4i9y

Structure of the C-terminal domain of Nup358

Method: X-RAY DIFFRACTION D_max: 115.0 Å Quality: EXCELLENT

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

E3 SUMO-protein ligase RanBP2

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 3062–3224	Not recorded	GOL GLYCEROL × 3 CL CHLORIDE ION × 1 TLA L(+)-TARTARIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.3；294 K；0.1 M TRIS-HCL, 0.2 M NaCl, 0.9 M K/Na Tartrate, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 1.75 Å R-free 0.158
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 3062–3224	Not recorded	GOL GLYCEROL × 5 CL CHLORIDE ION × 1 TLA L(+)-TARTARIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.3；294 K；0.1 M TRIS-HCL, 0.2 M NaCl, 0.9 M K/Na Tartrate, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 1.75 Å R-free 0.158
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 3062–3224	Not recorded	GOL GLYCEROL × 3 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.3；294 K；0.1 M TRIS-HCL, 0.2 M NaCl, 0.9 M K/Na Tartrate, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 1.75 Å R-free 0.158
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 3062–3224	Not recorded	GOL GLYCEROL × 5 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.3；294 K；0.1 M TRIS-HCL, 0.2 M NaCl, 0.9 M K/Na Tartrate, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 1.75 Å R-free 0.158
5	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain E； UniProt 3062–3224	Not recorded	GOL GLYCEROL × 2 CL CHLORIDE ION × 1 TLA L(+)-TARTARIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.3；294 K；0.1 M TRIS-HCL, 0.2 M NaCl, 0.9 M K/Na Tartrate, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 1.75 Å R-free 0.158
6	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain F； UniProt 3062–3224	Not recorded	GOL GLYCEROL × 3 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.3；294 K；0.1 M TRIS-HCL, 0.2 M NaCl, 0.9 M K/Na Tartrate, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 1.75 Å R-free 0.158

