4hcp

crystal structure of Burkholderia pseudomallei effector protein chbp in complex with nedd8

Method: X-RAY DIFFRACTION D_max: 65.6 Å Quality: EXCELLENT

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

Putative ATP/GTP binding protein

Burkholderia pseudomallei

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 78–328	Fragment：unp residues 78-382 Mutation：A156C	NEDD8 × 1 （Q15843） SO4 SULFATE ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION；pH 5.5；293 K；1.5 M ammonium sulfate and 100 mM citrate, pH 5.5, EVAPORATION, temperature 293K	Resolution 2.52 Å R-free 0.267

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 4HCP	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3EIR Crystal structure of CHBP, a Cif Homologue from Burkholderia pseudomallei Deposited 2008-09-17	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 48–328（281 aa） Fragment：residues 48-328	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；32% PEG1000, 100mM Sodium Cacodylate, 5% Glycerol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.10 Å R-free 0.254
3EIR Crystal structure of CHBP, a Cif Homologue from Burkholderia pseudomallei Deposited 2008-09-17	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 48–328（281 aa） Fragment：residues 48-328	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；32% PEG1000, 100mM Sodium Cacodylate, 5% Glycerol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.10 Å R-free 0.254
3EIT the 2.6 angstrom crystal structure of CHBP, the Cif Homologue from Burkholderia pseudomallei Deposited 2008-09-17	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 48–328（281 aa） Fragment：residues 48-328	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；32% PEG1000, 100mM Sodium Cacodylate, 5% Glycerol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.56 Å R-free 0.267
3EIT the 2.6 angstrom crystal structure of CHBP, the Cif Homologue from Burkholderia pseudomallei Deposited 2008-09-17	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 48–328（281 aa） Fragment：residues 48-328	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；32% PEG1000, 100mM Sodium Cacodylate, 5% Glycerol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.56 Å R-free 0.267
3GQM Crystal structure of Cell Inhibiting Factor (Cif) from Burkholderia pseudomallei (CifBp) Deposited 2009-03-24	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 67–328（262 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；10 % (w/v) PEG 8000, 100 mM HEPES 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K	Resolution 2.10 Å R-free 0.259
3GQM Crystal structure of Cell Inhibiting Factor (Cif) from Burkholderia pseudomallei (CifBp) Deposited 2009-03-24	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 67–328（262 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；10 % (w/v) PEG 8000, 100 mM HEPES 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K	Resolution 2.10 Å R-free 0.259
4HCN Crystal structure of Burkholderia pseudomallei effector protein CHBP in complex with ubiquitin Deposited 2012-09-30	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 78–328（251 aa） Fragment：unp RESIDUES 78-328	Mutation：A156C	PEG DI(HYDROXYETHYL)ETHER × 1 FMT FORMIC ACID × 2 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 7.2；293 K；12.5% PEG3350, 125MM MAGNESIUM FORMATE, pH 7.2, EVAPORATION, temperature 293K	Resolution 2.60 Å R-free 0.260

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

View Construct and Data Evidence

UniProt name	Q63KH5_BURPS
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–255； UniProt 78–328

NEDD8

Homo sapiens

UniProt Q15843

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 1–76	Fragment：unp residues 1-76	Putative ATP/GTP binding protein × 1 （Q63KH5） SO4 SULFATE ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION；pH 5.5；293 K；1.5 M ammonium sulfate and 100 mM citrate, pH 5.5, EVAPORATION, temperature 293K	Resolution 2.52 Å R-free 0.267

