolution 1.95 Å R-free 0.280
7NW1 Crystal structure of UFC1 in complex with UBA5 Deposited 2021-03-16	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain BBB 1–167（167 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；35 mM citric acid, 65 mM bis-tris propane, 19% PEG3350, 100 mM lithium chloride	Resolution 1.95 Å R-free 0.280
7OVC Structure of the human UFC1 protein in complex with the UBA5 C-terminal UFC1-binding motif. Deposited 2021-06-14	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–167（167 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.5；298 K；Ionic strength (raw mmCIF value) 100；Pressure AMBIENT NMR sample composition 1.0 mM [U-100% 13C; U-100% 15N] Ubiquitin-fold modifier-conjugating enzyme 1, 1.0 mM Ubiquitin-like modifier-activating enzyme 5, 50 mM TRIS, 100 mM sodium chloride, 2 mM TCEP, 5 mM AEBSF protease inhibitor, 0.15 mM DSS, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 1.2 mM Ubiquitin-fold modifier-conjugating enzyme 1, 0.3 mM [U-100% 13C; U-100% 15N] Ubiquitin-like modifier-activating enzyme 5, 50 mM TRIS, 100 mM sodium chloride, 2 mM TCEP, 5 mM AEBSF protease inhibitor, 0.15 mM DSS, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
8BZR UFC1-UFM1 conjugate Deposited 2022-12-15	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–167（167 aa）	Mutation：C116K	EDO 1,2-ETHANEDIOL × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；292 K；30% v/v PEG400, 0.1M Tris, 0.2M Na citrate	Resolution 1.78 Å R-free 0.226
9GLH Crystal Structure of UFC1 T106S Deposited 2024-08-27	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain AAA 1–167（167 aa）	Mutation：T106S	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；1.4M Sodium Malonate dibasic monohydrate pH 6.0.	Resolution 1.11 Å R-free 0.192
9GLI Crystal Structure of UFC1 T106C Deposited 2024-08-27	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain AAA 1–167（167 aa）	Not recorded	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；1M Ammonium Citrate tribasic pH 7.0, 0.1M Bis-Tris Propane pH 7.0.	Resolution 1.43 Å R-free 0.208
9GLJ Crystal Structure of UFC1 T106A Deposited 2024-08-27	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain AAA 1–167（167 aa）	Mutation：T106A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1M NaCl, 0.1M Bis-Tris pH 6.5, 1.5M Ammonium sulfate.	Resolution 1.21 Å R-free 0.199
9GLK Crystal Structure of UFC1 E149I Deposited 2024-08-27	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain AAA 1–167（167 aa）	Mutation：E149I	IMD IMIDAZOLE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.1M Bis-Tris pH 5.5, 2.0M Ammonium sulfate	Resolution 2.03 Å R-free 0.247
9GLL Crystal Structure of UFC1 T106L Deposited 2024-08-27	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain AAA 1–167（167 aa）	Mutation：T106L	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；293 K；1.4M Sodium potassium monobasic monohydrate/Potassium phosphate dibasic pH 9.0	Resolution 1.65 Å R-free 0.231
9GLM Crystal Structure of UFC1 W145F Deposited 2024-08-27	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain AAA 1–167（167 aa）	Mutation：W145F	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；1.5M Ammonium sulfate; 0.1M Bis-Tris propane pH 7.0	Resolution 1.79 Å R-free 0.238
9GLN Crystal Structure of UFC1 C116E Deposited 2024-08-27	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain AAA 1–167（167 aa）	Mutation：C116E	GOL GLYCEROL × 2 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.1 M Bis-Tris, pH 5.5, 1.8 M smmonium sulfate.	Resolution 1.92 Å R-free 0.227
9GLO Crystal Structure of UFC1 C116E&T106S Deposited 2024-08-27	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain AAA 1–167（167 aa）	Mutation：C116E, T106S	GOL GLYCEROL × 3 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.1 M Bis-Tris, pH 5.5, 2 M ammonium sulfate	Resolution 1.53 Å R-free 0.208
9GLP Crystal Structure of UFC1 C116E&T106I Deposited 2024-08-27	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain AAA 1–167（167 aa）	Mutation：C116E, T106I	GOL GLYCEROL × 2 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.1 M Bis-Tris, pH 5.5, 2 M ammonium sulfate.	Resolution 1.77 Å R-free 0.200
9GMM Crystal Structure of UFC1 T106I Deposited 2024-08-29	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain AAA 1–167（167 aa）	Mutation：T106I	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；1.5M Ammonium sulfate, 0.1M Bis-Tris Propane pH 7.0	Resolution 1.35 Å R-free 0.201
9GMN Crystal Structure of UFC1 T106V Deposited 2024-08-29	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain AAA 1–167（167 aa）	Mutation：T106V	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；1.5M Ammonium sulfate, 0.1M Tris pH 8.0.	Resolution 2.00 Å R-free 0.231
9GN8 Crystal Structure of UFC1 E149D Deposited 2024-08-31	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain AAA 1–167（167 aa）	Mutation：E149D	EDO 1,2-ETHANEDIOL × 1 FMT FORMIC ACID × 3 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；2% (v/v) Tacsimate Ph 7.0, 0.1M Hepes pH 7.5, 20% (w/v) PEG 3350	Resolution 1.96 Å R-free 0.257
9I9M Crystal structure of chimeric UFC1, TAK MotiF replaced with HPN motif of other E2 proteins Deposited 2025-02-06	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain AAA 1–167（167 aa）	Not recorded	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；0.1M sodium citrate tribasic dihydrate pH 5.5, 20% w/v 2-propanol, 20% w/v PEG 4000	Resolution 1.54 Å R-free 0.209
9I9N Crystal Structure of UFC1 C116E & K108A Deposited 2025-02-06	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain AAA 1–167（167 aa）	Mutation：C116E, K108A	GOL GLYCEROL × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.1M Tris pH 8.0, 2M Ammonium sulfate	Resolution 1.88 Å R-free 0.229
9I9O Crystal Structure of UFC1 K108M Deposited 2025-02-06	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain AAA 1–167（167 aa）	Mutation：K108M	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.15M Ammonium sulfate, 0.1M Sodium Hepes pH 7.0, 20%w/v PEG 4000	Resolution 2.05 Å R-free 0.253
9I9P Crystal Structure of UFC1 W145H Deposited 2025-02-06	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain AAA 1–167（167 aa）	Mutation：W145H	GOL GLYCEROL × 2 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.2M Lithium sulfate monohydrate, 0.1M HEPES pH 7.5, 25% w/v PEG 3350	Resolution 2.02 Å R-free 0.267
9IA8 Crystal Structure of UFC1 K108R Deposited 2025-02-08	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain AAA 1–167（167 aa）	Mutation：K08R	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；0.1M Bis-Tris pH 5.5, 2M Ammonium Sulfate	Resolution 1.90 Å R-free 0.247