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 4I9Y	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1RRP STRUCTURE OF THE RAN-GPPNHP-RANBD1 COMPLEX Deposited 1999-01-15	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1171–1304（134 aa）	Not recorded	MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.25；pH 6.25	Resolution 2.96 Å R-free 0.304
1RRP STRUCTURE OF THE RAN-GPPNHP-RANBD1 COMPLEX Deposited 1999-01-15	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1171–1304（134 aa）	Not recorded	MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.25；pH 6.25	Resolution 2.96 Å R-free 0.304
1RRP STRUCTURE OF THE RAN-GPPNHP-RANBD1 COMPLEX Deposited 1999-01-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain B 1171–1304（134 aa） Chain D 1171–1304（134 aa）	Not recorded	MG MAGNESIUM ION × 4 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.25；pH 6.25	Resolution 2.96 Å R-free 0.304
1RRP STRUCTURE OF THE RAN-GPPNHP-RANBD1 COMPLEX Deposited 1999-01-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1171–1304（134 aa） Chain D 1171–1304（134 aa）	Not recorded	MG MAGNESIUM ION × 2 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.25；pH 6.25	Resolution 2.96 Å R-free 0.304
1XKE Solution structure of the second Ran-binding domain from human RanBP2 Deposited 2004-09-28	Different construct 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 2028–2154（127 aa） Fragment：Ran-binding domain 2 (RanBD2)	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 150 mM Na2SO4；Pressure ambient NMR sample composition 1.4mM RanBD2 U-13C; U-15N; 150mM Na2SO4; 10mM DTE; 0.5 mM EDTA; 1mM NaN3; 0.1mM DSS; 10mM potassium phosphate buffer at pH 6.5; \| 92% H2O, 8%D2O NMR sample composition 0.7mM RanBD2 U-13C; U-15N; 150mM Na2SO4; 10mM DTE; 0.5mM EDTA; 1mM NaN3; 0.1mM DSS; 10mM potassium phosphate buffer at pH 6.5; \| 100% D2O NMR sample composition 1.0mM RanBD2 U-15N; 150mM Na2SO4; 10mM DTE; 0.5mM EDTA; 1mM NaN3; 0.1 mM DSS; 10mM potassium phosphate buffer at pH 6.5; \| 92% H2O, 8%D2O NMR sample composition 1.0mM RanBD2 U-15N; 150mM Na2SO4; 10mM DTE; 0.5mM EDTA; 1mM NaN3; 0.1mM DSS; 10mM potassium phosphate buffer at pH 6.5; \| 100% D2O	Resolution not provided
1Z5S Crystal structure of a complex between UBC9, SUMO-1, RANGAP1 and NUP358/RANBP2 Deposited 2005-03-19	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 D 2631–2711（81 aa） Fragment：IR1-M domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；291 K；18% PEG4000 (w/v), 0.1 M sodium citrate, 0.2 M ammonium acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.01 Å R-free 0.290
3UIN Complex between human RanGAP1-SUMO2, UBC9 and the IR1 domain from RanBP2 Deposited 2011-11-05	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 D 2629–2695（67 aa） Fragment：UNP residues 2629-2695	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；279 K；100 mM HEPES pH 7.5, 400 mM ammonium citrate, 2% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 279K	Resolution 2.60 Å R-free 0.264
3UIO Complex between human RanGAP1-SUMO2, UBC9 and the IR1 domain from RanBP2 containing IR2 Motif II Deposited 2011-11-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 2631–2695（65 aa） Fragment：UNP residues 2631-2695	Mutation：A2642V, Q2644E, L2647K, T2649D, K2650T 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；279 K；14% PEG4000, 100 mM sodium citrate pH 6.0, 200 mM ammonium acetate, vapor diffusion, hanging drop, temperature 279K	Resolution 2.60 Å R-free 0.251
3UIP Complex between human RanGAP1-SUMO1, UBC9 and the IR1 domain from RanBP2 containing IR2 Motif II Deposited 2011-11-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 2631–2695（65 aa） Fragment：UNP residues 2631-2695	Mutation：A2642V, Q2644E, L2647K, T2649D, K2650T Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；279 K；22% PEG4000, 100 mM HEPES pH 7.5, 400 mM ammonium citrate, 2% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 279K	Resolution 2.29 Å R-free 0.232
4GA0 Structure of the N-terminal domain of Nup358 Deposited 2012-07-24	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–145（145 aa） Fragment：unp residues 1-145	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；18 % (w/v) PEG 3350 200 mM lithium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.15 Å R-free 0.239
4L6E Crystal Structure of the RanBD1 fourth domain of E3 SUMO-protein ligase RanBP2. Northeast Structural Genomics Consortium (NESG) Target HR9193b Deposited 2013-06-12	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2907–3050（144 aa） Fragment：RanBD1 4 domain (UNP residues 2907-3050)	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions Microbatch crystallization under oil；pH 7；277 K；12% PEG 3350, 0.1M sodium acetate, pH 7.00, Microbatch crystallization under oil, temperature 277K	Resolution 2.50 Å R-free 0.222
4LQW Crystal structure of HIV-1 capsid N-terminal domain in complex with NUP358 cyclophilin Deposited 2013-07-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 3057–3224（168 aa） Fragment：UNP Residues 3057-3224	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；290 K；23 % v/v PEG 4000, 23 % glycerol, 8.5 % isopropanol, 85 mM HEPES pH 7.5, 20 mM spermine tetrahydrochloride, 100 mM glycine, VAPOR DIFFUSION, SITTING DROP, temperature 290K	Resolution 1.95 Å R-free 0.246