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 4HCP	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1NDD STRUCTURE OF NEDD8 Deposited 1998-08-21	Different construct 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 1–76（76 aa）	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.8；pH 4.8	Resolution 1.60 Å R-free 0.300
1NDD STRUCTURE OF NEDD8 Deposited 1998-08-21	Different construct 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 1–76（76 aa）	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.8；pH 4.8	Resolution 1.60 Å R-free 0.300
1NDD STRUCTURE OF NEDD8 Deposited 1998-08-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–76（76 aa）	Not recorded	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.8；pH 4.8	Resolution 1.60 Å R-free 0.300
1NDD STRUCTURE OF NEDD8 Deposited 1998-08-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 1–76（76 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.8；pH 4.8	Resolution 1.60 Å R-free 0.300
1NDD STRUCTURE OF NEDD8 Deposited 1998-08-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–76（76 aa） Chain B 1–76（76 aa） Chain C 1–76（76 aa） Chain D 1–76（76 aa）	Not recorded	CL CHLORIDE ION × 2 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.8；pH 4.8	Resolution 1.60 Å R-free 0.300
1R4M APPBP1-UBA3-NEDD8, an E1-ubiquitin-like protein complex Deposited 2003-10-07	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 I 1–76（76 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；PEG10K, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.00 Å R-free 0.280
1R4M APPBP1-UBA3-NEDD8, an E1-ubiquitin-like protein complex Deposited 2003-10-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain J 1–76（76 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；PEG10K, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.00 Å R-free 0.280
1R4M APPBP1-UBA3-NEDD8, an E1-ubiquitin-like protein complex Deposited 2003-10-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain K 1–76（76 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；PEG10K, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.00 Å R-free 0.280
1R4M APPBP1-UBA3-NEDD8, an E1-ubiquitin-like protein complex Deposited 2003-10-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain L 1–76（76 aa）	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；PEG10K, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.00 Å R-free 0.280
1R4N APPBP1-UBA3-NEDD8, an E1-ubiquitin-like protein complex with ATP Deposited 2003-10-07	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 I 1–76（76 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；peg10k, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.60 Å R-free 0.290
1R4N APPBP1-UBA3-NEDD8, an E1-ubiquitin-like protein complex with ATP Deposited 2003-10-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain J 1–76（76 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；peg10k, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.60 Å R-free 0.290
1R4N APPBP1-UBA3-NEDD8, an E1-ubiquitin-like protein complex with ATP Deposited 2003-10-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain K 1–76（76 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；peg10k, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.60 Å R-free 0.290
1R4N APPBP1-UBA3-NEDD8, an E1-ubiquitin-like protein complex with ATP Deposited 2003-10-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain L 1–76（76 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；peg10k, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.60 Å R-free 0.290
1XT9 Crystal Structure of Den1 in complex with Nedd8 Deposited 2004-10-21	Different construct Different ligand/ion 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	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；291 K；2M ammonium sulfate, 0.1M bicine, 4% tert-butanol, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.20 Å R-free 0.259
2BKR NEDD8 NEDP1 complex Deposited 2005-02-18	Different construct Different ligand/ion 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	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.5；CRYSTALS WERE GROWN BY SETTING-DROP METHOD BY MIXING THE NEDP1-NEDD8 COMPLEX (20MG/ML) WITH EQUAL VOLUME OF RESERVOIR SOLUTION CONTAINING 20%PEG8000, 200MM NACL, 100MM PHOSPHATE CITRATE PH4.5, pH 4.50	Resolution 1.90 Å R-free 0.209
