2fif

Crystal Structure of a Bovine Rabex-5 fragment complexed with ubiquitin

Method: X-RAY DIFFRACTION D_max: 100.2 Å Quality: GOOD

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

Ubiquitin

OrganismNot specified

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 1–76	Not recorded	Rab5 GDP/GTP exchange factor × 1 （O18973） SO4 SULFATE ION × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.6；295 K；20-25% PEG 4000, 0.2M lithium sulfate , pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.49 Å R-free 0.263
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 1–76	Not recorded	Rab5 GDP/GTP exchange factor × 1 （O18973） ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.6；295 K；20-25% PEG 4000, 0.2M lithium sulfate , pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.49 Å R-free 0.263
3	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain E； UniProt 1–76	Not recorded	Rab5 GDP/GTP exchange factor × 1 （O18973） ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.6；295 K；20-25% PEG 4000, 0.2M lithium sulfate , pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.49 Å R-free 0.263

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 2FIF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AAR STRUCTURE OF A DIUBIQUITIN CONJUGATE AND A MODEL FOR INTERACTION WITH UBIQUITIN CONJUGATING ENZYME (E2) Deposited 1992-04-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–76（76 aa） Chain B 1–76（76 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å
1P3Q Mechanism of Ubiquitin Recognition by the CUE Domain of VPS9 Deposited 2003-04-18	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain V 1–76（76 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；293 K；PEG 3350, magnesium chloride, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.70 Å R-free 0.277
1P3Q Mechanism of Ubiquitin Recognition by the CUE Domain of VPS9 Deposited 2003-04-18	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain U 1–76（76 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；293 K；PEG 3350, magnesium chloride, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.70 Å R-free 0.277
1V80 Solution structures of ubiquitin at 30 bar and 3 kbar Deposited 2003-12-27	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 4.6；293 K；Ionic strength (raw mmCIF value) 0.03；Pressure 30 NMR measurement conditions pH 4.6；293 K；Ionic strength (raw mmCIF value) 0.03；Pressure 1 NMR sample composition 10mM Ubiquitin; 30mM deutrated acetate buffer; 92% H2O, 8% D2O \| 92% H2O, 8% D2O NMR sample composition 3.0mM 15N-Ubiquitin; 30mM deutrated acetate buffer; 95% H2O, 5% D20 \| 95% H2O, 5% D20 NMR sample composition 1.8mM 15N-13C-Ubiquitin; 30mM deutrated acetate buffer; 95% H2O, 5% D2O \| 95% H2O, 5% D20	Resolution not provided
1V81 Solution structures of ubiquitin at 30 bar and 3 kbar Deposited 2003-12-27	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 4.6；293 K；Ionic strength (raw mmCIF value) 0.03；Pressure 3000 NMR sample composition 10mM Ubiquitin; 30mM deutrated acetate buffer; 92% H2O, 8% D2O \| 92% H2O, 8% D2O NMR sample composition 3mM 15N-Ubiquitin; 30mM deutrated acetate buffer; 95% H2O, 5% D2O \| 95% H2O/5% D2O NMR sample composition 1.8mM 15N-13C-Ubiquitin; 30mM deutrated acetate buffer; 95% H2O, 5% D2O \| 95% H2O/5% D2O	Resolution not provided
1WR6 Crystal structure of GGA3 GAT domain in complex with ubiquitin Deposited 2004-10-12	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 1–76（76 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；PEG3350, Ammonium formate, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.60 Å R-free 0.290
1WR6 Crystal structure of GGA3 GAT domain in complex with ubiquitin Deposited 2004-10-12	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 1–76（76 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；PEG3350, Ammonium formate, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.60 Å R-free 0.290
1WR6 Crystal structure of GGA3 GAT domain in complex with ubiquitin Deposited 2004-10-12	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 1–76（76 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；PEG3350, Ammonium formate, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.60 Å R-free 0.290
1WR6 Crystal structure of GGA3 GAT domain in complex with ubiquitin Deposited 2004-10-12	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 1–76（76 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；PEG3350, Ammonium formate, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.60 Å R-free 0.290
1WRD Crystal structure of Tom1 GAT domain in complex with ubiquitin Deposited 2004-10-14	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 6.5；293 K；sodium citrate, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.75 Å R-free 0.259
1WRD Crystal structure of Tom1 GAT domain in complex with ubiquitin Deposited 2004-10-14	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 48 PDB declaration: 48-meric	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 6.5；293 K；sodium citrate, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.75 Å R-free 0.259
1YD8 COMPLEX OF HUMAN GGA3 GAT DOMAIN AND UBIQUITIN Deposited 2004-12-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain U 1–76（76 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.80 Å R-free 0.297
1YD8 COMPLEX OF HUMAN GGA3 GAT DOMAIN AND UBIQUITIN Deposited 2004-12-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain V 1–76（76 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.80 Å R-free 0.297
2C7M Human Rabex-5 residues 1-74 in complex with Ubiquitin Deposited 2005-11-25	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	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；SITTING DROP 300 NL PLUS 300 NL 20 MG/ML PROTEIN SOLUTION 0.2 M LIS2SO4, 0.1 MES PH 6.5 25% PEG3350	Resolution 2.40 Å R-free 0.214
2C7N Human Rabex-5 residues 1-74 in complex with Ubiquitin Deposited 2005-11-25	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	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；SITTING DROP 300NL PLUS 300NL 0.2M AMMONIUM ACETATE 0.1M NACITRATE PH 6.5 25% PEG400	Resolution 2.10 Å R-free 0.238
2C7N Human Rabex-5 residues 1-74 in complex with Ubiquitin Deposited 2005-11-25	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–76（76 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；SITTING DROP 300NL PLUS 300NL 0.2M AMMONIUM ACETATE 0.1M NACITRATE PH 6.5 25% PEG400	Resolution 2.10 Å R-free 0.238
