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Solution Structure of the Ubiquitin-Associated Domain of Human BMSC-UbP and its Complex with Ubiquitin

Method: SOLUTION NMR Dmax: 51.3 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Immunoglobulin G-binding protein G,Ubiquitin-like protein 7

Homo sapiens

UniProt P06654

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 229–282 Fragment：UBA domain,UBA domain Mutation：I12A Polyubiquitin-B × 1 （J3QS39） SOLUTION NMR NMR measurement conditions：pH 6.5；298 K；Pressure ambient NMR sample composition：1mM HGB1-UBA | 20mM phosphate, 100mM NaCl, pH6.5 NMR sample composition：1mM Ubiquitin | 20mM phosphate, 100mM NaCl, pH6.5 Resolution not provided

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 2DEN Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1EM7 HELIX VARIANT OF THE B1 DOMAIN FROM STREPTOCOCCAL PROTEIN G Deposited 2000-03-16 Different construct Different mutation/modification 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 189–244（56 aa） Fragment：B1 DOMAIN
Mutation：A24E, K28R, Q32E, N35K, D36K No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；277 K；100 mM sodium acetate, 30% polyethylene glycol momomethyl Ether 2000, 200 mM ammonium sulfate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.00 Å R-free 0.267
1GB1 A NOVEL, HIGHLY STABLE FOLD OF THE IMMUNOGLOBULIN BINDING DOMAIN OF STREPTOCOCCAL PROTEIN G Deposited 1991-05-15 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 228–282（55 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
1IGC IGG1 FAB FRAGMENT (MOPC21) COMPLEX WITH DOMAIN III OF PROTEIN G FROM STREPTOCOCCUS Deposited 1994-08-05 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 293–352（60 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.60 Å
1IGD THE THIRD IGG-BINDING DOMAIN FROM STREPTOCOCCAL PROTEIN G: AN ANALYSIS BY X-RAY CRYSTALLOGRAPHY OF THE STRUCTURE ALONE AND IN A COMPLEX WITH FAB Deposited 1994-08-05 Different construct Different mutation/modification 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 293–352（60 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.10 Å
1LE3 NMR Structure of Tryptophan Zipper 4: A Stable Beta-Hairpin Peptide Based on the C-terminal Hairpin of the B1 Domain of Protein G Deposited 2002-04-09 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 267–282（16 aa） Fragment：C-terminal hairpin of the B1 domain of Protein G
Mutation：Y45W/F52W/V54W Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；288 K；Ionic strength (raw mmCIF value) 0；Pressure ambient
NMR sample composition 2mM trpzip4 | 92% H2O, 8% D2O, pH 6.0, 0.1mM DSS
Resolution not provided
1MPE Ensemble of 20 structures of the tetrameric mutant of the B1 domain of streptococcal protein G Deposited 2002-09-12 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 228–282（55 aa） Fragment：B1 domain, sequence database residues 228-282
Chain B 228–282（55 aa） Fragment：B1 domain, sequence database residues 228-282
Chain C 228–282（55 aa） Fragment：B1 domain, sequence database residues 228-282
Chain D 228–282（55 aa） Fragment：B1 domain, sequence database residues 228-282
Mutation：T2Q, L5V, A26F, F30V, Y33F, A34F Mutation：T2Q, L5V, A26F, F30V, Y33F, A34F Mutation：T2Q, L5V, A26F, F30V, Y33F, A34F Mutation：T2Q, L5V, A26F, F30V, Y33F, A34F No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 5.45；313 K；Ionic strength (raw mmCIF value) 50 mM sodium phosphate, 0.02% sodium azide；Pressure 1
NMR sample composition 3.5 mM (in monomer) U-15N,13C, 50 mM sodium phosphate buffer, 0.02% sodium azide | 90% H2O/10% D2O
NMR sample composition 2.89 mM (in monomer) U-15N, 50 mM sodium phosphate buffer, 0.02% sodium azide | 90% H2O/10% D2O
NMR sample composition 3.5 mM (in monomer) U-15N,13C, 50 mM sodium phosphate buffer, 0.02% sodium azide | 100% D2O
NMR sample composition 1.4 mM (in monomer) 1:1 mixture unlabelled:U-15N,13C, 50 mM sodium phosphate buffer, 0.02% sodium azide | 100% D2O
Resolution not provided
1MVK X-ray structure of the tetrameric mutant of the B1 domain of streptococcal protein G Deposited 2002-09-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 228–282（55 aa） Fragment：B1 domain, sequence database residues 228-282
Chain B 228–282（55 aa） Fragment：B1 domain, sequence database residues 228-282
Chain C 228–282（55 aa） Fragment：B1 domain, sequence database residues 228-282
Chain D 228–282（55 aa） Fragment：B1 domain, sequence database residues 228-282
Mutation：T2Q, L5V, A26F, F30V, Y33F, A34F Mutation：T2Q, L5V, A26F, F30V, Y33F, A34F Mutation：T2Q, L5V, A26F, F30V, Y33F, A34F Mutation：T2Q, L5V, A26F, F30V, Y33F, A34F SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；PEG 8000, ammonium sulfate, sodium acetate, sodium chloride, TrisHCl, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.50 Å R-free 0.283
1MVK X-ray structure of the tetrameric mutant of the B1 domain of streptococcal protein G Deposited 2002-09-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain E 228–282（55 aa） Fragment：B1 domain, sequence database residues 228-282
Chain F 228–282（55 aa） Fragment：B1 domain, sequence database residues 228-282
Chain G 228–282（55 aa） Fragment：B1 domain, sequence database residues 228-282
Chain H 228–282（55 aa） Fragment：B1 domain, sequence database residues 228-282
Mutation：T2Q, L5V, A26F, F30V, Y33F, A34F Mutation：T2Q, L5V, A26F, F30V, Y33F, A34F Mutation：T2Q, L5V, A26F, F30V, Y33F, A34F Mutation：T2Q, L5V, A26F, F30V, Y33F, A34F SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；PEG 8000, ammonium sulfate, sodium acetate, sodium chloride, TrisHCl, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.50 Å R-free 0.283
1MVK X-ray structure of the tetrameric mutant of the B1 domain of streptococcal protein G Deposited 2002-09-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain I 228–282（55 aa） Fragment：B1 domain, sequence database residues 228-282
Chain J 228–282（55 aa） Fragment：B1 domain, sequence database residues 228-282
Chain K 228–282（55 aa） Fragment：B1 domain, sequence database residues 228-282
Chain L 228–282（55 aa） Fragment：B1 domain, sequence database residues 228-282
Mutation：T2Q, L5V, A26F, F30V, Y33F, A34F Mutation：T2Q, L5V, A26F, F30V, Y33F, A34F Mutation：T2Q, L5V, A26F, F30V, Y33F, A34F Mutation：T2Q, L5V, A26F, F30V, Y33F, A34F SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；PEG 8000, ammonium sulfate, sodium acetate, sodium chloride, TrisHCl, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.50 Å R-free 0.283
1PGA TWO CRYSTAL STRUCTURES OF THE B1 IMMUNOGLOBULIN-BINDING DOMAIN OF STREPTOCOCCAL PROTEIN G AND COMPARISON WITH NMR Deposited 1993-11-23 Different construct Different mutation/modification 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 228–282（55 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.07 Å
