SAXSdb — 6b4e

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

Nucleoporin GLE1

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

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 243–538	Not recorded	Nucleoporin NUP42 × 1 （P49686） PRO PROLINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；294 K；0.1 M HEPES pH 8.2, 11 % (w/v/) PEG 3350, 0.2 M L-Proline	Resolution 1.75 Å R-free 0.211
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 243–538	Not recorded	Nucleoporin NUP42 × 1 （P49686） EDO 1,2-ETHANEDIOL × 2 PRO PROLINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；294 K；0.1 M HEPES pH 8.2, 11 % (w/v/) PEG 3350, 0.2 M L-Proline	Resolution 1.75 Å R-free 0.211

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 6B4E	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3PEU S. cerevisiae Dbp5 L327V C-terminal domain bound to Gle1 H337R and IP6 Deposited 2010-10-27	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 244–538（295 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 1 GOL GLYCEROL × 3 IHP INOSITOL HEXAKISPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；30% PEG 3350, 100 mM HEPES pH 8.0, 50 mM NaOAc, 200mM LiS04, 10 mM HEPES pH 7.5, 100mM NaCl, 1mM DTT, 0.5 mM IP6, 5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.60 Å R-free 0.213
3PEU S. cerevisiae Dbp5 L327V C-terminal domain bound to Gle1 H337R and IP6 Deposited 2010-10-27	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 244–538（295 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 1 GOL GLYCEROL × 3 IHP INOSITOL HEXAKISPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；30% PEG 3350, 100 mM HEPES pH 8.0, 50 mM NaOAc, 200mM LiS04, 10 mM HEPES pH 7.5, 100mM NaCl, 1mM DTT, 0.5 mM IP6, 5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.60 Å R-free 0.213
3PEV S. cerevisiae Dbp5 L327V C-terminal domain bound to Gle1 and IP6 Deposited 2010-10-27	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 244–538（295 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 1 GOL GLYCEROL × 3 IHP INOSITOL HEXAKISPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；291 K；30% PEG 3350, 100 mM HEPES pH 7.8, 200mM LiS04, 10mM HEPES pH 7.5, 150mM NaCl, 1mM DTT, 0.5 mM IP6, 5% glycerol , VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.50 Å R-free 0.238
3PEV S. cerevisiae Dbp5 L327V C-terminal domain bound to Gle1 and IP6 Deposited 2010-10-27	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 244–538（295 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 1 GOL GLYCEROL × 3 IHP INOSITOL HEXAKISPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；291 K；30% PEG 3350, 100 mM HEPES pH 7.8, 200mM LiS04, 10mM HEPES pH 7.5, 150mM NaCl, 1mM DTT, 0.5 mM IP6, 5% glycerol , VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.50 Å R-free 0.238
3RRM S. cerevisiae dbp5 l327v bound to nup159, gle1 h337r, ip6 and adp Deposited 2011-04-29	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 B 244–538（295 aa） Fragment：unp residues 244-538	Mutation：H337R	ADP ADENOSINE-5'-DIPHOSPHATE × 1 IHP INOSITOL HEXAKISPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；20% PEG 3350, 200 mM KOAc, 20 mM sarcosine, 10 mM HEPES, 100 mM NaCl, 1 mM DTT, 0.5 mM IP6, 10 mM MgCl2, 1 mM ADP, 5% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.90 Å R-free 0.261
3RRN S. cerevisiae dbp5 l327v bound to gle1 h337r and ip6 Deposited 2011-04-29	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 244–538（295 aa） Fragment：unp residues 244-538	Mutation：H337R	ADP ADENOSINE-5'-DIPHOSPHATE × 1 IHP INOSITOL HEXAKISPHOSPHATE × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；30% PEG 300, 100mM MES, 2% MPD, 10 mM HEPES, 100 mM NaCl, 1 mM DTT, 0.5 mM IP6, 0.5 mM ADP, 5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291K, pH 6.5	Resolution 4.00 Å R-free 0.239

4 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	GLE1_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–296； UniProt 243–538 Author chain B； PDBConstruct 1–296； UniProt 243–538