2C7N Human Rabex-5 residues 1-74 in complex with Ubiquitin Deposited 2005-11-25	Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 1–76（76 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；SITTING DROP 300NL PLUS 300NL 0.2M AMMONIUM ACETATE 0.1M NACITRATE PH 6.5 25% PEG400	Resolution 2.10 Å R-free 0.238
2C7N Human Rabex-5 residues 1-74 in complex with Ubiquitin Deposited 2005-11-25	Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 1–76（76 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；SITTING DROP 300NL PLUS 300NL 0.2M AMMONIUM ACETATE 0.1M NACITRATE PH 6.5 25% PEG400	Resolution 2.10 Å R-free 0.238
2C7N Human Rabex-5 residues 1-74 in complex with Ubiquitin Deposited 2005-11-25	Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain J 1–76（76 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；SITTING DROP 300NL PLUS 300NL 0.2M AMMONIUM ACETATE 0.1M NACITRATE PH 6.5 25% PEG400	Resolution 2.10 Å R-free 0.238
2C7N Human Rabex-5 residues 1-74 in complex with Ubiquitin Deposited 2005-11-25	Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 1–76（76 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；SITTING DROP 300NL PLUS 300NL 0.2M AMMONIUM ACETATE 0.1M NACITRATE PH 6.5 25% PEG400	Resolution 2.10 Å R-free 0.238
2D3G Double sided ubiquitin binding of Hrs-UIM Deposited 2005-09-28	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） 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 9.5；289 K；PEG400, CHES, pH 9.50, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 1.70 Å R-free 0.228
2DX5 The complex structure between the mouse EAP45-GLUE domain and ubiquitin Deposited 2006-08-24	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 7.5；277 K；18% PEG600, 0.1M HEPPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 3.35 Å R-free 0.329
2FID Crystal Structure of a Bovine Rabex-5 fragment complexed with ubiquitin Deposited 2005-12-29	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–76（76 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；295 K；20-25% PEG 4000, 0.2M lithium sulfate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.80 Å R-free 0.268
2OOB crystal structure of the UBA domain from Cbl-b ubiquitin ligase in complex with ubiquitin Deposited 2007-01-25	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 5；293 K；0.2M calcium chloride, 0.1M sodium acetate, 20% PEG6000, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.90 Å R-free 0.256
2QHO Crystal structure of the UBA domain from EDD ubiquitin ligase in complex with ubiquitin Deposited 2007-07-02	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–76（76 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；0.1M citric acid, 20% PEG 6000, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.85 Å R-free 0.258
2QHO Crystal structure of the UBA domain from EDD ubiquitin ligase in complex with ubiquitin Deposited 2007-07-02	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–76（76 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；0.1M citric acid, 20% PEG 6000, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.85 Å R-free 0.258
2QHO Crystal structure of the UBA domain from EDD ubiquitin ligase in complex with ubiquitin Deposited 2007-07-02	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 1–76（76 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；0.1M citric acid, 20% PEG 6000, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.85 Å R-free 0.258
2QHO Crystal structure of the UBA domain from EDD ubiquitin ligase in complex with ubiquitin Deposited 2007-07-02	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 1–76（76 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；0.1M citric acid, 20% PEG 6000, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.85 Å R-free 0.258
2WWZ TAB2 NZF DOMAIN IN COMPLEX WITH Lys63-linked di-ubiquitin, P212121 Deposited 2009-10-30	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–76（76 aa） Chain B 1–76（76 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.40 Å R-free 0.202
2WX0 TAB2 NZF DOMAIN IN COMPLEX WITH Lys63-linked di-ubiquitin, P21 Deposited 2009-10-30	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–76（76 aa） Chain B 1–76（76 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.40 Å R-free 0.236
2WX0 TAB2 NZF DOMAIN IN COMPLEX WITH Lys63-linked di-ubiquitin, P21 Deposited 2009-10-30	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 1–76（76 aa） Chain F 1–76（76 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.40 Å R-free 0.236
2WX1 TAB2 NZF DOMAIN IN COMPLEX WITH Lys63-linked tri-ubiquitin, P212121 Deposited 2009-10-30	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–76（76 aa） Chain B 1–76（76 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.00 Å R-free 0.269
3H1U Structure of ubiquitin in complex with Cd ions Deposited 2009-04-14	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	CD CADMIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；291.15 K；100mM HEPES pH 7.5, 50mm Cadmium sulfate, 1.0M Sodium citrate, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K	Resolution 3.00 Å R-free 0.257
3H1U Structure of ubiquitin in complex with Cd ions Deposited 2009-04-14	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	CD CADMIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；291.15 K；100mM HEPES pH 7.5, 50mm Cadmium sulfate, 1.0M Sodium citrate, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K	Resolution 3.00 Å R-free 0.257
3M3J A new crystal form of Lys48-linked diubiquitin Deposited 2010-03-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–76（76 aa） Chain B 1–76（76 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；30% PEG 4000, 0.2M lithium sulfate, 0.1 M Tris-HCl pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 1.60 Å R-free 0.229
3M3J A new crystal form of Lys48-linked diubiquitin Deposited 2010-03-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–76（76 aa） Chain D 1–76（76 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；30% PEG 4000, 0.2M lithium sulfate, 0.1 M Tris-HCl pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 1.60 Å R-free 0.229
3M3J A new crystal form of Lys48-linked diubiquitin Deposited 2010-03-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 1–76（76 aa） Chain F 1–76（76 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；30% PEG 4000, 0.2M lithium sulfate, 0.1 M Tris-HCl pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 1.60 Å R-free 0.229