1PGB TWO CRYSTAL STRUCTURES OF THE B1 IMMUNOGLOBULIN-BINDING DOMAIN OF STREPTOCCOCAL PROTEIN G AND COMPARISON WITH NMR Deposited 1993-11-23 Different construct Different mutation/modification 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 228–282（55 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.92 Å
1PGX THE 1.66 ANGSTROMS X-RAY STRUCTURE OF THE B2 IMMUNOGLOBULIN-BINDING DOMAIN OF STREPTOCOCCAL PROTEIN G AND COMPARISON TO THE NMR STRUCTURE OF THE B1 DOMAIN Deposited 1992-04-03 Different construct Different mutation/modification 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 284–366（83 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.66 Å
1PN5 NMR structure of the NALP1 Pyrin domain (PYD) Deposited 2003-06-12 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 228–282（55 aa） Fragment：Pyrin domain (PYD)
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；293 K；Pressure 1
NMR sample composition 1mM NALP1 PYD U-15N,13C; 50mM Na / PO4 - Buffer; 50mM NaCl; 1mM CHAPS; 20mM DTT (D10); 0.02% NaN3; 0.1mM EDTA; protease inhibitor cocktail (Complete, Roche); 95% H2O, 5% D2O | 95% H2O/5% D2O
Resolution not provided
1Q10 Ensemble of 40 Structures of the Dimeric Mutant of the B1 Domain of Streptococcal Protein G Deposited 2003-07-18 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 228–282（55 aa） Fragment：B1 Domain
Chain B 228–282（55 aa） Fragment：B1 Domain
Mutation：T228Q,L231V,F256V,Y259F,A260F Mutation：T228Q,L231V,F256V,Y259F,A260F No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 5.5；298 K；Ionic strength (raw mmCIF value) 50mM sodium phosphate buffer；Pressure ambient
NMR sample composition 1.7mM (in monomer) U-15N,13C, 50mM phosphate buffer, 0.02% NaN3, 92.5% H2O, 7.5% D2O | 92.5% H2O, 7.5% D2O
NMR sample composition 0.85mM (in monomer) U-15N,13C, 0.85mM (in monomer) unlabeled, 50mM phosphate buffer (pH 5.5), 0.02 % NaN3, 92.5% H2O, 7.5% D2O | 92.5% H2O, 7.5% D2O
NMR sample composition 0.85mM (in monomer) U-15N,13C, 0.85mM (in monomer) unlabeled, 50mM phosphate buffer, 0.02% NaN3, 100% D2O | 100% D2O
NMR sample composition 1.7mM (in monomer) unlabeled, 50mM phosphate buffer, 0.02% NaN3, 92.5% H2O, 7.5% D2O | 92.5% H2O, 7.5% D2O
NMR sample composition 1.7mM (in monomer) unlabeled, 50mM phosphate buffer, 0.02% NaN3, 100% D2O | 100% D2O
Resolution not provided
2CWB Solution Structure of the Ubiquitin-Associated Domain of Human BMSC-UbP and its Complex with Ubiquitin Deposited 2005-06-17 Different construct Different oligomeric state Different experimental conditions Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 229–282（54 aa） Fragment：C-TERMINAL UBA DOMAIN,C-TERMINAL UBA DOMAIN
Mutation：I12A No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 100mM NaCl；Pressure ambient
NMR sample composition 1mM HGB1-UBA U-15N,13C; 20mM phosphate buffer; 90% H2O, 10% D2O | 90% H2O/10% D2O
Resolution not provided
2GB1 A NOVEL, HIGHLY STABLE FOLD OF THE IMMUNOGLOBULIN BINDING DOMAIN OF STREPTOCOCCAL PROTEIN G Deposited 1991-05-15 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 228–282（55 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
2IGD ANISOTROPIC STRUCTURE OF PROTEIN G IGG-BINDING DOMAIN III AT 1.1 ANGSTROM RESOLUTION Deposited 1997-04-30 Different construct Different mutation/modification 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 293–352（60 aa） Fragment：IMMUNOGLOBULIN-BINDING DOMAIN III
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.8；CRYSTALS WERE GROWN BY HANGING DROP VAPOUR DIFFUSION FROM 24-26% PEG 4000, 10MM SODIUM ACETATE AT PH 4.8 AND 0.01% SODIUM AZIDE. CELL PARAMETERS ARE NOT THOSE DETERMINED EXPERIMENTALLY. THEY WERE ADJUSTED ON THE BASIS OF THE ENGH & HUBER DICTIONARY AT THE END OF REFINEMENT. THE EXPERIMENTAL ESTIMATES WERE KNOWN TO HAVE POTENTIAL ERRORS DUE TO INACCURACIES IN THE CRYSTAL-TO-DETECTOR AND WAVELENGTH CALIBRATION., vapor diffusion - hanging drop
Resolution 1.10 Å R-free 0.125
2IGH DETERMINATION OF THE SOLUTION STRUCTURES OF DOMAINS II AND III OF PROTEIN G FROM STREPTOCOCCUS BY 1H NMR Deposited 1992-08-26 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 292–352（61 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
2J52 Solution Structure of GB1 domain Protein G and low and high pressure. Deposited 2006-09-11 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 228–282（55 aa） Fragment：RESIDUES 228-282
Mutation：YES No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 5.4；287 K；Ionic strength (raw mmCIF value) 0.1；Pressure 30.0
NMR sample composition 90%WATER/10%D2O
Resolution not provided
2J53 Solution Structure of GB1 domain Protein G and low and high pressure. Deposited 2006-09-11 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 228–282（55 aa） Fragment：RESIDUES 228-282
Mutation：YES No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 5.4；287 K；Ionic strength (raw mmCIF value) 0.1；Pressure 2000.0
NMR sample composition 90%WATER/10%D2O
Resolution not provided
2JU6 Solid-State Protein Structure Determination with Proton-Detected Triple Resonance 3D Magic-Angle Spinning NMR Spectroscopy Deposited 2007-08-15 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain X 228–282（55 aa）
Mutation：T2Q No recorded non-water small molecule SOLID-STATE NMR
NMR measurement conditions pH 5.5；281 K；Pressure ambient
NMR sample composition 5 mM [U-13C; U-15N; U-2H] GB1, 50 % isopropyl alcohol, 25 % (4R)-2-Methylpentane-2,4-diol, 50 mM sodium phosphate, Solid Slurry | Solid Slurry
Resolution not provided
2K0P Determination of a Protein Structure in the Solid State from NMR Chemical Shifts Deposited 2008-02-11 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 228–282（55 aa） Fragment：GB1
Mutation：T2Q No recorded non-water small molecule SOLID-STATE NMR
NMR measurement conditions 278 K；Pressure 1
NMR sample composition 10 mg/mL [U-100% 13C; U-100% 15N] GB1, 0.5 v/v Methyl Pentane diol, 0.25 v/v Isopropanol | 0.5 v/v Methyl Pentane diol/0.25 v/v Isopropanol
Resolution not provided
2KBT Attachment of an NMR-invisible solubility enhancement tag (INSET) using a sortase-mediated protein ligation method Deposited 2008-12-07 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 228–282（55 aa） Fragment：SH3 2 domain of Proto-oncogene vav,UNP residues 228-282 of Immunoglobulin G-binding protein G
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 150；Pressure ambient
NMR sample composition 20 mM MES-1, 2 mM DTT-2, 150 mM NaCl-3, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2LGI Atomic Resolution Protein Structures using NMR Chemical Shift Tensors Deposited 2011-07-26 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 229–282（54 aa） Fragment：2-1 repeat region residues 229-282