4LQW Crystal structure of HIV-1 capsid N-terminal domain in complex with NUP358 cyclophilin Deposited 2013-07-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 3057–3224（168 aa） Fragment：UNP Residues 3057-3224	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；290 K；23 % v/v PEG 4000, 23 % glycerol, 8.5 % isopropanol, 85 mM HEPES pH 7.5, 20 mM spermine tetrahydrochloride, 100 mM glycine, VAPOR DIFFUSION, SITTING DROP, temperature 290K	Resolution 1.95 Å R-free 0.246
5CLL Truncated Ran wild type in complex with GDP-BeF and RanBD1 Deposited 2015-07-16	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1155–1321（167 aa） Fragment：Ran binding domain 1, residues 1155-1321	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.25；291 K；18 % PEG 4000, 250 mM ammonium sulfate, 100 mM MES pH 6.25, 1 mM BeF	Resolution 2.45 Å R-free 0.272
5CLL Truncated Ran wild type in complex with GDP-BeF and RanBD1 Deposited 2015-07-16	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1155–1321（167 aa） Fragment：Ran binding domain 1, residues 1155-1321	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.25；291 K；18 % PEG 4000, 250 mM ammonium sulfate, 100 mM MES pH 6.25, 1 mM BeF	Resolution 2.45 Å R-free 0.272
5CLQ Ran Y39A in complex with GPPNHP and RanBD1 Deposited 2015-07-16	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1155–1321（167 aa） Fragment：Ran binding domain 1, UNP residues 1155-1321	Not recorded	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；1.8M ammonium sulfate, 2.5% PEG 1500, 100 mM HEPES pH 7.5	Resolution 3.20 Å R-free 0.254
5CLQ Ran Y39A in complex with GPPNHP and RanBD1 Deposited 2015-07-16	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1155–1321（167 aa） Fragment：Ran binding domain 1, UNP residues 1155-1321	Not recorded	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；1.8M ammonium sulfate, 2.5% PEG 1500, 100 mM HEPES pH 7.5	Resolution 3.20 Å R-free 0.254
7MNJ Crystal structure of the N-terminal domain of NUP358/RanBP2 (residues 145-673) Deposited 2021-05-01	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 145–673（529 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；294 K；1% (w/v) PEG 2,000 MME; 0.8 M succinic acid; 0.1 M HEPES	Resolution 3.80 Å R-free 0.242
7MNJ Crystal structure of the N-terminal domain of NUP358/RanBP2 (residues 145-673) Deposited 2021-05-01	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 145–673（529 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；294 K；1% (w/v) PEG 2,000 MME; 0.8 M succinic acid; 0.1 M HEPES	Resolution 3.80 Å R-free 0.242
7MNJ Crystal structure of the N-terminal domain of NUP358/RanBP2 (residues 145-673) Deposited 2021-05-01	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 145–673（529 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；294 K；1% (w/v) PEG 2,000 MME; 0.8 M succinic acid; 0.1 M HEPES	Resolution 3.80 Å R-free 0.242
7MNK Crystal structure of the tetramerization element of NUP358/RanBP2 (residues 805-832) Deposited 2021-05-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 805–832（28 aa） Chain B 805–832（28 aa） Chain C 805–832（28 aa） Chain D 805–832（28 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 4 SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.5；294 K；2 M ammonium sulfate; 0.1 M citric acid	Resolution 1.10 Å R-free 0.167
7MNL Crystal structure of the N-terminal domain of NUP358/RanBP2 (residues 1-752) in complex with Fab fragment Deposited 2021-05-01	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 A 1–752（752 aa）	Mutation：I599M	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；294 K；3% (w/v) PEG 4,000; 0.15 M sodium acetate; 0.1 M sodium citrate	Resolution 3.95 Å R-free 0.241
7MNL Crystal structure of the N-terminal domain of NUP358/RanBP2 (residues 1-752) in complex with Fab fragment Deposited 2021-05-01	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 B 1–752（752 aa）	Mutation：I599M	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；294 K；3% (w/v) PEG 4,000; 0.15 M sodium acetate; 0.1 M sodium citrate	Resolution 3.95 Å R-free 0.241
7MNM Crystal structure of the N-terminal domain of NUP358/RanBP2 (residues 1-752) T585M mutant in complex with Fab fragment Deposited 2021-05-01	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 A 1–752（752 aa）	Mutation：I599M, T585M	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；294 K；2.5 % (w/v) PEG 4,000; 0.15 M sodium acetate; 0.1 M sodium citrate	Resolution 4.70 Å R-free 0.254
7MNM Crystal structure of the N-terminal domain of NUP358/RanBP2 (residues 1-752) T585M mutant in complex with Fab fragment Deposited 2021-05-01	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 B 1–752（752 aa）	Mutation：I599M, T585M	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；294 K；2.5 % (w/v) PEG 4,000; 0.15 M sodium acetate; 0.1 M sodium citrate	Resolution 4.70 Å R-free 0.254