2KO3 Nedd8 solution structure Deposited 2009-09-09	Different construct 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 1–76（76 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 200；Pressure ambient NMR sample composition 1 mM [U-100% 13C; U-100% 15N] Nedd8-1, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2N7K Unveiling the structural determinants of KIAA0323 binding preference for NEDD8 Deposited 2015-09-14	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–81（81 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.8；298 K；Ionic strength (raw mmCIF value) 0.02；Pressure ambient NMR sample composition 0.15-1.5 mM [U-100% 15N] protein, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2NVU Structure of APPBP1-UBA3~NEDD8-NEDD8-MgATP-Ubc12(C111A), a trapped ubiquitin-like protein activation complex Deposited 2006-11-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain I 1–76（76 aa） Chain J 1–76（76 aa）	Not recorded	MG MAGNESIUM ION × 1 ZN ZINC ION × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；291 K；17% v/v PEG 3350, 0.1 M HEPES pH 7.0, 0.2 M Disodium tartrate, VAPOR DIFFUSION, HANGING DROP, temperature 291K, pH 7.00	Resolution 2.80 Å R-free 0.274
3DBH Structural Dissection of a Gating Mechanism Preventing Misactivation of Ubiquitin by NEDD8's E1 (APPBP1-UBA3Arg190Ala-NEDD8Ala72Arg) Deposited 2008-05-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain J 1–76（76 aa）	Mutation：A172R	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.1 M Tris, 0.4 M ammonium acetate, 9-10% PEG 10K, 5 mM DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.85 Å R-free 0.274
3DBH Structural Dissection of a Gating Mechanism Preventing Misactivation of Ubiquitin by NEDD8's E1 (APPBP1-UBA3Arg190Ala-NEDD8Ala72Arg) Deposited 2008-05-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain I 1–76（76 aa）	Mutation：A172R	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.1 M Tris, 0.4 M ammonium acetate, 9-10% PEG 10K, 5 mM DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.85 Å R-free 0.274
3DBH Structural Dissection of a Gating Mechanism Preventing Misactivation of Ubiquitin by NEDD8's E1 (APPBP1-UBA3Arg190Ala-NEDD8Ala72Arg) Deposited 2008-05-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain L 1–76（76 aa）	Mutation：A172R	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.1 M Tris, 0.4 M ammonium acetate, 9-10% PEG 10K, 5 mM DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.85 Å R-free 0.274
3DBH Structural Dissection of a Gating Mechanism Preventing Misactivation of Ubiquitin by NEDD8's E1 (APPBP1-UBA3Arg190Ala-NEDD8Ala72Arg) Deposited 2008-05-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain K 1–76（76 aa）	Mutation：A172R	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.1 M Tris, 0.4 M ammonium acetate, 9-10% PEG 10K, 5 mM DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.85 Å R-free 0.274
3DBL Structural Dissection of a Gating Mechanism Preventing Misactivation of Ubiquitin by NEDD8's E1 (APPBP1-UBA3Arg190wt-NEDD8Ala72Gln) Deposited 2008-06-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain L 1–76（76 aa）	Mutation：A172Q	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.1 M Tris, 0.4 M ammonium acetate, 9-10% PEG 10K, 5 mM DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.90 Å R-free 0.274
3DBL Structural Dissection of a Gating Mechanism Preventing Misactivation of Ubiquitin by NEDD8's E1 (APPBP1-UBA3Arg190wt-NEDD8Ala72Gln) Deposited 2008-06-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain J 1–76（76 aa）	Mutation：A172Q	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.1 M Tris, 0.4 M ammonium acetate, 9-10% PEG 10K, 5 mM DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.90 Å R-free 0.274
3DBL Structural Dissection of a Gating Mechanism Preventing Misactivation of Ubiquitin by NEDD8's E1 (APPBP1-UBA3Arg190wt-NEDD8Ala72Gln) Deposited 2008-06-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain K 1–76（76 aa）	Mutation：A172Q	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.1 M Tris, 0.4 M ammonium acetate, 9-10% PEG 10K, 5 mM DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.90 Å R-free 0.274
3DBL Structural Dissection of a Gating Mechanism Preventing Misactivation of Ubiquitin by NEDD8's E1 (APPBP1-UBA3Arg190wt-NEDD8Ala72Gln) Deposited 2008-06-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain I 1–76（76 aa）	Mutation：A172Q	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.1 M Tris, 0.4 M ammonium acetate, 9-10% PEG 10K, 5 mM DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.90 Å R-free 0.274
3DBR Structural Dissection of a Gating Mechanism Preventing Misactivation of Ubiquitin by NEDD8's E1 (APPBP1-UBA3Arg190Gln-NEDD8Ala72Arg) Deposited 2008-06-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain K 1–76（76 aa）	Mutation：A172R	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；0.1 M Tris, 0.2 M NaCl, 10% PEG 10K, 8% PEG400, 5 mM DTT, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.05 Å R-free 0.280
3DBR Structural Dissection of a Gating Mechanism Preventing Misactivation of Ubiquitin by NEDD8's E1 (APPBP1-UBA3Arg190Gln-NEDD8Ala72Arg) Deposited 2008-06-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain L 1–76（76 aa）	Mutation：A172R	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；0.1 M Tris, 0.2 M NaCl, 10% PEG 10K, 8% PEG400, 5 mM DTT, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.05 Å R-free 0.280