Not recorded No recorded non-water small molecule SOLID-STATE NMR
NMR measurement conditions pH 5.5；273 K；Ionic strength (raw mmCIF value) 50；Pressure ambient
NMR sample composition 20 mg U-2-13C-glycerol; U-100% 15N GB1 | solid
Resolution not provided
2MBB Solution Structure of the human Polymerase iota UBM1-Ubiquitin Complex Deposited 2013-07-29 Different construct Different mutation/modification Different experimental conditions Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 229–282（54 aa） Fragment：UNP P06654 residues 229-282, UNP Q9UNA4 residues 516-555
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 3 mM [U-100% 15N] GB1-UBM1, 3 mM [U-100% 15N] ubiquitin, 100 mM potassium chloride, 25 mM sodium phosphate, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 3 mM [U-100% 13C; U-100% 15N] GB1-UBM1, 3 mM [U-100% 13C; U-100% 15N] ubiquitin, 100 mM potassium chloride, 25 mM sodium phosphate, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 3 mM [U-100% 13C; U-100% 15N] GB1-UBM1, 3 mM [U-100% 13C; U-100% 15N] ubiquitin, 100 mM potassium chloride, 25 mM sodium phosphate, 100% D2O | 100% D2O
NMR sample composition 3 mM [U-100% 13C; U-100% 15N] GB1-UBM1, 3 mM ubiquitin, 100 mM potassium chloride, 25 mM sodium phosphate, 100% D2O | 100% D2O
NMR sample composition 3 mM GB1-UBM1, 3 mM [U-100% 13C; U-100% 15N] ubiquitin, 100 mM potassium chloride, 25 mM sodium phosphate, 100% D2O | 100% D2O
Resolution not provided
2N7J Sidechain chi1 distribution in B3 domain of protein G from extensive sets of residual dipolar couplings Deposited 2015-09-12 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 299–352（54 aa） Fragment：residues 299-352
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；293 K；Ionic strength (raw mmCIF value) 0.05；Pressure ambient
NMR sample composition 2.5 mM [U-100% 13C; U-100% 15N] wild-type GB3, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 1.3 mM [U-13C; U-15N] GB3-K19A/V42E/D47K, 100% D2O | 100% D2O
NMR sample composition 1.3 mM [U-100% 13C; U-100% 15N; U-75% 2H] GB3-K19A/V42E/D47K, 100% D2O | 100% D2O
NMR sample composition 1.3 mM [U-13C; U-15N; U-2H] GB3-K19A/V42E/D47K, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 2.0 mM [U-100% 13C; U-100% 15N] GB3-K4A/K19E/V42E, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 2.0 mM [U-100% 13C; U-100% 15N] GB3-K4A/K19E/V42E, 100% D2O | 100% D2O
NMR sample composition 2.0 mM [U-100% 13C; U-100% 15N; U-75% 2H] GB3-K4A/K19E/V42E, 100% D2O | 100% D2O
NMR sample composition 2.0 mM [U-13C; U-15N; U-2H] GB3-K4A/K19E/V42E, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 2.5 mM [U-100% 13C; U-100% 15N] wild-type GB3, 100% D2O | 100% D2O
NMR sample composition 2.5 mM [U-100% 13C; U-100% 15N; U-75% 2H] GB3-K19A/V42E/D47K, 100% D2O | 100% D2O
NMR sample composition 2.5 mM [U-13C; U-15N; U-2H] wild-type GB3, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 0.9 mM [U-13C; U-15N] GB3-K4A/K19E/V42E-CHis6, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 0.9 mM [U-13C; U-15N] GB3-K4A/K19E/V42E-CHis6, 100% D2O | 100% D2O
NMR sample composition 0.9 mM [U-100% 13C; U-100% 15N; U-75% 2H] GB3-K4A/K19E/V42E-CHis6, 100% D2O | 100% D2O
NMR sample composition 0.9 mM [U-13C; U-15N; U-2H] GB3-K4A/K19E/V42E-CHis6, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 1.3 mM [U-13C; U-15N] GB3-K19A/V42E/D47K, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
2NMQ Simultaneous determination of protein structure and dynamics using rdcs Deposited 2006-10-23 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 298–352（55 aa） Fragment：protein GB3(residues 298-352)
Not recorded No recorded non-water small molecule SOLUTION NMR mmCIF provides none of the parsed conditions Resolution not provided
2RMM Solution structure of GB1 A34F mutant Deposited 2007-10-30 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 229–282（54 aa）
Chain B 229–282（54 aa）
Mutation：A34F Mutation：A34F No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 5.5；298 K；Ionic strength (raw mmCIF value) 0.05；Pressure ambient
NMR sample composition 2.0mM [U-99% 13C; U-99% 15N] entity, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2RPV Solution Structure of GB1 with LBT probe Deposited 2008-10-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 227–282（56 aa） Fragment：L2GB
Mutation：E38C LA LANTHANUM (III) ION × 1 SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 50；Pressure ambient
NMR sample composition 0.8mM [U-99% 13C; U-99% 15N] L2GB, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
3MP9 Structure of Streptococcal protein G B1 domain at pH 3.0 Deposited 2010-04-26 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 227–282（56 aa） Fragment：B1 domain (UNP residues 227-282)
Not recorded FMT FORMIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3；290 K；Crystals grown in 3.8M sodium formate, 8% isopropanol, 50mM sodium citrate, pH 5.5. Crystals then soaked in 3.8M sodium formate, 8% isopropanol, 50mM sodium citrate pH 3.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Resolution 1.20 Å R-free 0.181
3MP9 Structure of Streptococcal protein G B1 domain at pH 3.0 Deposited 2010-04-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 227–282（56 aa） Fragment：B1 domain (UNP residues 227-282)
Not recorded FMT FORMIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3；290 K；Crystals grown in 3.8M sodium formate, 8% isopropanol, 50mM sodium citrate, pH 5.5. Crystals then soaked in 3.8M sodium formate, 8% isopropanol, 50mM sodium citrate pH 3.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Resolution 1.20 Å R-free 0.181
3MP9 Structure of Streptococcal protein G B1 domain at pH 3.0 Deposited 2010-04-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 227–282（56 aa） Fragment：B1 domain (UNP residues 227-282)
Chain B 227–282（56 aa） Fragment：B1 domain (UNP residues 227-282)
Not recorded FMT FORMIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3；290 K；Crystals grown in 3.8M sodium formate, 8% isopropanol, 50mM sodium citrate, pH 5.5. Crystals then soaked in 3.8M sodium formate, 8% isopropanol, 50mM sodium citrate pH 3.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Resolution 1.20 Å R-free 0.181
6CNE Selenomethionine variant (V29SeM) of protein GB1 Deposited 2018-03-08 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 229–282（54 aa）
Mutation：L5Sem Non-standard monomer：Yes (specific site not provided by mmCIF) MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.9；283.15 K；47% MPD 20% IPA 25 mM sodium acetate pH 4.9 20 mg/ml protein in 25 mM sodium acetate buffer pH 5.5 Non-reducing conditions (no TCEP)
Resolution 1.20 Å R-free 0.198
