SAXSdb — 3ibv

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

Exportin-T

Schizosaccharomyces pombe

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 1–978	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；100mM MES, pH6.5, 30% PEG400, 160mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.10 Å R-free 0.313
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–978	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；100mM MES, pH6.5, 30% PEG400, 160mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.10 Å R-free 0.313

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 3IBV	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3ICQ Karyopherin nuclear state Deposited 2009-07-18	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 2 PDB declaration: trimeric	Chain T 1–978（978 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；100mM Bis-Tris, pH5.5, 20% PEG3350, 180mM sodium acetate at 18 degrees, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.20 Å R-free 0.294
3ICQ Karyopherin nuclear state Deposited 2009-07-18	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–RNA Heteromer；Protein × 2 PDB declaration: trimeric	Chain U 1–978（978 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；100mM Bis-Tris, pH5.5, 20% PEG3350, 180mM sodium acetate at 18 degrees, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.20 Å R-free 0.294

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

View Construct and Data Evidence

UniProt name	XPOT_SCHPO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–980； UniProt 1–978 Author chain B； PDBConstruct 3–980； UniProt 1–978

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	3ibv
Deposition date deposition_date	2009-07-17
Structure title title	Karyopherin cytosolic state
Keywords keywords	karyopherin, exportin, HEAT repeat, Cytoplasm, Nucleus, RNA-binding, Transport, tRNA processing, tRNA-binding, RNA BINDING PROTEIN; RNA BINDING 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	56.58 Å
Radius of gyration Rg (electron density) rg_electron	55.77 Å
Forward intensity I(0) i0	479300000.00
Molecular weight molecular_weight	182150.0 kDa
Excluded volume excluded_volume	227600 Å³
Envelope volume envelope_volume	410890 Å³
Hydration-shell volume shell_volume	63175 Å³
Envelope diameter envelope_diameter	211.3 Å
Shell Rg shell_rg	54.43 Å
Envelope Rg envelope_rg	56.48 Å
Shape Rg shape_rg	55.91 Å
Total Rg total_rg	55.22 Å
Total atoms total_atoms	12876
Residues n_residues	1819
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	198.9 Å
Rg (real space) rg_real	56.94 Å
Rg uncertainty (real space) rg_real_error	2.87 Å
I(0) (real space) i0_real	4.7930e+08
I(0) uncertainty (real space) i0_real_error	1.0250e+07
Rg (reciprocal space) rg_reciprocal	56.28 Å
I(0) (reciprocal space) i0_reciprocal	478800000.0000
Solution quality estimate total_estimate	0.8419
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	63.9 Å
Skewness Skewness skewness	0.457
Kurtosis Kurtosis kurtosis	-0.115
Angular range angular_range	— – 0.1400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	16430000.0000
Real-space data points n_real_points	29
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.811; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.955; Smooth: 0.552

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Exportin-T
Molecular weight formula_weight	110354.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	12876

GPMSAQDVENAVEAALDPSVGPIIKQQATDFIGSLRSSSTGWKICHEIFSEKTKYKPSTRLICLQTLSEKVREWNNESNLLELQMIRDSVWSYIKELSFLDEPAYISNAVQHLLTLLFLQLYPSNWNDFFASLQGVIAASSQSEFSNFYLKVLLSIGDEIADSLVLKTDVQIQKDNLVKDAIRANDMSDIVSFVYEMMLAYSNAKNYGTVGLCLQVYAQWVSWININLIVNEPCMNLLYSFLQIEELRCAACETMTEIVNKKMKPLEKLNLLNILNLNLFFSKSQEQSTDPNFDEHVAKLINAQGVELVAIKSDPSELSPELKENCSFQLYNLFPYLIRYLSDDYDETSTAVFPFLSDLLVSLRKESSSKELSASLKEFLKSLLEAIIKKMKYDESQEWDDDPDSEEEAEFQEMRKKLKIFQDTINSIDSSLFSSYMYSAITSSLSTAATLSPENSWQLIEFALYETYIFGEGLRGPDAFFNEVDKSPTVLSQILALVTTSQVCRHPHPLVQLLYMEILVRYASFFDYESAAIPALIEYFVGPRGIHNTNERVRPRAWYLFYRFVKSIKKQVVNYTESSLAMLGDLLNISVSPVTDMDAPVPTLNSSIRNSDFNSQLYLFETVGVLISSGNLTPEEQALYCDSLINALIGKANAALSSDLSALENIISVYCSLMAIGNFAKGFPARGSEEVAWLASFNKASDEIFLILDRMGFNEDIRGAVRFTSGRIINVVGPDMLPKVPQLISILLNSIDMNELVDVLSFISQLIHIYKDNMMEITNRMLPTLLMRIFSSLSAAPQGTDDAVKQNDLRKSYISFILQLLNKGFGSILFTEENQVYFDPLINSILHFANLVGEPATQKSSIALVSKMVSLWGGKDGIAGFENFTLSLTPLCFEMPVNPNFNTRDGQSLVVLGELAGLQKIILEKLGDIYKSYLVTVYFPTVNFPDVMASEYLQALSNLDSRSFKQFFQKFIQALKSGNV

来源 Source

来源生物 organism	Schizosaccharomyces pombe
通用名 common_name	Fission yeast
NCBI Class编号 ncbi_taxonomy_id	4896
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	4

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3ibva_
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.1 — ARM repeat
Family Family family	a.118.1.19 — Exportin HEAT-like repeat

Domain ID domain_id	d3ibvb_
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.1 — ARM repeat
Family Family family	a.118.1.19 — Exportin HEAT-like repeat

CATH v4.4 (2 domains)

Domain ID domain_id	3ibvA00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	10 — Leucine-rich Repeat Variant
Homologous superfamily homologous superfamily	10 — Leucine-rich Repeat Variant

Domain ID domain_id	3ibvB00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	10 — Leucine-rich Repeat Variant
Homologous superfamily homologous superfamily	10 — Leucine-rich Repeat Variant

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8. Citations (1)

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Unit-cell length a length_a	119.900 Å
Unit-cell length b length_b	130.100 Å
Unit-cell length c length_c	173.900 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	8

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	3.100 Å
Low-resolution limit resolution_low	29.900 Å
R factor r_factor	—
R_work r_work	0.2750
R_free r_free	0.3130

fit	/app/data/saxs_computation/ib/3ibv/3ibv.fit
pddf	/app/data/pr_computation/ib/3ibv/3ibv.pr.out
profile	/app/data/saxs_computation/ib/3ibv/3ibv.dat

Karyopherin cytosolic state

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

Exportin-T

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