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7mnj

Crystal structure of the N-terminal domain of NUP358/RanBP2 (residues 145-673)

Method: X-RAY DIFFRACTION Dmax: 125.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

E3 SUMO-protein ligase RanBP2

Homo sapiens

UniProt P49792

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 145–673 Not recorded No other associated polymer 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
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 145–673 Not recorded No other associated polymer 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
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain C； UniProt 145–673 Not recorded No other associated polymer 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

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 7MNJ 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 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 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 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 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 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 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
4I9Y Structure of the C-terminal domain of Nup358 Deposited 2012-12-05 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 3062–3224（163 aa）
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
4I9Y Structure of the C-terminal domain of Nup358 Deposited 2012-12-05 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 3062–3224（163 aa）
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
4I9Y Structure of the C-terminal domain of Nup358 Deposited 2012-12-05 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 3062–3224（163 aa）
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
4I9Y Structure of the C-terminal domain of Nup358 Deposited 2012-12-05 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 3062–3224（163 aa）
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
4I9Y Structure of the C-terminal domain of Nup358 Deposited 2012-12-05 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain E 3062–3224（163 aa）
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
4I9Y Structure of the C-terminal domain of Nup358 Deposited 2012-12-05 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain F 3062–3224（163 aa）
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
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 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 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 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
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 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 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 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 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 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 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 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 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 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 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 66 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 1–529； UniProt 145–673 Author chain B； PDBConstruct 1–529； UniProt 145–673 Author chain C； PDBConstruct 1–529； UniProt 145–673

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 7mnj

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7mnj
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7mnj
Deposition date deposition_date2021-05-01
Structure title titleCrystal structure of the N-terminal domain of NUP358/RanBP2 (residues 145-673)
Keywords keywordsNUCLEAR PORE COMPLEX COMPONENT, NUCLEOCYTOPLASMIC TRANSPORT, TRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier38.30 Å
Radius of gyration Rg (electron density) rg_electron37.70 Å
Forward intensity I(0) i0484299000.00
Molecular weight molecular_weight180240.0 kDa
Excluded volume excluded_volume226190 ų
Envelope volume envelope_volume295860 ų
Hydration-shell volume shell_volume64101 ų
Envelope diameter envelope_diameter125.5 Å
Shell Rg shell_rg44.65 Å
Envelope Rg envelope_rg37.33 Å
Shape Rg shape_rg37.71 Å
Total Rg total_rg38.09 Å
Total atoms total_atoms25365
Residues n_residues1586
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax125.4 Å
Rg (real space) rg_real38.17 Å
Rg uncertainty (real space) rg_real_error0.84 Å
I(0) (real space) i0_real4.8430e+08
I(0) uncertainty (real space) i0_real_error8.4930e+06
Rg (reciprocal space) rg_reciprocal38.25 Å
I(0) (reciprocal space) i0_reciprocal484300000.0000
Solution quality estimate total_estimate0.8851
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary48.9 Å
Skewness Skewness skewness0.267
Kurtosis Kurtosis kurtosis-0.369
Angular range angular_range— – 0.2050 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha114500000.0000
Real-space data points n_real_points42
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.866; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.908
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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8. Citations (1)

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9. Files and Curves (10)