6CNE Selenomethionine variant (V29SeM) of protein GB1 Deposited 2018-03-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 229–282（54 aa）
Mutation：L5Sem Non-standard monomer：Yes (specific site not provided by mmCIF) MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.9；283.15 K；47% MPD 20% IPA 25 mM sodium acetate pH 4.9 20 mg/ml protein in 25 mM sodium acetate buffer pH 5.5 Non-reducing conditions (no TCEP)
Resolution 1.20 Å R-free 0.198
6L91 X-ray structure of synthetic GB1 domain with the mutation K10(DVA). Deposited 2019-11-07 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 227–282（56 aa）
Mutation：K10(DVA) Non-standard monomer：Yes (specific site not provided by mmCIF) GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；294 K；0.1M NaCacodylate (pH 5.5), 20% PEG 4000
Resolution 1.84 Å R-free 0.186
6L9B X-ray structure of synthetic GB1 domain with mutations K10(DVA), T11A Deposited 2019-11-08 Different construct Different mutation/modification 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 227–282（56 aa）
Mutation：K10(DVA), T11A 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 4.6；293 K；0.2M CaCl2, 0.1M sodium acetate (pH 4.6), 30% Isopropanol
Resolution 1.95 Å R-free 0.250
6L9D X-ray structure of synthetic GB1 domain with mutations K10(DVA), T11S Deposited 2019-11-08 Different construct Different mutation/modification 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 227–282（56 aa）
Mutation：K10DVA, T11S 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 6；293 K；0.1M Sodium Cacodylate (pH 6), 20% PEG 4000
Resolution 1.73 Å R-free 0.243
6LJI X-ray structure of synthetic GB1 domain with mutations K10(DVA), T11V Deposited 2019-12-16 Different construct Different mutation/modification 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 227–282（56 aa） Fragment：GB1 domain
Mutation：K10(DVA), T11V 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 6；294 K；20% PEG 4000, 0.1M MES pH 6.0
Resolution 1.84 Å R-free 0.328
6LJI X-ray structure of synthetic GB1 domain with mutations K10(DVA), T11V Deposited 2019-12-16 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 227–282（56 aa） Fragment：GB1 domain
Mutation：K10(DVA), T11V 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 6；294 K；20% PEG 4000, 0.1M MES pH 6.0
Resolution 1.84 Å R-free 0.328
6V9I cryo-EM structure of Cullin5 bound to RING-box protein 2 (Cul5-Rbx2) Deposited 2019-12-13 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 229–282（54 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；4 second blot time, blot force 20
Resolution 5.20 Å
7QTR GB1 in mammalian cells, 50 uM Deposited 2022-01-15 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 229–282（54 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.4；283 K；Ionic strength (raw mmCIF value) 0；Pressure AMBIENT
NMR sample composition 50 uM [U-13C; U-15N] B1 domain of streptococcal protein G (GB1), 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
7QTS GB1 in mammalian cells, 10 uM Deposited 2022-01-15 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 229–282（54 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.4；283 K；Ionic strength (raw mmCIF value) 0；Pressure AMBIENT
NMR sample composition 10 uM [U-13C; U-15N] GB1, in-cell | in-cell
Resolution not provided
7RXC CryoEM structure of KDELR with Legobody Deposited 2021-08-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric
Chain B 295–352（58 aa）
Not recorded POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7RXD CryoEM structure of RBD domain of COVID-19 in complex with Legobody Deposited 2021-08-22 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric
Chain B 295–352（58 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8JXR Structure of nanobody-bound DRD1_LSD complex Deposited 2023-07-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric
Chain C 295–352（58 aa）
Mutation：E360Q,K363A,D364F,T367I,R368L 7LD (8alpha)-N,N-diethyl-6-methyl-9,10-didehydroergoline-8-carboxamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.57 Å
8JXS Structure of nanobody-bound DRD1_PF-6142 complex Deposited 2023-07-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric
Chain C 295–352（58 aa）
Mutation：E360Q,K363A,D364F,T367I,R368L,D404E,A405H V6X 4-[3-methyl-4-(6-methylimidazo[1,2-a]pyrazin-5-yl)phenoxy]furo[3,2-c]pyridine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
8T0G Backbone Dialkylation in Peptide Hairpins: Natural Backbone Prototype Deposited 2023-06-01 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 267–282（16 aa）
Mutation：T13A Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.3；298 K；Ionic strength (raw mmCIF value) 250；Pressure 1
NMR sample composition 2 mM GB1 C-terminal Hairpin Mutant: Ala13 variant, 50 mM sodium phosphate, 0.2 mM DSS, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
9BDT Apolipoprotein B 100 bound to LDL receptor and legobody Deposited 2024-04-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 7 PDB declaration: heptameric
Chain B 295–352（58 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 CA CALCIUM ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.40 Å
9CHT Human E3 ligase E6AP in complex with HPV16-E6 and p53 Deposited 2024-07-02 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 228–282（55 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.54 Å
9COO Nanobody 4 bound to Apolipoprotein B 100 Deposited 2024-07-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric
Chain B 295–352（58 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 CA CALCIUM ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.73 Å
9G4T Beta carbonic anhydrase CsoSCA from the Halothiobacillus neapolitanus alpha-carboxysome Deposited 2024-07-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 6 PDB declaration: monomeric
Chain A 229–282（54 aa）
Not recorded ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.51 Å
9JA5 Cryo-EM structure of Tdk1-Bdf1 complex Deposited 2024-08-24 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 228–282（55 aa）
Chain B 228–282（55 aa）
Chain C 228–282（55 aa）
Chain D 228–282（55 aa）
Chain E 228–282（55 aa）
Chain F 228–282（55 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE；blot for 5 seconds before plunging
Resolution 2.70 Å
9JA6 Cryo-EM structure of Tdk1 tetramer complex Deposited 2024-08-24 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 228–282（55 aa）
Chain B 228–282（55 aa）
Chain C 228–282（55 aa）
Chain D 228–282（55 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE；blot for 5 seconds before plunging
Resolution 4.40 Å
9W3K GPR151-Legobody complex Deposited 2025-07-29 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric
Chain C 295–352（58 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.08 Å

