SAXSdb — 5jiu

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

Ran-binding protein 9

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 108–350 Chain B； UniProt 108–350	Fragment：UNP RESIDUES 108-350	Probable ATP-dependent RNA helicase DDX4 × 2 （Q61496） CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；20~25% (w/v) PEG 3350, 0.1 M Bis-Tris, pH 6.5, 0.2 M NaCl	Resolution 2.05 Å R-free 0.203

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 5JIU	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5JI7 The Crystal Structure Of IUS-SPRY Domain From RanBPM/9 Deposited 2016-04-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 108–350（243 aa） Fragment：IUS-SPRY DOMAIN, UNP RESIDUES 108-350	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；0.1M NA-CACODYLATE, PH 6.5, 6% PEG 4000, 0.2M KCL, 0.02M MGCL2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K	Resolution 1.51 Å R-free 0.191
5JI9 The Crystal Structure Of IUS-SPRY Domain From RanBPM/9 Deposited 2016-04-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 108–350（243 aa） Fragment：IUS-SPRY DOMAIN, UNP RESIDUES 108-350	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；0.1M NA-CACODYLATE, PH 6.5, 6% PEG 4000, 0.2M KCL, 0.02M MGCL2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K	Resolution 2.50 Å R-free 0.227
7NSC Substrate receptor scaffolding module of human CTLH E3 ubiquitin ligase Deposited 2021-03-05	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–729（729 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RANB9_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–243； UniProt 108–350 Author chain B； PDBConstruct 1–243； UniProt 108–350

Probable ATP-dependent RNA helicase DDX4

OrganismNot specified

UniProt Q61496

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain C； UniProt 201–220 Chain D； UniProt 201–220	Fragment：UNP RESIDUES 201-220	Ran-binding protein 9 × 2 （Q96S59） CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；20~25% (w/v) PEG 3350, 0.1 M Bis-Tris, pH 6.5, 0.2 M NaCl	Resolution 2.05 Å R-free 0.203

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	DDX4_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–20； UniProt 201–220 Author chain D； PDBConstruct 1–20； UniProt 201–220

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	5jiu
Deposition date deposition_date	2016-04-22
Structure title title	The crystal structure of RanBPM/9 IUS-SPRY domain in complex with DDX-4 peptide
Keywords keywords	beta sandwich, Ran binding protein, TRANSPORT PROTEIN, RAN BINDING PROTEIN-PEPTIDE complex; RAN BINDING PROTEIN/PEPTIDE
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	26.81 Å
Radius of gyration Rg (electron density) rg_electron	26.27 Å
Forward intensity I(0) i0	40430400.00
Molecular weight molecular_weight	48003.0 kDa
Excluded volume excluded_volume	59373 Å³
Envelope volume envelope_volume	69733 Å³
Hydration-shell volume shell_volume	23510 Å³
Envelope diameter envelope_diameter	90.5 Å
Shell Rg shell_rg	31.76 Å
Envelope Rg envelope_rg	26.16 Å
Shape Rg shape_rg	26.29 Å
Total Rg total_rg	26.81 Å
Total atoms total_atoms	3384
Residues n_residues	430
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	87.8 Å
Rg (real space) rg_real	27.04 Å
Rg uncertainty (real space) rg_real_error	0.67 Å
I(0) (real space) i0_real	4.0430e+07
I(0) uncertainty (real space) i0_real_error	5.8180e+05
Rg (reciprocal space) rg_reciprocal	26.97 Å
I(0) (reciprocal space) i0_reciprocal	40430000.0000
Solution quality estimate total_estimate	0.8316
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.8 Å
Skewness Skewness skewness	0.474
Kurtosis Kurtosis kurtosis	-0.560
Angular range angular_range	— – 0.2950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	13830000.0000
Real-space data points n_real_points	60
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.742; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.712; Smooth: 0.868

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Ran-binding protein 9
Molecular weight formula_weight	26344.5 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	3660

LAAGPGPAGGAPTPALVAGSSAAAPFPHGDSALNEQEKELQRRLKRLYPAVDEQETPLPRSWSPKDKFSYIGLSQNNLRVHYKGHGKTPKDAASVRATHPIPAACGIYYFEVKIVSKGRDGYMGIGLSAQGVNMNRLPGWDKHSYGYHGDDGHSFCSSGTGQPYGPTFTTGDVIGCCVNLINNTCFYTKNGHSLGIAFTDLPPNLYPTVGLQTPGEVVDANFGQHPFVFDIEDYMREWRTKIQ

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	Probable ATP-dependent RNA helicase DDX4
Molecular weight formula_weight	2101.2 kDa
EC 编号 ec_number	3.6.4.13
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

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

KSETEGGESSDSQGPKVTYI

Entity 3 Entity 3 non-polymer

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

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	276

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	5jiuA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	920 — SPRY domain

Domain ID domain_id	5jiuB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	920 — SPRY domain

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8. Citations (1)

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Unit-cell length a length_a	123.318 Å
Unit-cell length b length_b	123.318 Å
Unit-cell length c length_c	91.986 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	I 4
Space-group number int_tables_number	79
Crystal system crystal_system	—

Resolution resolution	2.054 Å
Low-resolution limit resolution_low	32.058 Å
R factor r_factor	0.1678
R_work r_work	0.1661
R_free r_free	0.2025

fit	/app/data/saxs_computation/ji/5jiu/5jiu.fit
pddf	/app/data/pr_computation/ji/5jiu/5jiu.pr.out
profile	/app/data/saxs_computation/ji/5jiu/5jiu.dat

The crystal structure of RanBPM/9 IUS-SPRY domain in complex with DDX-4 peptide

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

Ran-binding protein 9

State in the Current Structure

Other States of the Same Protein in the Database

Probable ATP-dependent RNA helicase DDX4

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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 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)