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6h77

E1 enzyme for ubiquitin like protein activation in complex with UBL

Method: X-RAY DIFFRACTION Dmax: 133.0 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Ubiquitin-like modifier-activating enzyme 5

Homo sapiens

UniProt Q9GZZ9

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 36–346 Chain B； UniProt 36–346 Not recorded Ubiquitin-fold modifier 1 × 2 （P61960） ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 4 ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 18 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.1；293.15 K；0.2 M Lithium Nitrate, 21% PEG 3350, 0.2 M Magnesium chloride hexahydrate and 3.5 % v/v Pentaerythritol ethoxylate (3/4 EO/OH) Resolution 2.10 Å R-free 0.221
2 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain C； UniProt 36–346 Chain D； UniProt 36–346 Not recorded Ubiquitin-fold modifier 1 × 2 （P61960） ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 4 ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 17 PEG DI(HYDROXYETHYL)ETHER × 3 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.1；293.15 K；0.2 M Lithium Nitrate, 21% PEG 3350, 0.2 M Magnesium chloride hexahydrate and 3.5 % v/v Pentaerythritol ethoxylate (3/4 EO/OH) Resolution 2.10 Å R-free 0.221

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 6H77 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3GUC Human Ubiquitin-activating Enzyme 5 in Complex with AMPPNP Deposited 2009-03-29 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 57–329（273 aa）
Chain B 57–329（273 aa）
Not recorded ZN ZINC ION × 2 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.2；287 K；1 M LITHIUM SULPHATE, 0.3 M AMMONIUM SULPHATE,0.1 M SODIUM CITRATE, PH 6.2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 287K
Resolution 2.25 Å R-free 0.255
3H8V Human Ubiquitin-activating Enzyme 5 in Complex with ATP Deposited 2009-04-29 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 57–329（273 aa） Fragment：residues 57-329
Chain B 57–329（273 aa） Fragment：residues 57-329
Not recorded ZN ZINC ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.2；287 K；1 M LITHIUM SULPHATE, 0.3 M AMMONIUM SULPHATE, 0.1 M SODIUM CITRATE, PH 6.2 , VAPOR DIFFUSION, HANGING DROP, temperature 287K
Resolution 2.00 Å R-free 0.224
5IAA Crystal structure of human UBA5 in complex with UFM1 Deposited 2016-02-21 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 57–346（290 aa） Fragment：UNP residues 57-346
Chain B 57–346（290 aa） Fragment：UNP residues 57-346
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；8% Tascimate, pH 7.0 and 16% PEG3350
Resolution 1.85 Å R-free 0.206
5L95 Crystal structure of human UBA5 in complex with UFM1 and AMP Deposited 2016-06-09 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 68–346（279 aa）
Chain B 68–346（279 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；0.1M HEPES pH7.5, 10% PEG 6000 and 5% 2-Methyl-2,4-pentanediol (MPD)
Resolution 2.10 Å R-free 0.222
6H78 E1 enzyme for ubiquitin like protein activation. Deposited 2018-07-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 36–335（300 aa）
Chain B 36–335（300 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 4 ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；293.13 K；0.2M sodium citrate tribasic dihydrate pH 7.9, 20% PEG 3350.
Resolution 2.70 Å R-free 0.242
6H78 E1 enzyme for ubiquitin like protein activation. Deposited 2018-07-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 36–335（300 aa）
Chain D 36–335（300 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 4 ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；293.13 K；0.2M sodium citrate tribasic dihydrate pH 7.9, 20% PEG 3350.
Resolution 2.70 Å R-free 0.242
6H78 E1 enzyme for ubiquitin like protein activation. Deposited 2018-07-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain E 36–335（300 aa）
Chain F 36–335（300 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 4 ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；293.13 K；0.2M sodium citrate tribasic dihydrate pH 7.9, 20% PEG 3350.
Resolution 2.70 Å R-free 0.242
6H78 E1 enzyme for ubiquitin like protein activation. Deposited 2018-07-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain G 36–335（300 aa）
Chain H 36–335（300 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 4 ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；293.13 K；0.2M sodium citrate tribasic dihydrate pH 7.9, 20% PEG 3350.
Resolution 2.70 Å R-free 0.242
6H78 E1 enzyme for ubiquitin like protein activation. Deposited 2018-07-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain I 36–335（300 aa）
Chain J 36–335（300 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 4 ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；293.13 K；0.2M sodium citrate tribasic dihydrate pH 7.9, 20% PEG 3350.
Resolution 2.70 Å R-free 0.242
6H78 E1 enzyme for ubiquitin like protein activation. Deposited 2018-07-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 6 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain K 36–335（300 aa）
Chain L 36–335（300 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 4 ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 5 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；293.13 K；0.2M sodium citrate tribasic dihydrate pH 7.9, 20% PEG 3350.
Resolution 2.70 Å R-free 0.242
6H78 E1 enzyme for ubiquitin like protein activation. Deposited 2018-07-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 7 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain M 36–335（300 aa）
Chain N 36–335（300 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 4 ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；293.13 K；0.2M sodium citrate tribasic dihydrate pH 7.9, 20% PEG 3350.
Resolution 2.70 Å R-free 0.242
6H78 E1 enzyme for ubiquitin like protein activation. Deposited 2018-07-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 8 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain O 36–335（300 aa）
Chain P 36–335（300 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 4 ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；293.13 K；0.2M sodium citrate tribasic dihydrate pH 7.9, 20% PEG 3350.
Resolution 2.70 Å R-free 0.242
6H8C Structure of the human GABARAPL2 protein in complex with the UBA5 LIR motif Deposited 2018-08-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 333–348（16 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 100；Pressure AMBIENT
NMR sample composition 0.6 mM [U-99% 13C; U-99% 15N] GABARAPL2, 1.0 mM No Ubiquitin-like modifier-activating enzyme 5 (UBA5) LIR motif, 50 mM No sodium phosphate, 100 mM No sodium chloride, 4.6 mM No sodium azide, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 1.0 mM No GABARAPL2, 0.6 mM [U-99% 13C; U-99% 15N] Ubiquitin-like modifier-activating enzyme 5 (UBA5) LIR motif, 50 mM No sodium phosphate, 100 mM No sodium chloride, 4.6 mM No sodium azide, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
7NVK Crystal structure of UBA5 fragment fused to the N-terminus of UFC1 Deposited 2021-03-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain AAA 347–404（58 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 construct 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 FFF 389–404（16 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain CCC 389–404（16 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 381–404（24 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