48 other PDB entries and 54 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SPG1_STRSG
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 9–62； UniProt 229–282

Immunoglobulin G-binding protein G,Ubiquitin-like protein 7

Homo sapiens

UniProt Q96S82

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 336–380 Fragment：UBA domain,UBA domain Mutation：I12A Polyubiquitin-B × 1 （J3QS39） SOLUTION NMR NMR measurement conditions：pH 6.5；298 K；Pressure ambient NMR sample composition：1mM HGB1-UBA | 20mM phosphate, 100mM NaCl, pH6.5 NMR sample composition：1mM Ubiquitin | 20mM phosphate, 100mM NaCl, pH6.5 Resolution not provided

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 2DEN Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2CWB Solution Structure of the Ubiquitin-Associated Domain of Human BMSC-UbP and its Complex with Ubiquitin Deposited 2005-06-17 Different construct Different oligomeric state Different experimental conditions Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 336–380（45 aa） Fragment：C-TERMINAL UBA DOMAIN,C-TERMINAL UBA DOMAIN
Mutation：I12A No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 100mM NaCl；Pressure ambient
NMR sample composition 1mM HGB1-UBA U-15N,13C; 20mM phosphate buffer; 90% H2O, 10% D2O | 90% H2O/10% D2O
Resolution not provided

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name UBL7_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 64–108； UniProt 336–380

Polyubiquitin-B

Homo sapiens

UniProt J3QS39

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 1–76 Not recorded Immunoglobulin G-binding protein G,Ubiquitin-like protein 7 × 1 （P06654,Q96S82） SOLUTION NMR NMR measurement conditions：pH 6.5；298 K；Pressure ambient NMR sample composition：1mM HGB1-UBA | 20mM phosphate, 100mM NaCl, pH6.5 NMR sample composition：1mM Ubiquitin | 20mM phosphate, 100mM NaCl, pH6.5 Resolution not provided