19 other PDB entries and 37 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	UBIQ_BOVIN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–76； UniProt 1–76 Author chain C； PDBConstruct 1–76； UniProt 1–76 Author chain E； PDBConstruct 1–76； UniProt 1–76

Rab5 GDP/GTP exchange factor

Bos taurus

UniProt O18973

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 9–73	Fragment：A20 zinc finger and inverted ubiquitin interacting motif domains	Ubiquitin × 1 （P62990） SO4 SULFATE ION × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.6；295 K；20-25% PEG 4000, 0.2M lithium sulfate , pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.49 Å R-free 0.263
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 9–73	Fragment：A20 zinc finger and inverted ubiquitin interacting motif domains	Ubiquitin × 1 （P62990） ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.6；295 K；20-25% PEG 4000, 0.2M lithium sulfate , pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.49 Å R-free 0.263
3	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain F； UniProt 9–73	Fragment：A20 zinc finger and inverted ubiquitin interacting motif domains	Ubiquitin × 1 （P62990） ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.6；295 K；20-25% PEG 4000, 0.2M lithium sulfate , pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.49 Å R-free 0.263

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 2FIF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2FID Crystal Structure of a Bovine Rabex-5 fragment complexed with ubiquitin Deposited 2005-12-29	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 9–73（65 aa） Fragment：A20 zinc finger and inverted ubiquitin interacting motif domains	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；295 K；20-25% PEG 4000, 0.2M lithium sulfate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.80 Å R-free 0.268

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

View Construct and Data Evidence

UniProt name	RABX5_BOVIN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 6–70； UniProt 9–73 Author chain D； PDBConstruct 6–70； UniProt 9–73 Author chain F； PDBConstruct 6–70； UniProt 9–73