9 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name UBA5_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–311； UniProt 36–346 Author chain B； PDBConstruct 1–311； UniProt 36–346 Author chain C； PDBConstruct 1–311； UniProt 36–346 Author chain D； PDBConstruct 1–311； UniProt 36–346

Ubiquitin-fold modifier 1

Homo sapiens

UniProt P61960

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain Q； UniProt 1–78 Chain T； UniProt 1–78 Not recorded Ubiquitin-like modifier-activating enzyme 5 × 2 （Q9GZZ9） ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 4 ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 18 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.1；293.15 K；0.2 M Lithium Nitrate, 21% PEG 3350, 0.2 M Magnesium chloride hexahydrate and 3.5 % v/v Pentaerythritol ethoxylate (3/4 EO/OH) Resolution 2.10 Å R-free 0.221
2 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain R； UniProt 1–78 Chain S； UniProt 1–78 Not recorded Ubiquitin-like modifier-activating enzyme 5 × 2 （Q9GZZ9） ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 4 ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 17 PEG DI(HYDROXYETHYL)ETHER × 3 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.1；293.15 K；0.2 M Lithium Nitrate, 21% PEG 3350, 0.2 M Magnesium chloride hexahydrate and 3.5 % v/v Pentaerythritol ethoxylate (3/4 EO/OH) Resolution 2.10 Å R-free 0.221