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 2DEN Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2MBH NMR structure of EKLF(22-40)/Ubiquitin Complex Deposited 2013-07-31 Different oligomeric state Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；300 K；Ionic strength (raw mmCIF value) 20
NMR sample composition 4 mM Ubi_unl, 0.8 mM [U-100% 15N] EKLF, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 4 mM EKLF_unl, 0.8 mM [U-100% 15N] Ubiquitin, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 4 mM EKLF_unl, 0.8 mM [U-100% 13C; U-100% 15N] Ubiquitin, 100% D2O | 100% D2O
NMR sample composition 4 mM Ubi_unl, 0.8 mM [U-100% 13C; U-100% 15N] EKLF, 100% D2O | 100% D2O
Resolution not provided
3PRM Structural analysis of a viral OTU domain protease from the Crimean-Congo Hemorrhagic Fever virus in complex with human ubiquitin Deposited 2010-11-30 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–75（75 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 6.5；298 K；22-26% PEG 8000, 0.1 M Na cacodylate, 0.2 M Mg acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.30 Å R-free 0.267
3PRM Structural analysis of a viral OTU domain protease from the Crimean-Congo Hemorrhagic Fever virus in complex with human ubiquitin Deposited 2010-11-30 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–75（75 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 6.5；298 K；22-26% PEG 8000, 0.1 M Na cacodylate, 0.2 M Mg acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.30 Å R-free 0.267
3PRP Structural analysis of a viral OTU domain protease from the Crimean-Congo Hemorrhagic Fever virus in complex with human ubiquitin Deposited 2010-11-30 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–75（75 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 6.5；298 K；22-28% PEG 8000, 100 mM Na cacodylate pH 6.5, 100-250 mM Mg acetate, and 2% n-Octyl- -D-glucoside, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.70 Å R-free 0.212
3PRP Structural analysis of a viral OTU domain protease from the Crimean-Congo Hemorrhagic Fever virus in complex with human ubiquitin Deposited 2010-11-30 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–75（75 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 6.5；298 K；22-28% PEG 8000, 100 mM Na cacodylate pH 6.5, 100-250 mM Mg acetate, and 2% n-Octyl- -D-glucoside, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.70 Å R-free 0.212
5TXK CRYSTAL STRUCTURE OF USP35 C450S IN COMPLEX WITH UBIQUITIN Deposited 2016-11-17 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 1–76（76 aa）
Not recorded SO4 SULFATE ION × 3 EDO 1,2-ETHANEDIOL × 3 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；296 K；0.95 M ammonium sulphate 0.1 M HEPES
Resolution 1.84 Å R-free 0.183
5YDR Structure of DNMT1 RFTS domain in complex with ubiquitin Deposited 2017-09-14 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 × 3 PDB declaration: trimeric
Chain A 1–73（73 aa） Fragment：UNP residues 1-73
Chain D 1–73（73 aa） Fragment：UNP residues 1-73
Not recorded PO4 PHOSPHATE ION × 2 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 8；291 K；20mM Tris-HCl, 200mM sodium acetate, 25% PEG 4000
Resolution 2.00 Å R-free 0.233
6K4I The partially disordered conformation of ubiquitin (Q41N variant) Deposited 2019-05-24 Different mutation/modification Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa）
Mutation：Q41N No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 4；278 K；Ionic strength (raw mmCIF value) 30；Pressure 2500
NMR sample composition 1.0 mM [U-99% 13C; U-99% 15N] ubiquitin, 30 mM D D-acetate, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.3 mM [U-99% 15N] ubiquitin, 30 mM D D-acetate, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
6KOW Retracted state of S65/T66 double-phosphorylated ubiquitin Deposited 2019-08-13 Different mutation/modification Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.4；298 K；Ionic strength (raw mmCIF value) 150；Pressure 760
NMR sample composition 20 mM HEPES, 150 mM sodium chloride, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
6KOX Relaxed state of S65/T66 double-phosphorylated ubiquitin Deposited 2019-08-13 Different mutation/modification Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.4；298 K；Ionic strength (raw mmCIF value) 150；Pressure 760
NMR sample composition 20 mM HEPES, 150 mM sodium chloride, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
6NJG Ubiquitin Variant in Complex with Ubiquitin Interacting Motif Deposited 2019-01-03 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–78（78 aa）
Mutation：K6Q, L8I, G10V, K11M, T12R, T14A, K48M, Q62K, K63R, E64D, T66N, H68Y, L71S, R72S, G75S, G76L, M77R, Q78A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；2.1 M DL-Malic acid
Resolution 2.35 Å R-free 0.244
6NOG Poised-state Dot1L bound to the H2B-Ubiquitinated nucleosome Deposited 2019-01-16 Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain L 1–76（76 aa）
Mutation：G76C No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；Solutions were prepared on the day of freezing and filtered though a 0.2 um filter prior to use.
cryo-EM vitrification conditions Cryogen ETHANE；Blot once for 3.5 seconds before freezing
Resolution 3.90 Å
6O96 Dot1L bound to the H2BK120 Ubiquitinated nucleosome Deposited 2019-03-13 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain L 1–76（76 aa）
Mutation：G76C SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen PROPANE；blotted for 3s before plunging
Resolution 3.50 Å
6OAM Crystal Structure of ChlaDUB2 DUB domain Deposited 2019-03-17 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–75（75 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 7.5；298 K；0.1 M HEPES sodium pH 7.5, 0.8 M sodium phosphate monobasic monohydrate, 0.8 M sodium phosphate monobasic, 0.1M Cesium chloride
Resolution 2.50 Å R-free 0.306
6OAM Crystal Structure of ChlaDUB2 DUB domain Deposited 2019-03-17 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–75（75 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 7.5；298 K；0.1 M HEPES sodium pH 7.5, 0.8 M sodium phosphate monobasic monohydrate, 0.8 M sodium phosphate monobasic, 0.1M Cesium chloride
Resolution 2.50 Å R-free 0.306
6PZV Crystal Structure of Bovine DNMT1 RFTS domain in complex with H3K9me3 and Ubiquitin Deposited 2019-08-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–76（76 aa）
Chain B 1–76（76 aa）
Not recorded FLC CITRATE ANION × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.5；277 K；0.1M citric acid (pH 3.5), 28% PEG8000
Resolution 3.01 Å R-free 0.272
6PZV Crystal Structure of Bovine DNMT1 RFTS domain in complex with H3K9me3 and Ubiquitin Deposited 2019-08-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain E 1–76（76 aa）
Chain F 1–76（76 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.5；277 K；0.1M citric acid (pH 3.5), 28% PEG8000
Resolution 3.01 Å R-free 0.272
6QF8 Solution NMR ensemble for human ubiquitin at 298K compiled using the CoMAND method Deposited 2019-01-09 Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 5.8；298 K；Ionic strength (raw mmCIF value) 100；Pressure 1
NMR sample composition 1.0 mM [U-99% 13C; U-99% 15N] human ubiquitin, 40 mM sodium phosphate, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
6TBM Structure of SAGA bound to TBP, including Spt8 and DUB Deposited 2019-11-01 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain R 1–75（75 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 20.00 Å
6UH5 Structural basis of COMPASS eCM recognition of the H2Bub nucleosome Deposited 2019-09-26 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 17 PDB declaration: nonadecameric
Chain Q 1–76（76 aa）
Mutation：G76C ZN ZINC ION × 1 SAM S-ADENOSYLMETHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6XAA SARS CoV-2 PLpro in complex with ubiquitin propargylamide Deposited 2020-06-04 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 1–76（76 aa）
Mutation：G76 replaced with propargylamide Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；30% PEG4000, 0.2 M sodium acetate, 0.1 M Tris chloride, pH 8.5
Resolution 2.70 Å R-free 0.260
6XQC UbKEKS Deposited 2020-07-09 Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.4；298 K；Ionic strength (raw mmCIF value) 100；Pressure 1
NMR sample composition 500 uM [U-13C; U-15N] UbKEKS, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 500 uM [U-13C; U-15N] UbKEKS, 100% D2O | 100% D2O
Resolution not provided
7BBD Crystal structure of monoubiquitinated TRIM21 RING (Ub-RING) In complex with ubiquitin charged Ube2N (Ube2N~Ub) and Ube2V2 Deposited 2020-12-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–74（74 aa）