7MNN Crystal structure of the N-terminal domain of NUP358/RanBP2 (residues 1-752) T653I mutant in complex with Fab fragment Deposited 2021-05-01	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 A 1–752（752 aa）	Mutation：I599M, T653I	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；294 K；4 (w/v) % PEG 4,000; 0.15 M sodium acetate; 0.1 M sodium citrate	Resolution 6.70 Å R-free 0.263
7MNN Crystal structure of the N-terminal domain of NUP358/RanBP2 (residues 1-752) T653I mutant in complex with Fab fragment Deposited 2021-05-01	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 B 1–752（752 aa）	Mutation：I599M, T653I	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；294 K；4 (w/v) % PEG 4,000; 0.15 M sodium acetate; 0.1 M sodium citrate	Resolution 6.70 Å R-free 0.263
7MNO Crystal structure of the N-terminal domain of NUP358/RanBP2 (residues 1-752) I656V mutant in complex with Fab fragment Deposited 2021-05-01	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 A 1–752（752 aa）	Mutation：I599M, I656V	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；294 K；3.5 % (w/v) PEG 4,000; 0.15 M sodium acetate; 0.1 M sodium citrate	Resolution 6.73 Å R-free 0.254
7MNO Crystal structure of the N-terminal domain of NUP358/RanBP2 (residues 1-752) I656V mutant in complex with Fab fragment Deposited 2021-05-01	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 B 1–752（752 aa）	Mutation：I599M, I656V	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；294 K；3.5 % (w/v) PEG 4,000; 0.15 M sodium acetate; 0.1 M sodium citrate	Resolution 6.73 Å R-free 0.254
7MNP Crystal Structure of the ZnF2 of Nucleoporin NUP358/RanBP2 in complex with Ran-GDP Deposited 2021-05-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1407–1443（37 aa）	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；294 K；17 % (w/v) PEG 3,350; 0.1M Bis-Tris	Resolution 2.05 Å R-free 0.231
7MNP Crystal Structure of the ZnF2 of Nucleoporin NUP358/RanBP2 in complex with Ran-GDP Deposited 2021-05-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1407–1443（37 aa）	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；294 K；17 % (w/v) PEG 3,350; 0.1M Bis-Tris	Resolution 2.05 Å R-free 0.231
7MNQ Crystal Structure of the ZnF2 of Nucleoporin NUP358/RanBP2 in complex with Ran-GDP Deposited 2021-05-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1407–1443（37 aa）	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；21% (w/v) PEG 3350; 0.1 M Bis-Tris	Resolution 2.05 Å R-free 0.208
7MNR Crystal Structure of the ZnF3 of Nucleoporin NUP358/RanBP2 in complex with Ran-GDP Deposited 2021-05-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1471–1507（37 aa）	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；19% (w/v) PEG 3350; 0.1 M Bis-Tris	Resolution 1.80 Å R-free 0.196
7MNS Crystal Structure of the ZnF4 of Nucleoporin NUP358/RanBP2 in complex with Ran-GDP Deposited 2021-05-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1535–1571（37 aa）	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；18 % (w/v) PEG 3,350; 0.1M Bis-Tris	Resolution 2.10 Å R-free 0.203
7MNT Crystal Structure of the ZnF5 or ZnF6 of Nucleoporin NUP358/RanBP2 in complex with Ran-GDP Deposited 2021-05-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1598–1634（37 aa）	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；19 % (w/v) PEG 3,350; 0.1M Bis-Tris	Resolution 2.45 Å R-free 0.257
7MNT Crystal Structure of the ZnF5 or ZnF6 of Nucleoporin NUP358/RanBP2 in complex with Ran-GDP Deposited 2021-05-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1598–1634（37 aa）	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；19 % (w/v) PEG 3,350; 0.1M Bis-Tris	Resolution 2.45 Å R-free 0.257
7MNU Crystal Structure of the ZnF7 of Nucleoporin NUP358/RanBP2 in complex with Ran-GDP Deposited 2021-05-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1716–1752（37 aa）	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；19% (w/v) PEG 3350; 0.1 M Bis-Tris	Resolution 2.00 Å R-free 0.224
7MNV Crystal Structure of the ZnF8 of Nucleoporin NUP358/RanBP2 in complex with Ran-GDP Deposited 2021-05-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1773–1809（37 aa）	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 1 GOL GLYCEROL × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.7；294 K；19% (w/v) PEG 3350; 0.1 M Bis-Tris	Resolution 1.80 Å R-free 0.185
7MNW Crystal Structure of Nup358/RanBP2 Ran-binding domain 1 in complex with Ran-GPPNHP Deposited 2021-05-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1171–1306（136 aa） Fragment：RAN-binding domain 1 of the E3 SUMO-PROTEIN LIGASE RANBP2 (UNP residues 1171-1306)	Not recorded	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；20% w/v PEG3350, 0.2 M potassium sodium tartrate tetrahydrate	Resolution 2.40 Å R-free 0.242
7MNW Crystal Structure of Nup358/RanBP2 Ran-binding domain 1 in complex with Ran-GPPNHP Deposited 2021-05-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1171–1306（136 aa） Fragment：RAN-binding domain 1 of the E3 SUMO-PROTEIN LIGASE RANBP2 (UNP residues 1171-1306)	Not recorded	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；20% w/v PEG3350, 0.2 M potassium sodium tartrate tetrahydrate	Resolution 2.40 Å R-free 0.242
