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2ec1

Solution structure of the RanBD1 domain from human Nucleoporin 50 kDa

Method: SOLUTION NMR Dmax: 52.2 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Nucleoporin 50 kDa

Homo sapiens

UniProt Q9UKX7

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 351–468 Fragment：RanBP domain No other associated polymer SOLUTION NMR NMR measurement conditions：pH 7；298 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient NMR sample composition：1.14 mM 13C, 15N-labeled protein; 20mM d-Tris-HCl(pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O | 90% H2O/10% D2O Resolution not provided

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 2EC1 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3TJ3 Structure of importin a5 bound to the N-terminus of Nup50 Deposited 2011-08-23 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–109（109 aa） Fragment：N-terminal domain (UNP residues 1-109)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；24% PEG3350, 100 mM Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.70 Å R-free 0.255
3TJ3 Structure of importin a5 bound to the N-terminus of Nup50 Deposited 2011-08-23 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–109（109 aa） Fragment：N-terminal domain (UNP residues 1-109)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；24% PEG3350, 100 mM Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.70 Å R-free 0.255
7MO0 Crystal Structure of Nucleoporin NUP50 Ran-Binding Domain in Complex with Ran-GPPNHP Deposited 2021-05-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 337–468（132 aa） Fragment：RAN-binding domain of NUP50 (UNP residues 337-468)
Non-standard monomer：Yes (specific site not provided by mmCIF) GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；25% w/v PEG3350, 0.2 M ammonium sulfate, 0.1 M HEPES
Resolution 2.45 Å R-free 0.239
7MO0 Crystal Structure of Nucleoporin NUP50 Ran-Binding Domain in Complex with Ran-GPPNHP Deposited 2021-05-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 337–468（132 aa） Fragment：RAN-binding domain of NUP50 (UNP residues 337-468)
Non-standard monomer：Yes (specific site not provided by mmCIF) GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；25% w/v PEG3350, 0.2 M ammonium sulfate, 0.1 M HEPES
Resolution 2.45 Å R-free 0.239

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

View Construct and Data Evidence
UniProt name NUP50_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 8–125； UniProt 351–468

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 2ec1

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2ec1
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2ec1
Deposition date deposition_date2007-02-09
Structure title titleSolution structure of the RanBD1 domain from human Nucleoporin 50 kDa
Keywords keywords;RanBP domain, Nucleoporin 50 kDa, Nuclear pore-associated protein 60 kDa-like, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, TRANSPORT PROTEIN ;; TRANSPORT PROTEIN
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier14.82 Å
Radius of gyration Rg (electron density) rg_electron14.31 Å
Forward intensity I(0) i0920251000.00
Molecular weight molecular_weight266370.0 kDa
Excluded volume excluded_volume338040 ų
Envelope volume envelope_volume32834 ų
Hydration-shell volume shell_volume16449 ų
Envelope diameter envelope_diameter61.9 Å
Shell Rg shell_rg22.98 Å
Envelope Rg envelope_rg17.29 Å
Shape Rg shape_rg14.32 Å
Total Rg total_rg14.47 Å
Total atoms total_atoms38240
Residues n_residues2360
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 dmax52.2 Å
Rg (real space) rg_real14.73 Å
Rg uncertainty (real space) rg_real_error0.43 Å
I(0) (real space) i0_real9.2030e+08
I(0) uncertainty (real space) i0_real_error1.0260e+07
Rg (reciprocal space) rg_reciprocal14.74 Å
I(0) (reciprocal space) i0_reciprocal920300000.0000
Solution quality estimate total_estimate0.7601
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary19.2 Å
Skewness Skewness skewness0.113
Kurtosis Kurtosis kurtosis-0.134
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha231300.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.628; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.000
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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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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id2ec1A00
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology29 — PH-domain like
Homologous superfamily homologous superfamily30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)
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8. Citations (1)

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9. Files and Curves (10)