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9yb5

Cryo-EM structure of human importin Beta:Ran-GDP:RanBP1 complex

Method: ELECTRON MICROSCOPY D_max: 101.2 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9yb5
deposition_date	2025-09-16
title	Cryo-EM structure of human importin Beta:Ran-GDP:RanBP1 complex
keywords	Importins, TRANSPORT PROTEIN, Ran, Ran binding protein; TRANSPORT PROTEIN
method	ELECTRON MICROSCOPY

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	31.83 Å
rg_electron	31.18 Å
i0	132105000.00
molecular_weight	91176.0 kDa
excluded_volume	114210 Å³
envelope_volume	149990 Å³
shell_volume	40355 Å³
envelope_diameter	105.4 Å
shell_rg	38.22 Å
envelope_rg	31.07 Å
shape_rg	31.18 Å
total_rg	31.81 Å
total_atoms	6402
n_residues	804
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	101.2 Å
rg_real	31.77 Å
rg_real_error	0.58 Å
i0_real	1.3210e+08
i0_real_error	1.8660e+06
rg_reciprocal	31.80 Å
i0_reciprocal	132100000.0000
total_estimate	0.9047
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	38.4 Å
skewness	0.254
kurtosis	-0.524
angular_range	— – 0.2500 Å⁻¹
current_alpha	0.0000
highest_alpha	28570000.0000
n_real_points	51
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.941; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.935

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Importin subunit beta-1
formula_weight	51071.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B
atom_count	6402

ELITILEKTVSPDRLELEAAQKFLERAAVENLPTFLVELSRVLANPGNSQVARVAAGLQIKNSLTSKDPDIKAQYQQRWLAIDANARREVKNYVLQTLGTETYRPSSASQCVAGIACAEIPVNQWPELIPQLVANVTNPNSTEHMKESTLEAIGYICQDIDPEQLQDKSNEILTAIIQGMRKEEPSNNVKLAATNALLNSLEFTKANFDKESERHFIMQVVCEATQCPDTRVRVAALQNLVKIMSLYYQYMETYMGPALFAITIEAMKSDIDEVALQGIEFWSNVCDEEMDLAIEASEAAEQGRPPEHTSKFYAKGALQYLVPILTQTLTKQDENDDDDDWNPCKAAGVCLMLLATCCEDDIVPHVLPFIKEHIKNPDWRYRDAAVMAFGCILEGPEPSQLKPLVIQAMPTLIELMKDPSVVVRDTAAWTVGRICELLPEAAINDVYLAPLLQCLIEG

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 polymer

description	GTP-binding nuclear protein Ran
formula_weight	23712.3 kDa
ec_number	3.6.5.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	D

AAQVQFKLVLVGDGGTGKTTFVKRHLTGEFEKKYVATLGVEVHPLVFHTNRGPIKFNVWDTAGQEKFGGLRDGYYIQAQCAIIMFDVTSRVTYKNVPNWHRDLVRVCENIPIVLCGNKVDIKDRKVKAKSIVFHRKKNLQYYDISAKSNYNFEKPFLWLARKLIGDPNLEFVAMPALAPPEVVMDPALAAQYEHDLEVAQTTALPDEDAA

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 3 polymer

description	Ran-specific GTPase-activating protein
formula_weight	16109.4 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

PDEQEIATLEEDEEELFCNRAKLFRFASENDLPEWKERGTGDVKLLKHKEKGAIRLLMRRDKTLKICANHYITPMMELKPNAGSDRAWVWNTHADFADECPKPELLAIRFLNAENAQKFKTKFEECRKEIEEREKK

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 4 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	GUANOSINE-5'-DIPHOSPHATE
formula_weight	443.2 kDa
src_method	syn
entity_count	1

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	3.200 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.20 Å
resolution_method	—
num_particles	241237

fit	/app/data/saxs_computation/yb/9yb5/9yb5.fit
pddf	/app/data/pr_computation/yb/9yb5/9yb5.pr.out
profile	/app/data/saxs_computation/yb/9yb5/9yb5.dat

Cryo-EM structure of human importin Beta:Ran-GDP:RanBP1 complex

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

EM 3D

5. Entities & Polymer Info (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 non-polymer

Entity 5 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)