7MNW Crystal Structure of Nup358/RanBP2 Ran-binding domain 1 in complex with Ran-GPPNHP Deposited 2021-05-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 1171–1306（136 aa） Fragment：RAN-binding domain 1 of the E3 SUMO-PROTEIN LIGASE RANBP2 (UNP residues 1171-1306)	Not recorded	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；20% w/v PEG3350, 0.2 M potassium sodium tartrate tetrahydrate	Resolution 2.40 Å R-free 0.242
7MNW Crystal Structure of Nup358/RanBP2 Ran-binding domain 1 in complex with Ran-GPPNHP Deposited 2021-05-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 1171–1306（136 aa） Fragment：RAN-binding domain 1 of the E3 SUMO-PROTEIN LIGASE RANBP2 (UNP residues 1171-1306)	Not recorded	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；20% w/v PEG3350, 0.2 M potassium sodium tartrate tetrahydrate	Resolution 2.40 Å R-free 0.242
7MNX Crystal Structure of Nup358/RanBP2 Ran-binding domain 2 in complex with Ran-GPPNHP Deposited 2021-05-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 2012–2148（137 aa） Fragment：RAN-binding domain 2 of the E3 SUMO-PROTEIN LIGASE RANBP2 (UNP residues 2012-2148)	Not recorded	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；294 K；15% w/v PEG3350, 0.125 M magnesium formate	Resolution 2.40 Å R-free 0.230
7MNX Crystal Structure of Nup358/RanBP2 Ran-binding domain 2 in complex with Ran-GPPNHP Deposited 2021-05-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 2012–2148（137 aa） Fragment：RAN-binding domain 2 of the E3 SUMO-PROTEIN LIGASE RANBP2 (UNP residues 2012-2148)	Not recorded	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；294 K；15% w/v PEG3350, 0.125 M magnesium formate	Resolution 2.40 Å R-free 0.230
7MNX Crystal Structure of Nup358/RanBP2 Ran-binding domain 2 in complex with Ran-GPPNHP Deposited 2021-05-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 2012–2148（137 aa） Fragment：RAN-binding domain 2 of the E3 SUMO-PROTEIN LIGASE RANBP2 (UNP residues 2012-2148)	Not recorded	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；294 K；15% w/v PEG3350, 0.125 M magnesium formate	Resolution 2.40 Å R-free 0.230
7MNX Crystal Structure of Nup358/RanBP2 Ran-binding domain 2 in complex with Ran-GPPNHP Deposited 2021-05-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 2012–2148（137 aa） Fragment：RAN-binding domain 2 of the E3 SUMO-PROTEIN LIGASE RANBP2 (UNP residues 2012-2148)	Not recorded	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；294 K；15% w/v PEG3350, 0.125 M magnesium formate	Resolution 2.40 Å R-free 0.230
7MNX Crystal Structure of Nup358/RanBP2 Ran-binding domain 2 in complex with Ran-GPPNHP Deposited 2021-05-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain J 2012–2148（137 aa） Fragment：RAN-binding domain 2 of the E3 SUMO-PROTEIN LIGASE RANBP2 (UNP residues 2012-2148)	Not recorded	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；294 K；15% w/v PEG3350, 0.125 M magnesium formate	Resolution 2.40 Å R-free 0.230
7MNX Crystal Structure of Nup358/RanBP2 Ran-binding domain 2 in complex with Ran-GPPNHP Deposited 2021-05-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 2012–2148（137 aa） Fragment：RAN-binding domain 2 of the E3 SUMO-PROTEIN LIGASE RANBP2 (UNP residues 2012-2148)	Not recorded	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；294 K；15% w/v PEG3350, 0.125 M magnesium formate	Resolution 2.40 Å R-free 0.230
7MNY Crystal Structure of Nup358/RanBP2 Ran-binding domain 3 in complex with Ran-GPPNHP Deposited 2021-05-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 2309–2443（135 aa） Fragment：RAN-binding domain 3 of the E3 SUMO-PROTEIN LIGASE RANBP2 (UNP residues 2309-2443)	Not recorded	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；294 K；20% w/v PEG3350, 0.2 M sodium formate	Resolution 2.70 Å R-free 0.262
7MNY Crystal Structure of Nup358/RanBP2 Ran-binding domain 3 in complex with Ran-GPPNHP Deposited 2021-05-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 2309–2443（135 aa） Fragment：RAN-binding domain 3 of the E3 SUMO-PROTEIN LIGASE RANBP2 (UNP residues 2309-2443)	Not recorded	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；294 K；20% w/v PEG3350, 0.2 M sodium formate	Resolution 2.70 Å R-free 0.262
7MNY Crystal Structure of Nup358/RanBP2 Ran-binding domain 3 in complex with Ran-GPPNHP Deposited 2021-05-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 2309–2443（135 aa） Fragment：RAN-binding domain 3 of the E3 SUMO-PROTEIN LIGASE RANBP2 (UNP residues 2309-2443)	Not recorded	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；294 K；20% w/v PEG3350, 0.2 M sodium formate	Resolution 2.70 Å R-free 0.262
7MNY Crystal Structure of Nup358/RanBP2 Ran-binding domain 3 in complex with Ran-GPPNHP Deposited 2021-05-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 2309–2443（135 aa） Fragment：RAN-binding domain 3 of the E3 SUMO-PROTEIN LIGASE RANBP2 (UNP residues 2309-2443)	Not recorded	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；294 K；20% w/v PEG3350, 0.2 M sodium formate	Resolution 2.70 Å R-free 0.262