3DBR Structural Dissection of a Gating Mechanism Preventing Misactivation of Ubiquitin by NEDD8's E1 (APPBP1-UBA3Arg190Gln-NEDD8Ala72Arg) Deposited 2008-06-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain J 1–76（76 aa）	Mutation：A172R	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；0.1 M Tris, 0.2 M NaCl, 10% PEG 10K, 8% PEG400, 5 mM DTT, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.05 Å R-free 0.280
3DBR Structural Dissection of a Gating Mechanism Preventing Misactivation of Ubiquitin by NEDD8's E1 (APPBP1-UBA3Arg190Gln-NEDD8Ala72Arg) Deposited 2008-06-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain I 1–76（76 aa）	Mutation：A172R	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；0.1 M Tris, 0.2 M NaCl, 10% PEG 10K, 8% PEG400, 5 mM DTT, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.05 Å R-free 0.280
3DQV Structural Insights into NEDD8 Activation of Cullin-RING Ligases: Conformational Control of Conjugation Deposited 2008-07-09	Different construct Different mutation/modification 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 1–76（76 aa） Fragment：NEDD8 C-terminus covalently linked to Cul5 Lys724	Mutation：L162M Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions 277 K；with ~19% PEG3350, 275mM (NH4)2PO4, 5mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 3.00 Å R-free 0.299
3DQV Structural Insights into NEDD8 Activation of Cullin-RING Ligases: Conformational Control of Conjugation Deposited 2008-07-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–76（76 aa） Fragment：NEDD8 C-terminus covalently linked to Cul5 Lys724	Mutation：L162M Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions 277 K；with ~19% PEG3350, 275mM (NH4)2PO4, 5mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 3.00 Å R-free 0.299
3DQV Structural Insights into NEDD8 Activation of Cullin-RING Ligases: Conformational Control of Conjugation Deposited 2008-07-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–76（76 aa） Fragment：NEDD8 C-terminus covalently linked to Cul5 Lys724 Chain B 1–76（76 aa） Fragment：NEDD8 C-terminus covalently linked to Cul5 Lys724	Mutation：L162M Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：L162M Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions 277 K；with ~19% PEG3350, 275mM (NH4)2PO4, 5mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 3.00 Å R-free 0.299
3GZN Structure of NEDD8-activating enzyme in complex with NEDD8 and MLN4924 Deposited 2009-04-07	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 I 1–76（76 aa）	Not recorded	ZN ZINC ION × 1 B39 [(1S,2S,4R)-4-{4-[(1S)-2,3-dihydro-1H-inden-1-ylamino]-7H-pyrrolo[2,3-d]pyrimidin-7-yl}-2-hydroxycyclopentyl]methyl sulfamate × 1	X-RAY DIFFRACTION X-ray crystallization conditions 293 K；1.8 M tri-ammonium citrate pH 7.0, 4% (v/v) 1,3 butanediol, temperature 293K	Resolution 3.00 Å R-free 0.287
3GZN Structure of NEDD8-activating enzyme in complex with NEDD8 and MLN4924 Deposited 2009-04-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain J 1–76（76 aa）	Not recorded	ZN ZINC ION × 1 B39 [(1S,2S,4R)-4-{4-[(1S)-2,3-dihydro-1H-inden-1-ylamino]-7H-pyrrolo[2,3-d]pyrimidin-7-yl}-2-hydroxycyclopentyl]methyl sulfamate × 1	X-RAY DIFFRACTION X-ray crystallization conditions 293 K；1.8 M tri-ammonium citrate pH 7.0, 4% (v/v) 1,3 butanediol, temperature 293K	Resolution 3.00 Å R-free 0.287
4F8C Structure of the Cif:Nedd8 complex - Yersinia pseudotuberculosis Cycle Inhibiting Factor in complex with human Nedd8 Deposited 2012-05-17	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–81（81 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；289 K；2.2M sodium malonate, 44mM bis-tris propane (pH 7.0), 66mM bis-tris propane (pH 8.0), VAPOR DIFFUSION, SITTING DROP, temperature 289K	Resolution 1.95 Å R-free 0.235
4F8C Structure of the Cif:Nedd8 complex - Yersinia pseudotuberculosis Cycle Inhibiting Factor in complex with human Nedd8 Deposited 2012-05-17	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–81（81 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；289 K；2.2M sodium malonate, 44mM bis-tris propane (pH 7.0), 66mM bis-tris propane (pH 8.0), VAPOR DIFFUSION, SITTING DROP, temperature 289K	Resolution 1.95 Å R-free 0.235
4FBJ Structure of the Cif:Nedd8 complex - Photorhabdus luminescens Cycle Inhibiting Factor in complex with human Nedd8 Deposited 2012-05-23	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–81（81 aa）	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.7；289 K；20% PEG 4000, 200mM sodium acetate, 100mM MES pH 6.7, VAPOR DIFFUSION, SITTING DROP, temperature 289K	Resolution 1.60 Å R-free 0.236
4P5O Structure of an RBX1-UBC12~NEDD8-CUL1-DCN1 complex: a RING-E3-E2~ubiquitin-like protein-substrate intermediate trapped in action Deposited 2014-03-18	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain K 1–76（76 aa）	Not recorded	ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；11% PEG3350, 0.2M ammonium citrate, 10mM ATP	Resolution 3.11 Å R-free 0.284