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；290.15 K；MOPSO, Bis-Tris, PEG 4K, 1,2,6-hexanetriol, Li, Na, K
Resolution 2.20 Å R-free 0.252
7BU0 Crystal structure of a OTU deubiquitinase in complex with Ub-PA Deposited 2020-04-03 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 × 4 PDB declaration: tetrameric
Chain C 1–75（75 aa）
Chain D 1–75（75 aa）
Not recorded AYE prop-2-en-1-amine × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；289.15 K；0.1M Magnesium formate dihydrate 15% w/v PEG 3350
Resolution 2.43 Å R-free 0.255
7E8I Structural insight into BRCA1-BARD1 complex recruitment to damaged chromatin Deposited 2021-03-01 Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain L 1–76（76 aa）
Mutation：G76C No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7NBB Branched Lys48- and Lys63-linked tri-ubiquitin (K48-K63-Ub3) in complex with synthetic nanobody NbSL3 Deposited 2021-01-26 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 × 4 PDB declaration: tetrameric
Chain A 1–72（72 aa）
Chain B 1–76（76 aa）
Chain C 1–76（76 aa）
Mutation：K48R K63R Mutation：K48R K63R MG MAGNESIUM ION × 4 GOL GLYCEROL × 1 CL CHLORIDE ION × 2 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；277.15 K；0.1 M Bis-Tris pH 7.2 0.28 M MgCl2 21% PEG3350 0.15 M NaCl 0.05 M Tris/HCl pH 7.5
Resolution 1.55 Å R-free 0.212
7NBB Branched Lys48- and Lys63-linked tri-ubiquitin (K48-K63-Ub3) in complex with synthetic nanobody NbSL3 Deposited 2021-01-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain E 1–72（72 aa）
Chain F 1–76（76 aa）
Chain G 1–76（76 aa）
Mutation：K48R K63R Mutation：K48R K63R MG MAGNESIUM ION × 3 GOL GLYCEROL × 1 CL CHLORIDE ION × 5 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；277.15 K；0.1 M Bis-Tris pH 7.2 0.28 M MgCl2 21% PEG3350 0.15 M NaCl 0.05 M Tris/HCl pH 7.5
Resolution 1.55 Å R-free 0.212
7NPO Branched K48-K63-Ub3 Deposited 2021-02-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–72（72 aa）
Chain B 1–76（76 aa）
Chain C 1–76（76 aa）
Mutation：K48R K63R Mutation：K48R K63R GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；0.2 M Ammonium acetate, 20 mM Tris pH 7.5, 50 mM NaCl, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 30% w/v PEG 4000; 22 mg/ml
Resolution 2.19 Å R-free 0.284
7QO4 26S proteasome WT-Ubp6-UbVS complex in the si state (ATPases, Rpn1, Ubp6, and UbVS) Deposited 2021-12-23 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 × 9 PDB declaration: nonameric
Chain 9 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ATP ADENOSINE-5'-TRIPHOSPHATE × 5 MG MAGNESIUM ION × 6 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.00 Å
7QO6 26S proteasome Rpt1-RK -Ubp6-UbVS complex in the s2 state Deposited 2021-12-23 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 × 49 PDB declaration: 49-meric
Chain 9 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ATP ADENOSINE-5'-TRIPHOSPHATE × 5 MG MAGNESIUM ION × 6 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.30 Å
7UD5 Complex between MLL1-WRAD and an H2B-ubiquitinated nucleosome Deposited 2022-03-18 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric
Chain O 1–76（76 aa）
Mutation：G76C SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.25 Å
7US1 Structure of parkin (R0RB) bound to two phospho-ubiquitin molecules Deposited 2022-04-22 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 × 3 PDB declaration: trimeric
Chain B 1–74（74 aa）
Chain C 1–74（74 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 6 PEG DI(HYDROXYETHYL)ETHER × 1 EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277.15 K；0.1M Bis-Tris propane pH 7.5, 20.5% PEG3350, 0.2M NaI
Resolution 2.48 Å R-free 0.258
7W3U USP34 catalytic domain in complex with UbPA Deposited 2021-11-26 Different construct 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 D 1–75（75 aa）
Not recorded ZN ZINC ION × 1 AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；15% w/v PEG 3350, 0.8M Magnesium chloride hexahydrate, 0.6mM Lyso PG, 1 mM Facade R-EPC
Resolution 3.13 Å R-free 0.245
7W3U USP34 catalytic domain in complex with UbPA Deposited 2021-11-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 1–75（75 aa）
Not recorded ZN ZINC ION × 1 AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；15% w/v PEG 3350, 0.8M Magnesium chloride hexahydrate, 0.6mM Lyso PG, 1 mM Facade R-EPC
Resolution 3.13 Å R-free 0.245
7W3U USP34 catalytic domain in complex with UbPA Deposited 2021-11-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 1–75（75 aa）
Not recorded ZN ZINC ION × 1 AYE prop-2-en-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；15% w/v PEG 3350, 0.8M Magnesium chloride hexahydrate, 0.6mM Lyso PG, 1 mM Facade R-EPC
Resolution 3.13 Å R-free 0.245
7W54 Crystal structure of a bacterial OTU DUB with Ub-PA Deposited 2021-11-29 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 × 6 PDB declaration: hexameric
Chain C 1–75（75 aa）
Chain D 1–75（75 aa）
Chain E 1–75（75 aa）
Chain F 1–75（75 aa）
Not recorded AYE prop-2-en-1-amine × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；299 K；100 mM Magnesium formate, 15% (w/v) PEG 3350, pH 8.0
Resolution 2.64 Å R-free 0.253
7YQK cryo-EM structure of gammaH2AXK15ub-H4K20me2 nucleosome bound to 53BP1 Deposited 2022-08-07 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain O 1–75（75 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.38 Å
8A67 Branched Lys48- and Lys63-linked tri-ubiquitin (K48-K63-Ub3) in complex with matured synthetic nanobody NbSL3.3Q (3rd generation) Deposited 2022-06-16 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 × 4 PDB declaration: tetrameric
Chain A 1–72（72 aa）
Chain B 1–76（76 aa）
Chain C 1–76（76 aa）
Mutation：K48R K63R Mutation：K48R K63R GOL GLYCEROL × 1 IPA ISOPROPYL ALCOHOL × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293.15 K；Protein concentrated to 14.5 mg/ml in 20 mM HEPES pH 7.5, 150 mM NaCl. Mixed 200 nl protein with 100 nl mother liquor (0.1 M HEPES pH 7.5, 10% 2-propanol, 20% PEG4000). Crystals harvested and cryo-protected with Mother liquor supplemented with 30% glycerol.
Resolution 1.86 Å R-free 0.245
8A67 Branched Lys48- and Lys63-linked tri-ubiquitin (K48-K63-Ub3) in complex with matured synthetic nanobody NbSL3.3Q (3rd generation) Deposited 2022-06-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain E 1–72（72 aa）
Chain F 1–76（76 aa）
Chain G 1–76（76 aa）
Mutation：K48R K63R Mutation：K48R K63R GOL GLYCEROL × 1 IPA ISOPROPYL ALCOHOL × 1 ZN ZINC ION × 1 CL CHLORIDE ION × 1 NA SODIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293.15 K；Protein concentrated to 14.5 mg/ml in 20 mM HEPES pH 7.5, 150 mM NaCl. Mixed 200 nl protein with 100 nl mother liquor (0.1 M HEPES pH 7.5, 10% 2-propanol, 20% PEG4000). Crystals harvested and cryo-protected with Mother liquor supplemented with 30% glycerol.
Resolution 1.86 Å R-free 0.245
8DU4 Complex between RbBP5-WDR5 and an H2B-ubiquitinated nucleosome Deposited 2022-07-26 Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain O 1–76（76 aa）
Mutation：G76C No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.55 Å
8HQY Cryo-EM structure of SSX1 bound to the H2AK119Ub nucleosome at a resolution of 3.05 angstrom Deposited 2022-12-14 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain U 1–74（74 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
8K6E LnaB-Actin-PRUb ternary complex Deposited 2023-07-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–75（75 aa）
Not recorded ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 AR6 [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；289 K；PEG 8000; Sodium chloride; Sodium HEPES
Resolution 2.74 Å R-free 0.245
8T2D Ubiquitin variant i53:Mutant T12Y.T14E.L67R with 53BP1 Tudor domain Deposited 2023-06-05 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–74（74 aa）
Mutation：T12Y, T14E, L67R No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；290 K；0.1 M MES pH 6.0, 0.2 M Trimethylamine N-oxide dehydrate, 13% w/v PEG MME 2000
Resolution 1.75 Å R-free 0.273
8WG5 Cryo-EM structure of USP16 bound to H2AK119Ub nucleosome Deposited 2023-09-20 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain U 1–75（75 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
9KQO cryo-EM structure of RNF20/RNF40-RAD6A-Ub in complex with H2BS112GlcNAc nucleosome Deposited 2024-11-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain B 1–75（75 aa）
Not recorded ZN ZINC ION × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.48 Å
9NY4 USP21 bound to H2AK119ub nucleosome Deposited 2025-03-26 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain U 1–76（76 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.98 Å