7MNY Crystal Structure of Nup358/RanBP2 Ran-binding domain 3 in complex with Ran-GPPNHP Deposited 2021-05-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain J 2309–2443（135 aa） Fragment：RAN-binding domain 3 of the E3 SUMO-PROTEIN LIGASE RANBP2 (UNP residues 2309-2443)	Not recorded	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；294 K；20% w/v PEG3350, 0.2 M sodium formate	Resolution 2.70 Å R-free 0.262
7MNY Crystal Structure of Nup358/RanBP2 Ran-binding domain 3 in complex with Ran-GPPNHP Deposited 2021-05-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 2309–2443（135 aa） Fragment：RAN-binding domain 3 of the E3 SUMO-PROTEIN LIGASE RANBP2 (UNP residues 2309-2443)	Not recorded	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；294 K；20% w/v PEG3350, 0.2 M sodium formate	Resolution 2.70 Å R-free 0.262
7MNZ Crystal Structure of Nup358/RanBP2 Ran-binding domain 4 in complex with Ran-GPPNHP Deposited 2021-05-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 2911–3045（135 aa） Fragment：;RAN-binding domain 4 of the E3 SUMO-PROTEIN LIGASE RANBP2 (UNP residues 2911-3045), WHTMKNYY/QNYDNKQV mutant (UNP residues 2962-2969) ;	Mutation：W2962Q, H2963N, T2964Y, M2965D, K2966N, N2967K, Y2928Q, Y2969V	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；294 K；20% w/v PEG3350, 0.1 M ammonium sulfate, 0.1 M HEPES	Resolution 2.35 Å R-free 0.225
7MNZ Crystal Structure of Nup358/RanBP2 Ran-binding domain 4 in complex with Ran-GPPNHP Deposited 2021-05-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 2911–3045（135 aa） Fragment：;RAN-binding domain 4 of the E3 SUMO-PROTEIN LIGASE RANBP2 (UNP residues 2911-3045), WHTMKNYY/QNYDNKQV mutant (UNP residues 2962-2969) ;	Mutation：W2962Q, H2963N, T2964Y, M2965D, K2966N, N2967K, Y2928Q, Y2969V	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；294 K；20% w/v PEG3350, 0.1 M ammonium sulfate, 0.1 M HEPES	Resolution 2.35 Å R-free 0.225
7MNZ Crystal Structure of Nup358/RanBP2 Ran-binding domain 4 in complex with Ran-GPPNHP Deposited 2021-05-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 2911–3045（135 aa） Fragment：;RAN-binding domain 4 of the E3 SUMO-PROTEIN LIGASE RANBP2 (UNP residues 2911-3045), WHTMKNYY/QNYDNKQV mutant (UNP residues 2962-2969) ;	Mutation：W2962Q, H2963N, T2964Y, M2965D, K2966N, N2967K, Y2928Q, Y2969V	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；294 K；20% w/v PEG3350, 0.1 M ammonium sulfate, 0.1 M HEPES	Resolution 2.35 Å R-free 0.225
7MNZ Crystal Structure of Nup358/RanBP2 Ran-binding domain 4 in complex with Ran-GPPNHP Deposited 2021-05-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 2911–3045（135 aa） Fragment：;RAN-binding domain 4 of the E3 SUMO-PROTEIN LIGASE RANBP2 (UNP residues 2911-3045), WHTMKNYY/QNYDNKQV mutant (UNP residues 2962-2969) ;	Mutation：W2962Q, H2963N, T2964Y, M2965D, K2966N, N2967K, Y2928Q, Y2969V	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；294 K；20% w/v PEG3350, 0.1 M ammonium sulfate, 0.1 M HEPES	Resolution 2.35 Å R-free 0.225
7MNZ Crystal Structure of Nup358/RanBP2 Ran-binding domain 4 in complex with Ran-GPPNHP Deposited 2021-05-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain J 2911–3045（135 aa） Fragment：;RAN-binding domain 4 of the E3 SUMO-PROTEIN LIGASE RANBP2 (UNP residues 2911-3045), WHTMKNYY/QNYDNKQV mutant (UNP residues 2962-2969) ;	Mutation：W2962Q, H2963N, T2964Y, M2965D, K2966N, N2967K, Y2928Q, Y2969V	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；294 K；20% w/v PEG3350, 0.1 M ammonium sulfate, 0.1 M HEPES	Resolution 2.35 Å R-free 0.225
7MNZ Crystal Structure of Nup358/RanBP2 Ran-binding domain 4 in complex with Ran-GPPNHP Deposited 2021-05-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 2911–3045（135 aa） Fragment：;RAN-binding domain 4 of the E3 SUMO-PROTEIN LIGASE RANBP2 (UNP residues 2911-3045), WHTMKNYY/QNYDNKQV mutant (UNP residues 2962-2969) ;	Mutation：W2962Q, H2963N, T2964Y, M2965D, K2966N, N2967K, Y2928Q, Y2969V	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；294 K；20% w/v PEG3350, 0.1 M ammonium sulfate, 0.1 M HEPES	Resolution 2.35 Å R-free 0.225
7R5J Human nuclear pore complex (dilated) Deposited 2022-02-10	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 × 808 PDB declaration: 808-meric	Chain 00 1–3224（3224 aa） Chain 01 1–3224（3224 aa） Chain 02 1–3224（3224 aa） Chain 03 1–3224（3224 aa） Chain 04 1–3224（3224 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 50.00 Å
7R5K Human nuclear pore complex (constricted) Deposited 2022-02-10	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 × 808 PDB declaration: 808-meric	Chain 00 1–3224（3224 aa） Chain 01 1–3224（3224 aa） Chain 02 1–3224（3224 aa） Chain 03 1–3224（3224 aa） Chain 04 1–3224（3224 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 12.00 Å
9B62 Human RANBP2/RAN(GTP)/RANGAP1-SUMO1/UBC9/CRM1/RAN(GTP) - composite map and model Deposited 2024-03-23	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 E 2446–3060（615 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8；20 mM Tris-Cl pH 8.0, 50 mM NaCl, 0.1 mM TCEP supplemented with 0.02% (v/v) IGEPAL CA-630 cryo-EM vitrification conditions Cryogen ETHANE；30 s wait time, blot for 2.5 s before plunging	Resolution 2.90 Å