26 other PDB entries and 30 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	UFC1_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–167； UniProt 1–167 Author chain F； PDBConstruct 1–167； UniProt 1–167

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8c0d
Deposition date deposition_date	2022-12-16
Structure title title	UFL1/DDRGK1 bound to UFC1
Keywords keywords	UFM1, E3 ligase, ubiquitin, UFBP1, LIGASE; LIGASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	43.09 Å
Radius of gyration Rg (electron density) rg_electron	43.57 Å
Forward intensity I(0) i0	129716000.00
Molecular weight molecular_weight	92111.0 kDa
Excluded volume excluded_volume	115440 Å³
Envelope volume envelope_volume	167870 Å³
Hydration-shell volume shell_volume	37048 Å³
Envelope diameter envelope_diameter	188.5 Å
Shell Rg shell_rg	40.98 Å
Envelope Rg envelope_rg	44.27 Å
Shape Rg shape_rg	43.57 Å
Total Rg total_rg	43.39 Å
Total atoms total_atoms	12900
Residues n_residues	850
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	183.4 Å
Rg (real space) rg_real	46.69 Å
Rg uncertainty (real space) rg_real_error	1.72 Å
I(0) (real space) i0_real	1.3160e+08
I(0) uncertainty (real space) i0_real_error	2.4780e+06
Rg (reciprocal space) rg_reciprocal	43.09 Å
I(0) (reciprocal space) i0_reciprocal	129600000.0000
Solution quality estimate total_estimate	0.5238
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	44.6 Å
Skewness Skewness skewness	0.819
Kurtosis Kurtosis kurtosis	0.410
Angular range angular_range	— – 0.1850 Å⁻¹
Current regularization parameter α current_alpha	1.1210
Highest regularization parameter α highest_alpha	8433000.0000
Real-space data points n_real_points	38
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.416; Stabil: 0.822; Sysdev: 0.000; Positv: 1.000; Valcen: 0.341; Smooth: 0.787

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	E3 UFM1-protein ligase 1
Molecular weight formula_weight	22350.3 kDa
EC 编号 ec_number	2.3.2.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D
Atom count atom_count	12907

MGHHHHHHENLYFQGMADAWEEIRRLAADFQRAQFAEATQRLSERNCIEIVNKLIAQKQLEVVHTLDGKEYITPAQISKEMRDELHVRGGRVNIVDLQQVINVDLIHIENRIGDIIKSEKHVQLVLGQLIDENYLDRLAEEVNDKLQESGQVTISELCKTYDLPGNFLTQALTQRLGRIISGHIDLDNRGVIFT

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	DDRGK domain-containing protein 1
Molecular weight formula_weight	12177.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,E

ETMTEEQSQSFLTEFINYIKQSKVVLLEDLASQVGLRTQDTINRIQDLLAEGTITGVIDDRGKFIYITPEELAAVANFIRQRGRVSIAELAQASNSLIAWGRESPAQAPA

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Ubiquitin-fold modifier-conjugating enzyme 1
Molecular weight formula_weight	19569.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,F

MADEATRRVVSEIPVLKTNAGPRDRELWVQRLKEEYQSLIRYVENNKNADNDWFRLESNKEGTRWFGKCWYIHDLLKYEFDIEFDIPITYPTTAPEIAVPELDGKTAKMYRGGKIKLTDHFKPLWARNVPKFGLAHLMALGLGPWLAVEIPDLIQKGVIQHKEKCNQG

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	7

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8. Citations (1)

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Unit-cell length a length_a	79.210 Å
Unit-cell length b length_b	124.565 Å
Unit-cell length c length_c	131.292 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.564 Å
Low-resolution limit resolution_low	65.732 Å
R factor r_factor	—
R_work r_work	0.2320
R_free r_free	0.2858

fit	/app/data/saxs_computation/c0/8c0d/8c0d.fit
pddf	/app/data/pr_computation/c0/8c0d/8c0d.pr.out
profile	/app/data/saxs_computation/c0/8c0d/8c0d.dat

UFL1/DDRGK1 bound to UFC1

1. Protein Identity and Related Structures Protein Identity & Related Structures

E3 UFM1-protein ligase 1

State in the Current Structure

Other States of the Same Protein in the Database

DDRGK domain-containing protein 1

State in the Current Structure

Other States of the Same Protein in the Database

Ubiquitin-fold modifier-conjugating enzyme 1

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)