38 other PDB entries and 46 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name J3QS39_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–76； UniProt 1–76

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 2den

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2den
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2den
Deposition date deposition_date2006-02-14
Structure title titleSolution Structure of the Ubiquitin-Associated Domain of Human BMSC-UbP and its Complex with Ubiquitin
Keywords keywordsA:alpha-alpha-alpha, B:beta-beta-helix-helix-beta-beta-helix-beta, PROTEIN BINDING; PROTEIN BINDING
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier15.26 Å
Radius of gyration Rg (electron density) rg_electron14.75 Å
Forward intensity I(0) i0259672000.00
Molecular weight molecular_weight134690.0 kDa
Excluded volume excluded_volume168700 ų
Envelope volume envelope_volume26085 ų
Hydration-shell volume shell_volume14172 ų
Envelope diameter envelope_diameter54.3 Å
Shell Rg shell_rg21.44 Å
Envelope Rg envelope_rg16.08 Å
Shape Rg shape_rg14.75 Å
Total Rg total_rg14.93 Å
Total atoms total_atoms19120
Residues n_residues1220
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 dmax51.3 Å
Rg (real space) rg_real15.75 Å
Rg uncertainty (real space) rg_real_error0.12 Å
I(0) (real space) i0_real2.5870e+08
I(0) uncertainty (real space) i0_real_error2.5300e+06
Rg (reciprocal space) rg_reciprocal15.25 Å
I(0) (reciprocal space) i0_reciprocal259700000.0000
Solution quality estimate total_estimate0.6469
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary16.9 Å
Skewness Skewness skewness0.428
Kurtosis Kurtosis kurtosis-0.165
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha7.7960
Highest regularization parameter α highest_alpha492800.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.758; Stabil: 0.907; Sysdev: 0.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.464
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd2dena_
Class classa — All alpha proteins
Fold Fold folda.5 — RuvA C-terminal domain-like
Superfamily Superfamily superfamilya.5.2 — UBA-like
Family Family familya.5.2.0 — automated matches
Domain ID domain_idd2denb_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.1 — Ubiquitin-like
Family Family familyd.15.1.1 — Ubiquitin-related

CATH v4.4 (2 domains)

Domain ID domain_id2denA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily10 — Ubiquitin-associated (UBA) domain
Domain ID domain_id2denB00
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)