31 other PDB entries and 63 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RBP2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–167； UniProt 3062–3224 Author chain B； PDBConstruct 5–167； UniProt 3062–3224 Author chain C； PDBConstruct 5–167； UniProt 3062–3224 Author chain D； PDBConstruct 5–167； UniProt 3062–3224 Author chain E； PDBConstruct 5–167； UniProt 3062–3224 Author chain F； PDBConstruct 5–167； UniProt 3062–3224

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	4i9y
Deposition date deposition_date	2012-12-05
Structure title title	Structure of the C-terminal domain of Nup358
Keywords keywords	Nuclear Pore Complex, TRANSPORT PROTEIN; TRANSPORT PROTEIN
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	36.53 Å
Radius of gyration Rg (electron density) rg_electron	36.05 Å
Forward intensity I(0) i0	203393000.00
Molecular weight molecular_weight	112760.0 kDa
Excluded volume excluded_volume	139920 Å³
Envelope volume envelope_volume	178090 Å³
Hydration-shell volume shell_volume	42075 Å³
Envelope diameter envelope_diameter	119.9 Å
Shell Rg shell_rg	41.75 Å
Envelope Rg envelope_rg	35.58 Å
Shape Rg shape_rg	36.02 Å
Total Rg total_rg	36.49 Å
Total atoms total_atoms	15652
Residues n_residues	1002
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	115.0 Å
Rg (real space) rg_real	36.50 Å
Rg uncertainty (real space) rg_real_error	0.94 Å
I(0) (real space) i0_real	2.0340e+08
I(0) uncertainty (real space) i0_real_error	3.5610e+06
Rg (reciprocal space) rg_reciprocal	36.52 Å
I(0) (reciprocal space) i0_reciprocal	203400000.0000
Solution quality estimate total_estimate	0.9064
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	45.5 Å
Skewness Skewness skewness	0.191
Kurtosis Kurtosis kurtosis	-0.709
Angular range angular_range	— – 0.2150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	33660000.0000
Real-space data points n_real_points	44
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.954; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.970; Smooth: 0.947