4P5O Structure of an RBX1-UBC12~NEDD8-CUL1-DCN1 complex: a RING-E3-E2~ubiquitin-like protein-substrate intermediate trapped in action Deposited 2014-03-18	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain H 1–76（76 aa）	Not recorded	ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；11% PEG3350, 0.2M ammonium citrate, 10mM ATP	Resolution 3.11 Å R-free 0.284
6R7F Structural basis of Cullin-2 RING E3 ligase regulation by the COP9 signalosome Deposited 2019-03-28	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain N 1–76（76 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；15 mM HEPES pH 7.5 100 mM NaCL 0.5 mM DTT 1% Glycerol cryo-EM vitrification conditions Cryogen ETHANE	Resolution 8.20 Å
6TTU Ubiquitin Ligation to substrate by a cullin-RING E3 ligase at 3.7A resolution: NEDD8-CUL1-RBX1 N98R-SKP1-monomeric b-TRCP1dD-IkBa-UB~UBE2D2 Deposited 2019-12-30	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain N 1–76（76 aa）	Not recorded	ZN ZINC ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.70 Å
7B5L Ubiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 super-assembly: NEDD8-CUL1-RBX1-SKP1-SKP2-CKSHS1-Cyclin A-CDK2-p27-UBE2L3~Ub~ARIH1. Transition State 1 Deposited 2020-12-04	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain N 1–76（76 aa）	Not recorded	ZN ZINC ION × 9 SY8 5-azanylpentan-2-one × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
7B5N Ubiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 super-assembly: NEDD8-CUL1-RBX1-UBE2L3~Ub~ARIH1. Deposited 2020-12-05	Different construct 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 N 1–81（81 aa）	Not recorded	ZN ZINC ION × 9 SY8 5-azanylpentan-2-one × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
7ONI Structure of Neddylated CUL5 C-terminal region-RBX2-ARIH2* Deposited 2021-05-25	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain N 1–81（81 aa）	Not recorded	ZN ZINC ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
8B3G C(N)RL4CSA-UVSSA-E2-ubiquitin complex. Deposited 2022-09-16	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain N 1–76（76 aa）	Not recorded	ZN ZINC ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.40 Å
8B3I CRL4CSA-E2-Ub (state 2) Deposited 2022-09-16	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain N 1–76（76 aa）	Not recorded	ZN ZINC ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
8CAF N8C_Fab3b in complex with NEDD8-CUL1(WHB) Deposited 2023-01-24	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain F 1–76（76 aa） Fragment：UNP residues 1-76	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；2.0-2.1M Ammonium Sulfate, 0.1M Citrate pH 6.0, 10mM TCEP	Resolution 2.66 Å R-free 0.263
8CAF N8C_Fab3b in complex with NEDD8-CUL1(WHB) Deposited 2023-01-24	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain G 1–76（76 aa） Fragment：UNP residues 1-76	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；2.0-2.1M Ammonium Sulfate, 0.1M Citrate pH 6.0, 10mM TCEP	Resolution 2.66 Å R-free 0.263
8H38 Cryo-EM Structure of the KBTBD2-CRL3~N8-CSN(mutate) complex Deposited 2022-10-08	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric	Chain N 1–76（76 aa）	Not recorded	ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8	Resolution 4.25 Å
8Q7H Structure of CUL9-RBX1 ubiquitin E3 ligase complex in unneddylated and neddylated conformation - focused cullin dimer Deposited 2023-08-16	Different construct 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 N 1–81（81 aa）	Not recorded	ZN ZINC ION × 10	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.10 Å
8RX0 (NEDD8)-CRL2VHL-MZ1-Brd4BD2-Ub(G76S, K48C)-UBE2R1(C93K, S138C, C191S, C223S)-Ub Deposited 2024-02-05	Different construct 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 N 1–76（76 aa）	Not recorded	759 (2~{S},4~{R})-1-[(2~{S})-2-[2-[2-[2-[2-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethanoylamino]-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-2,3-dihydro-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 ZN ZINC ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
8WQC cryo-EM structure of neddylated CUL2-RBX1-ELOB-ELOC-FEM1B bound with the C-degron of CDK5R1 Deposited 2023-10-11	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 × 12 PDB declaration: dodecameric	Chain K 1–76（76 aa） Chain N 1–76（76 aa）	Not recorded	ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.54 Å
8WQG cryo-EM structure of neddylated CUL2-RBX1-ELOB-ELOC-FEM1B bound with the C-degron of CCDC89 (conformation 1) Deposited 2023-10-11	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 × 12 PDB declaration: dodecameric	Chain K 1–76（76 aa） Chain N 1–76（76 aa）	Not recorded	ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.09 Å