Nucleoporin NUP42

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P49686

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 D； UniProt 397–430	Not recorded	Nucleoporin GLE1 × 1 （Q12315） PRO PROLINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；294 K；0.1 M HEPES pH 8.2, 11 % (w/v/) PEG 3350, 0.2 M L-Proline	Resolution 1.75 Å R-free 0.211
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 397–430	Not recorded	Nucleoporin GLE1 × 1 （Q12315） EDO 1,2-ETHANEDIOL × 2 PRO PROLINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；294 K；0.1 M HEPES pH 8.2, 11 % (w/v/) PEG 3350, 0.2 M L-Proline	Resolution 1.75 Å R-free 0.211

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	NUP42_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 6–39； UniProt 397–430 Author chain D； PDBConstruct 6–39； UniProt 397–430

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	6b4e
Deposition date deposition_date	2017-09-26
Structure title title	Crystal structure of Saccharomyces cerevisiae 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	30.50 Å
Radius of gyration Rg (electron density) rg_electron	30.01 Å
Forward intensity I(0) i0	85165600.00
Molecular weight molecular_weight	76246.0 kDa
Excluded volume excluded_volume	96967 Å³
Envelope volume envelope_volume	120390 Å³
Hydration-shell volume shell_volume	34403 Å³
Envelope diameter envelope_diameter	112.7 Å
Shell Rg shell_rg	36.17 Å
Envelope Rg envelope_rg	30.08 Å
Shape Rg shape_rg	30.00 Å
Total Rg total_rg	30.63 Å
Total atoms total_atoms	10861
Residues n_residues	662
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	108.4 Å
Rg (real space) rg_real	30.63 Å
Rg uncertainty (real space) rg_real_error	1.07 Å
I(0) (real space) i0_real	8.5170e+07
I(0) uncertainty (real space) i0_real_error	1.4660e+06
Rg (reciprocal space) rg_reciprocal	30.58 Å
I(0) (reciprocal space) i0_reciprocal	85160000.0000
Solution quality estimate total_estimate	0.8488
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	33.4 Å
Skewness Skewness skewness	0.501
Kurtosis Kurtosis kurtosis	-0.125
Angular range angular_range	— – 0.2600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	18310000.0000
Real-space data points n_real_points	53
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.728; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.885; Smooth: 0.962

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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	34258.7 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	14170

MTNFDKISKMFWHYKDKIAQIKQDIVLPIKKADVNVRNLLSRHKRKINPKFGQLTNSNQQLFKIQNELTQLINDTKGDSLAYHWILNFIAKAVVHQAETEVRVKPESALPLGKLTLYLLVQFPELQELFMARLVKKCPFVIGFTCEIDTEKGRQNMGWKRNNENKWEDNTSYDERMGGILSLFAIITRLQLPQEFITTTSHPFPIALSWHILARICNTPLNLITNTHFVILGSWWDAAAVQFLQAYGNQASKLLILIGEELTSRMAEKKYVGAARLRILLEAWQNNNMESFPEMSP

来源 Source

来源生物 organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
通用名 common_name	;Baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Nucleoporin NUP42
Molecular weight formula_weight	4076.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

GPSGSELADLAEETLKIFRANKFELGLVPDIPPPPALVA

来源 Source

来源生物 organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
通用名 common_name	;Baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	PROLINE
Molecular weight formula_weight	115.1 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	628

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	6b4eA00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	510 — GLE1-like

Domain ID domain_id	6b4eB00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	510 — GLE1-like

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8. Citations (1)

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Unit-cell length a length_a	67.470 Å
Unit-cell length b length_b	67.470 Å
Unit-cell length c length_c	361.651 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	1.750 Å
Low-resolution limit resolution_low	47.299 Å
R factor r_factor	0.1855
R_work r_work	0.1849
R_free r_free	0.2107

fit	/app/data/saxs_computation/b4/6b4e/6b4e.fit
pddf	/app/data/pr_computation/b4/6b4e/6b4e.pr.out
profile	/app/data/saxs_computation/b4/6b4e/6b4e.dat

Crystal structure of Saccharomyces cerevisiae 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 NUP42

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

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)