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 6H77 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1WXS Solution Structure of Ufm1, a ubiquitin-fold modifier Deposited 2005-02-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–85（85 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；303 K；Ionic strength (raw mmCIF value) 100mM；Pressure ambient
NMR sample composition 0.1mM Ufm1 U-13C,15N; 10mM phosphate buffer NA; 100mM NaCl; 90% H2O, 10% D2O | 90% H2O/10% D2O
Resolution not provided
5HKH Crystal structure of Ufm1 in complex with UBA5 Deposited 2016-01-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 2–83（82 aa）
Chain C 2–83（82 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M ammonium acetate, 0.01 M magnesium acetate, 30% polyethylene glycol 8000, 0.05 M sodium cacodylate, pH 8.0
Resolution 2.55 Å R-free 0.248
5IA7 Crystal structure of Ubiquitin fold modifier 1 (Ufm1) Deposited 2016-02-21 Different construct 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 1–83（83 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；0.2M Ammonium acetate, 0.1M Sodium citrate tribasic dihydrate and 30% PEG 4000
Resolution 2.00 Å R-free 0.230
5IA7 Crystal structure of Ubiquitin fold modifier 1 (Ufm1) Deposited 2016-02-21 Different construct 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 1–83（83 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；0.2M Ammonium acetate, 0.1M Sodium citrate tribasic dihydrate and 30% PEG 4000
Resolution 2.00 Å R-free 0.230
5IA8 Structure of a Ubiquitin like protein with an E1 fragment Deposited 2016-02-21 Different construct Different mutation/modification 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 1–83（83 aa） Fragment：UNP residues 334-346,UNP residues 1-83
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；0.2M Potassium phosphate dibasic and 20% PEG 3350
Resolution 2.00 Å R-free 0.236
5IA8 Structure of a Ubiquitin like protein with an E1 fragment Deposited 2016-02-21 Different construct Different mutation/modification 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 1–83（83 aa） Fragment：UNP residues 334-346,UNP residues 1-83
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；0.2M Potassium phosphate dibasic and 20% PEG 3350
Resolution 2.00 Å R-free 0.236
5IAA Crystal structure of human UBA5 in complex with UFM1 Deposited 2016-02-21 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–83（83 aa）
Chain D 1–83（83 aa）
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；8% Tascimate, pH 7.0 and 16% PEG3350
Resolution 1.85 Å R-free 0.206
5L95 Crystal structure of human UBA5 in complex with UFM1 and AMP Deposited 2016-06-09 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 4–83（80 aa）
Chain D 4–83（80 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；0.1M HEPES pH7.5, 10% PEG 6000 and 5% 2-Methyl-2,4-pentanediol (MPD)
Resolution 2.10 Å R-free 0.222
7W3N Crystal structure of Ufm1 fused to UFBP1 UFIM Deposited 2021-11-25 Different construct Different mutation/modification 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 1–83（83 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
8BZR UFC1-UFM1 conjugate Deposited 2022-12-15 Different construct 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 B 1–83（83 aa）
Not recorded 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
8OHD 60S ribosomal subunit bound to the E3-UFM1 complex - state 3 (native) Deposited 2023-03-21 Different construct Different mutation/modification 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 D 1–85（85 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 mutation/modification 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 D 1–85（85 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 mutation/modification 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 D 1–85（85 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
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 mutation/modification 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 D 1–85（85 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

12 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name UFM1_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain Q； PDBConstruct 1–78； UniProt 1–78 Author chain R； PDBConstruct 1–78； UniProt 1–78 Author chain S； PDBConstruct 1–78； UniProt 1–78 Author chain T； PDBConstruct 1–78； UniProt 1–78

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

SAXS profile for 6h77

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6h77
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6h77
Deposition date deposition_date2018-07-30
Structure title titleE1 enzyme for ubiquitin like protein activation in complex with UBL
Keywords keywordsUbiquitin like protein activating enzyme, signaling protein; SIGNALING PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier38.83 Å
Radius of gyration Rg (electron density) rg_electron38.97 Å
Forward intensity I(0) i0448217000.00
Molecular weight molecular_weight171820.0 kDa
Excluded volume excluded_volume214790 ų
Envelope volume envelope_volume274350 ų
Hydration-shell volume shell_volume58189 ų
Envelope diameter envelope_diameter152.1 Å
Shell Rg shell_rg44.35 Å
Envelope Rg envelope_rg39.51 Å
Shape Rg shape_rg38.99 Å
Total Rg total_rg39.19 Å
Total atoms total_atoms11997
Residues n_residues1517
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax133.0 Å
Rg (real space) rg_real38.95 Å
Rg uncertainty (real space) rg_real_error1.22 Å
I(0) (real space) i0_real4.4820e+08
I(0) uncertainty (real space) i0_real_error7.7940e+06
Rg (reciprocal space) rg_reciprocal38.88 Å
I(0) (reciprocal space) i0_reciprocal448200000.0000
Solution quality estimate total_estimate0.8022
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary42.2 Å
Skewness Skewness skewness0.430
Kurtosis Kurtosis kurtosis-0.289
Angular range angular_range— – 0.2050 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha106000000.0000
Real-space data points n_real_points42
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.814; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.982; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (8)

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7. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id6h77A01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id6h77B01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id6h77C01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id6h77D01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id6h77Q00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Domain ID domain_id6h77R00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Domain ID domain_id6h77S00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Domain ID domain_id6h77T00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
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8. Citations (1)

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9. Files and Curves (10)