8WZN ParkinK211N in complex with phospho NEDD8 Deposited 2023-11-02	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–76（76 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 8 PEG DI(HYDROXYETHYL)ETHER × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；291 K；0.1 M, MMT, 7.0, 25% w/v, PEG 1500	Resolution 1.80 Å R-free 0.212
8WZO Parkin in complex with phospho NEDD8 Deposited 2023-11-02	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–76（76 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 8 EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；277 K；0.02 M Sodium/potassium phosphate, 0.1 M Bis-Tris propane, 7.5, 20% w/v PEG 3350	Resolution 2.25 Å R-free 0.248
9E77 Cryo-EM structure of CSN-N8 in complex with CSN5i-3 Deposited 2024-11-01	Different construct 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 I 1–81（81 aa）	Not recorded	6LT 3-(difluoromethyl)-N-{6-[(5S,6S)-6-hydroxy-6,7,8,9-tetrahydro-5H-imidazo[1,5-a]azepin-5-yl][1,1'-biphenyl]-3-yl}-1-(propan-2-yl)-1H-pyrazole-5-carboxamide × 1 ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
9EFM Cryo-EM structure of COP9 signalosome precatalytic state with neddylated cullin-1 Deposited 2024-11-20	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric	Chain I 1–81（81 aa）	Not recorded	ZN ZINC ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.16 Å
9EFQ Cryo-EM structure of COP9 signalosome precatalytic state with neddylated cullin-2 Deposited 2024-11-20	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric	Chain I 1–81（81 aa）	Not recorded	ZN ZINC ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.96 Å
9EFV Cryo-EM structure of CSN-N8CUL1 in complex with CSN5i-3 Deposited 2024-11-20	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric	Chain I 1–81（81 aa）	Not recorded	6LT 3-(difluoromethyl)-N-{6-[(5S,6S)-6-hydroxy-6,7,8,9-tetrahydro-5H-imidazo[1,5-a]azepin-5-yl][1,1'-biphenyl]-3-yl}-1-(propan-2-yl)-1H-pyrazole-5-carboxamide × 1 ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.03 Å
9EG1 COP9 signalosome deneddylation complex with cullin-5 Deposited 2024-11-20	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric	Chain I 1–81（81 aa）	Not recorded	ZN ZINC ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.52 Å
9EG8 Cryo-EM structure of COP9 signalosome precatalytic state with neddylated cullin-4A Deposited 2024-11-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric	Chain I 1–81（81 aa）	Not recorded	ZN ZINC ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.39 Å
9EGL Cryo-EM structure of COP9 signalosome precatalytic state with neddylated cullin-3 Deposited 2024-11-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric	Chain I 1–81（81 aa）	Not recorded	ZN ZINC ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.93 Å
9QO0 Pre-activated 9-subunit COP9 signalosome and neddylated SCF (Skp1-Skp2-Cks1) complex structure Deposited 2025-03-25	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: 15-meric	Chain K 1–76（76 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.26 Å
9QO1 Activated 9-subunit COP9 signalosome and neddylated SCF (SKP1-SKP2-CKS1) complex structure Deposited 2025-03-25	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: 12-meric	Chain K 1–76（76 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.23 Å
9SDX Structure of RBR binding E2 variant crosslinked with NEDD8-CUL5-RBX2 bound ARIH2 and Ub Deposited 2025-08-15	Different construct 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 N 1–81（81 aa）	Not recorded	ZN ZINC ION × 7 SY8 5-azanylpentan-2-one × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 2.97 Å
9T7V Structure of LRRC58-EloB/C-CDO1 in complex with NEDD8-CUL5-RBX2-ARIH2-Ub Deposited 2025-11-12	Different construct 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 N 1–76（76 aa）	Not recorded	FE FE (III) ION × 1 SY8 5-azanylpentan-2-one × 1 ZN ZINC ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.95 Å
9UUM Cryo-EM structure of mezigdomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub ubiquitylation assembly Deposited 2025-05-07	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain N 1–76（76 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 3.41 Å
9V0A Cryo-EM structure of pomalidomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub ubiquitylation assembly Deposited 2025-05-17	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain N 1–76（76 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 3.69 Å
9V0B Cryo-EM structure of avadomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub ubiquitylation assembly Deposited 2025-05-17	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain N 1–76（76 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 3.54 Å
9V0F Cryo-EM structure of cemsidomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub ubiquitylation assembly Deposited 2025-05-17	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain N 1–76（76 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 3.71 Å

