SAXSdb — 6b4f

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

Nucleoporin GLE1

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 383–698	Not recorded	Nucleoporin like 2 × 1 （Q3B7J4） CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；294 K；0.2 M sodium potassium phosphate pH 7.6, 26 % (w/v) PEG 3350	Resolution 2.81 Å R-free 0.274
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 383–698	Not recorded	Nucleoporin like 2 × 1 （Q3B7J4） PO4 PHOSPHATE ION × 2 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；294 K；0.2 M sodium potassium phosphate pH 7.6, 26 % (w/v) PEG 3350	Resolution 2.81 Å R-free 0.274

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 6B4F	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6B4I Crystal structure of human Gle1 CTD-Nup42 GBM-DDX19B(ADP) complex Deposited 2017-09-26	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 383–698（316 aa）	Not recorded	PO4 PHOSPHATE ION × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；13 % (w/v) PEG 3350, 0.2 M sodium potassium phosphate	Resolution 3.62 Å R-free 0.281
6B4I Crystal structure of human Gle1 CTD-Nup42 GBM-DDX19B(ADP) complex Deposited 2017-09-26	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 383–698（316 aa）	Not recorded	PO4 PHOSPHATE ION × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；13 % (w/v) PEG 3350, 0.2 M sodium potassium phosphate	Resolution 3.62 Å R-free 0.281
6B4J Crystal structure of human Gle1 CTD-Nup42 GBM-DDX19B(AMPPNP) complex Deposited 2017-09-26	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 383–698（316 aa）	Not recorded	PO4 PHOSPHATE ION × 4 MG MAGNESIUM ION × 1 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；15 % (w/v) PEG 3350, 0.3 M sodium potassium phosphate pH 6.6	Resolution 3.40 Å R-free 0.313
6B4J Crystal structure of human Gle1 CTD-Nup42 GBM-DDX19B(AMPPNP) complex Deposited 2017-09-26	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 383–698（316 aa）	Not recorded	PO4 PHOSPHATE ION × 2 MG MAGNESIUM ION × 1 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；15 % (w/v) PEG 3350, 0.3 M sodium potassium phosphate pH 6.6	Resolution 3.40 Å R-free 0.313

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

View Construct and Data Evidence

UniProt name	GLE1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–317； UniProt 383–698 Author chain B； PDBConstruct 2–317； UniProt 383–698

Nucleoporin like 2

Homo sapiens

UniProt Q3B7J4

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 381–423	Not recorded	Nucleoporin GLE1 × 1 （Q53GS7） CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；294 K；0.2 M sodium potassium phosphate pH 7.6, 26 % (w/v) PEG 3350	Resolution 2.81 Å R-free 0.274
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 381–423	Not recorded	Nucleoporin GLE1 × 1 （Q53GS7） PO4 PHOSPHATE ION × 2 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；294 K；0.2 M sodium potassium phosphate pH 7.6, 26 % (w/v) PEG 3350	Resolution 2.81 Å R-free 0.274

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 6B4F	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6B4I Crystal structure of human Gle1 CTD-Nup42 GBM-DDX19B(ADP) complex Deposited 2017-09-26	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 381–423（43 aa）	Not recorded	PO4 PHOSPHATE ION × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；13 % (w/v) PEG 3350, 0.2 M sodium potassium phosphate	Resolution 3.62 Å R-free 0.281
6B4I Crystal structure of human Gle1 CTD-Nup42 GBM-DDX19B(ADP) complex Deposited 2017-09-26	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 381–423（43 aa）	Not recorded	PO4 PHOSPHATE ION × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；13 % (w/v) PEG 3350, 0.2 M sodium potassium phosphate	Resolution 3.62 Å R-free 0.281

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

View Construct and Data Evidence

UniProt name	Q3B7J4_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 8–50； UniProt 381–423 Author chain D； PDBConstruct 8–50； UniProt 381–423

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	6b4f
Deposition date deposition_date	2017-09-26
Structure title title	Crystal structure of human Gle1 CTD-Nup42 GBM complex
Keywords keywords	Complex, Nuclear Pore Complex, mRNA export, DEAD-box helicase, 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	29.80 Å
Radius of gyration Rg (electron density) rg_electron	28.79 Å
Forward intensity I(0) i0	100996000.00
Molecular weight molecular_weight	82479.0 kDa
Excluded volume excluded_volume	104670 Å³
Envelope volume envelope_volume	132540 Å³
Hydration-shell volume shell_volume	37680 Å³
Envelope diameter envelope_diameter	101.3 Å
Shell Rg shell_rg	36.58 Å
Envelope Rg envelope_rg	29.08 Å
Shape Rg shape_rg	28.73 Å
Total Rg total_rg	29.77 Å
Total atoms total_atoms	11682
Residues n_residues	718
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	98.4 Å
Rg (real space) rg_real	29.76 Å
Rg uncertainty (real space) rg_real_error	0.69 Å
I(0) (real space) i0_real	1.0100e+08
I(0) uncertainty (real space) i0_real_error	1.4890e+06
Rg (reciprocal space) rg_reciprocal	29.78 Å
I(0) (reciprocal space) i0_reciprocal	101000000.0000
Solution quality estimate total_estimate	0.6871
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	33.4 Å
Skewness Skewness skewness	0.320
Kurtosis Kurtosis kurtosis	-0.343
Angular range angular_range	— – 0.2650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	24850000.0000
Real-space data points n_real_points	54
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.865; Stabil: 1.000; Sysdev: 0.135; Positv: 1.000; Valcen: 0.999; Smooth: 0.928

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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	Nucleoporin GLE1
Molecular weight formula_weight	36375.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,A
Atom count atom_count	11711

MQDITMQWYQQLQDASMQCVLTFEGLTNSKDSQAKKIKMDLQKAATIPVSQISTIAGSKLKEIFDKIHSLLSGKPVQSGGRSVSVTLNPQGLDFVQYKLAEKFVKQGEEEVASHHEAAFPIAVVASGIWELHPRVGDLILAHLHKKCPYSVPFYPTFKEGMALEDYQRMLGYQVKDSKVEQQDNFLKRMSGMIRLYAAIIQLRWPYGNRQEIHPHGLNHGWRWLAQILNMEPLSDVTATLLFDFLEVCGNALMKQYQVQFWKMLILIKEDYFPRIEAITSSGQMGSFIRLKQFLEKCLQHKDIPVPKGFLTSSFWRS

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 polymer

Description description	Nucleoporin like 2
Molecular weight formula_weight	5526.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

GPSGSIIATDNVLFTPRDKLTVEELEQFQSKKFTLGKIPLKPPPLELLNV

来源 Source

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

Entity 3 Entity 3 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	29

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8. Citations (1)

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Unit-cell length a length_a	164.660 Å
Unit-cell length b length_b	69.710 Å
Unit-cell length c length_c	93.570 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.66 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	2.811 Å
Low-resolution limit resolution_low	46.782 Å
R factor r_factor	0.2469
R_work r_work	0.2454
R_free r_free	0.2735

fit	/app/data/saxs_computation/b4/6b4f/6b4f.fit
pddf	/app/data/pr_computation/b4/6b4f/6b4f.pr.out
profile	/app/data/saxs_computation/b4/6b4f/6b4f.dat

Crystal structure of human Gle1 CTD-Nup42 GBM complex

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

Nucleoporin GLE1

State in the Current Structure

Other States of the Same Protein in the Database

Nucleoporin like 2

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)