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	2fif
Deposition date deposition_date	2005-12-29
Structure title title	Crystal Structure of a Bovine Rabex-5 fragment complexed with ubiquitin
Keywords keywords	zinc finger, helix, PROTEIN TURNOVER-ENDOCYTOSIS COMPLEX; PROTEIN TURNOVER/ENDOCYTOSIS
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	31.05 Å
Radius of gyration Rg (electron density) rg_electron	30.54 Å
Forward intensity I(0) i0	36127900.00
Molecular weight molecular_weight	45814.0 kDa
Excluded volume excluded_volume	56924 Å³
Envelope volume envelope_volume	82586 Å³
Hydration-shell volume shell_volume	23764 Å³
Envelope diameter envelope_diameter	102.0 Å
Shell Rg shell_rg	35.87 Å
Envelope Rg envelope_rg	29.79 Å
Shape Rg shape_rg	30.54 Å
Total Rg total_rg	31.08 Å
Total atoms total_atoms	3209
Residues n_residues	392
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	100.2 Å
Rg (real space) rg_real	31.17 Å
Rg uncertainty (real space) rg_real_error	0.84 Å
I(0) (real space) i0_real	3.6130e+07
I(0) uncertainty (real space) i0_real_error	5.5730e+05
Rg (reciprocal space) rg_reciprocal	31.12 Å
I(0) (reciprocal space) i0_reciprocal	36130000.0000
Solution quality estimate total_estimate	0.8893
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	29.5 Å
Skewness Skewness skewness	0.282
Kurtosis Kurtosis kurtosis	-0.716
Angular range angular_range	— – 0.2550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2532000.0000
Real-space data points n_real_points	52
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.942; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.817; Smooth: 0.912

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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	Ubiquitin
Molecular weight formula_weight	8576.8 kDa
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E
Atom count atom_count	3228

MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG

Entity 2 Entity 2 polymer

Description description	Rab5 GDP/GTP exchange factor
Molecular weight formula_weight	8124.0 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,F

GAMGSGIHVDQSELLCKKGCGYYGNPAWQGFCSKCWREEYHKARQKQIQEDWELAERLQREEEEAFASSQ

来源 Source

来源生物 organism	Bos taurus
通用名 common_name	cattle
NCBI Class编号 ncbi_taxonomy_id	9913
宿主生物 host_organism	Escherichia coli BL21(DE3)

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	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	19

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d2fifa_
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	d2fifb_
Class class	g — Small proteins
Fold Fold fold	g.39 — Glucocorticoid receptor-like (DNA-binding domain)
Superfamily Superfamily superfamily	g.39.1 — Glucocorticoid receptor-like (DNA-binding domain)
Family Family family	g.39.1.15 — A20-like zinc finger

Domain ID domain_id	d2fifc_
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	d2fifd_
Class class	g — Small proteins
Fold Fold fold	g.39 — Glucocorticoid receptor-like (DNA-binding domain)
Superfamily Superfamily superfamily	g.39.1 — Glucocorticoid receptor-like (DNA-binding domain)
Family Family family	g.39.1.15 — A20-like zinc finger

Domain ID domain_id	d2fife_
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	d2fiff_
Class class	g — Small proteins
Fold Fold fold	g.39 — Glucocorticoid receptor-like (DNA-binding domain)
Superfamily Superfamily superfamily	g.39.1 — Glucocorticoid receptor-like (DNA-binding domain)
Family Family family	g.39.1.15 — A20-like zinc finger

CATH v4.4 (6 domains)

Domain ID domain_id	2fifA00
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

Domain ID domain_id	2fifB01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	4770 —

Domain ID domain_id	2fifC00
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

Domain ID domain_id	2fifD01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	4770 —

Domain ID domain_id	2fifE00
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

Domain ID domain_id	2fifF01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	4770 —

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8. Citations (1)

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Unit-cell length a length_a	192.200 Å
Unit-cell length b length_b	44.420 Å
Unit-cell length c length_c	69.170 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	108.98 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

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

Resolution resolution	2.490 Å
Low-resolution limit resolution_low	90.910 Å
R factor r_factor	0.2300
R_work r_work	0.2282
R_free r_free	0.2635

fit	/app/data/saxs_computation/fi/2fif/2fif.fit
pddf	/app/data/pr_computation/fi/2fif/2fif.pr.out
profile	/app/data/saxs_computation/fi/2fif/2fif.dat

Crystal Structure of a Bovine Rabex-5 fragment complexed with ubiquitin

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

Ubiquitin

State in the Current Structure

Other States of the Same Protein in the Database

Rab5 GDP/GTP exchange factor

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

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) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)