46 other PDB entries and 71 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NEDD8_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 3–78； 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

P(r) Distance Distribution P(r) Distribution

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

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4hcp
Deposition date deposition_date	2012-10-01
Structure title title	crystal structure of Burkholderia pseudomallei effector protein chbp in complex with nedd8
Keywords keywords	deamidase, Alpha/Beta/Alpha fold, Deamidation, NEDD8/Ubiquitin, bacterial cytosol, PROTEIN BINDING; PROTEIN BINDING
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	20.84 Å
Radius of gyration Rg (electron density) rg_electron	19.66 Å
Forward intensity I(0) i0	22342000.00
Molecular weight molecular_weight	36034.0 kDa
Excluded volume excluded_volume	45209 Å³
Envelope volume envelope_volume	52075 Å³
Hydration-shell volume shell_volume	21816 Å³
Envelope diameter envelope_diameter	67.2 Å
Shell Rg shell_rg	26.38 Å
Envelope Rg envelope_rg	19.92 Å
Shape Rg shape_rg	19.64 Å
Total Rg total_rg	20.61 Å
Total atoms total_atoms	2535
Residues n_residues	320
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	65.6 Å
Rg (real space) rg_real	20.73 Å
Rg uncertainty (real space) rg_real_error	0.29 Å
I(0) (real space) i0_real	2.2340e+07
I(0) uncertainty (real space) i0_real_error	2.3660e+05
Rg (reciprocal space) rg_reciprocal	20.75 Å
I(0) (reciprocal space) i0_reciprocal	22340000.0000
Solution quality estimate total_estimate	0.9002
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	26.6 Å
Skewness Skewness skewness	0.171
Kurtosis Kurtosis kurtosis	-0.469
Angular range angular_range	— – 0.3800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5592000.0000
Real-space data points n_real_points	70
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.904; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.992

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Putative ATP/GTP binding protein
Molecular weight formula_weight	28557.4 kDa
Mutation mutation	A156C
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2629

SGRPLKHRVTLRKATLASLMQSLSGESSNRVMWNDRYDTLLIARDPREIKNAIEKSVTDFGGLENYKELTGGADPFALMTPVAGLSANNIFKLMTEKDVPIDPTSIEYLENTSFAEHVNTLDSHKNYVVIVNDGRLGHKFLIDLPALTQGPRTAYIIQSDLGGGALPAVRVEDWISRRGSDPVSLDELNQLLSKDFSKMPDDVQTRLLASILQIDKDPHKVDIKKLHLDGKLRFASHEYDFRQFQRNAQYVAGLG

来源 Source

来源生物 organism	Burkholderia pseudomallei
NCBI Class编号 ncbi_taxonomy_id	272560
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	NEDD8
Molecular weight formula_weight	8716.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

AAMLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLALRGG

来源 Source

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

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	94

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d4hcpb1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.1 — Ubiquitin-related

Domain ID domain_id	d4hcpb2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id	4hcpB00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

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8. Citations (1)

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Unit-cell length a length_a	127.389 Å
Unit-cell length b length_b	44.973 Å
Unit-cell length c length_c	67.303 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	110.83 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.520 Å
Low-resolution limit resolution_low	19.840 Å
R factor r_factor	0.2034
R_work r_work	0.2000
R_free r_free	0.2668

fit	/app/data/saxs_computation/hc/4hcp/4hcp.fit
pddf	/app/data/pr_computation/hc/4hcp/4hcp.pr.out
profile	/app/data/saxs_computation/hc/4hcp/4hcp.dat

crystal structure of Burkholderia pseudomallei effector protein chbp in complex with nedd8

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

Putative ATP/GTP binding protein

State in the Current Structure

Other States of the Same Protein in the Database

NEDD8

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)