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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	E3 SUMO-protein ligase RanBP2
Molecular weight formula_weight	18386.8 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	17923

GPHMTNPVVFFDVCADGEPLGRITMELFSNIVPRTAENFRALCTGEKGFGFKNSIFHRVIPDFVCQGGDITKHDGTGGQSIYGDKFEDENFDVKHTGPGLLSMANQGQNTNNSQFVITLKKAEHLDFKHVVFGFVKDGMDTVKKIESFGSPKGSVCRRITITECGQI

来源 Source

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

Entity 2 Entity 2 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	21

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

Description description	L(+)-TARTARIC ACID
Molecular weight formula_weight	150.1 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	1533

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7. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d4i9ya1
Class class	b — All beta proteins
Fold Fold fold	b.62 — Cyclophilin-like
Superfamily Superfamily superfamily	b.62.1 — Cyclophilin-like
Family Family family	b.62.1.1 — Cyclophilin (peptidylprolyl isomerase)

Domain ID domain_id	d4i9ya2
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

Domain ID domain_id	d4i9yb1
Class class	b — All beta proteins
Fold Fold fold	b.62 — Cyclophilin-like
Superfamily Superfamily superfamily	b.62.1 — Cyclophilin-like
Family Family family	b.62.1.1 — Cyclophilin (peptidylprolyl isomerase)

Domain ID domain_id	d4i9yb2
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

Domain ID domain_id	d4i9yc1
Class class	b — All beta proteins
Fold Fold fold	b.62 — Cyclophilin-like
Superfamily Superfamily superfamily	b.62.1 — Cyclophilin-like
Family Family family	b.62.1.1 — Cyclophilin (peptidylprolyl isomerase)

Domain ID domain_id	d4i9yc2
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

Domain ID domain_id	d4i9yd1
Class class	b — All beta proteins
Fold Fold fold	b.62 — Cyclophilin-like
Superfamily Superfamily superfamily	b.62.1 — Cyclophilin-like
Family Family family	b.62.1.1 — Cyclophilin (peptidylprolyl isomerase)

Domain ID domain_id	d4i9yd2
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

Domain ID domain_id	d4i9ye1
Class class	b — All beta proteins
Fold Fold fold	b.62 — Cyclophilin-like
Superfamily Superfamily superfamily	b.62.1 — Cyclophilin-like
Family Family family	b.62.1.1 — Cyclophilin (peptidylprolyl isomerase)

Domain ID domain_id	d4i9ye2
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

Domain ID domain_id	d4i9yf1
Class class	b — All beta proteins
Fold Fold fold	b.62 — Cyclophilin-like
Superfamily Superfamily superfamily	b.62.1 — Cyclophilin-like
Family Family family	b.62.1.1 — Cyclophilin (peptidylprolyl isomerase)

Domain ID domain_id	d4i9yf2
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 (6 domains)

Domain ID domain_id	4i9yA00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	100 — Cyclophilin
Homologous superfamily homologous superfamily	10 — Cyclophilin-like

Domain ID domain_id	4i9yB00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	100 — Cyclophilin
Homologous superfamily homologous superfamily	10 — Cyclophilin-like

Domain ID domain_id	4i9yC00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	100 — Cyclophilin
Homologous superfamily homologous superfamily	10 — Cyclophilin-like

Domain ID domain_id	4i9yD00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	100 — Cyclophilin
Homologous superfamily homologous superfamily	10 — Cyclophilin-like

Domain ID domain_id	4i9yE00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	100 — Cyclophilin
Homologous superfamily homologous superfamily	10 — Cyclophilin-like

Domain ID domain_id	4i9yF00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	100 — Cyclophilin
Homologous superfamily homologous superfamily	10 — Cyclophilin-like

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8. Citations (1)

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Unit-cell length a length_a	104.062 Å
Unit-cell length b length_b	97.132 Å
Unit-cell length c length_c	108.151 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	117.38 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.750 Å
Low-resolution limit resolution_low	48.566 Å
R factor r_factor	0.1248
R_work r_work	0.1230
R_free r_free	0.1576

fit	/app/data/saxs_computation/i9/4i9y/4i9y.fit
pddf	/app/data/pr_computation/i9/4i9y/4i9y.pr.out
profile	/app/data/saxs_computation/i9/4i9y/4i9y.dat