5jia

The Crystal Structure Of IUS-SPRY Domain From RanBP10

Method: X-RAY DIFFRACTION

▼

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

Ran-binding protein 10

Mus musculus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	IMIDAZOLE × 1 water × 1	Consistent with protein count
10	Protein monomer	Monomer	Protein 1	IMIDAZOLE × 1 water × 1	Consistent with protein count
11	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
12	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
13	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
14	Protein monomer	Monomer	Protein 1	IMIDAZOLE × 1 water × 1	Consistent with protein count
15	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
16	Protein monomer	Monomer	Protein 1	IMIDAZOLE × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	IMIDAZOLE × 1 water × 1	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	IMIDAZOLE × 1 water × 1	Consistent with protein count
6	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
7	Protein monomer	Monomer	Protein 1	IMIDAZOLE × 1 water × 1	Consistent with protein count
8	Protein monomer	Monomer	Protein 1	IMIDAZOLE × 1 water × 1	Consistent with protein count
9	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RBP10_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–210； UniProt 29–238 Author chain B； PDBConstruct 1–210； UniProt 29–238 Author chain C； PDBConstruct 1–210； UniProt 29–238 Author chain D； PDBConstruct 1–210； UniProt 29–238 Author chain E； PDBConstruct 1–210； UniProt 29–238 Author chain F； PDBConstruct 1–210； UniProt 29–238 Author chain G； PDBConstruct 1–210； UniProt 29–238 Author chain H； PDBConstruct 1–210； UniProt 29–238 Author chain I； PDBConstruct 1–210； UniProt 29–238 Author chain J； PDBConstruct 1–210； UniProt 29–238 Author chain K； PDBConstruct 1–210； UniProt 29–238 Author chain L； PDBConstruct 1–210； UniProt 29–238 Author chain M； PDBConstruct 1–210； UniProt 29–238 Author chain N； PDBConstruct 1–210； UniProt 29–238 Author chain O； PDBConstruct 1–210； UniProt 29–238 Author chain P； PDBConstruct 1–210； UniProt 29–238

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	5jia
Deposition date deposition_date	2016-04-22
Structure title title	The Crystal Structure Of IUS-SPRY Domain From RanBP10
Keywords keywords	BETA SANDWICH, TRANSPORT PROTEIN, RAN-BINDING PROTEIN; RAN-BINDING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

▼

3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

5jia__assembly_4__model_1

Assembly 4 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

5jia__assembly_4__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5jia__assembly_4__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	17.50 Å
Rg (electron density)	16.20 Å
Total Rg	17.26 Å
Atom count	1645
Residues	210
Excluded volume	28840 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5jia__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5jia__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`5jia__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`5jia__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`5jia__assembly_5__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`5jia__assembly_6__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`5jia__assembly_7__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
8	1	`5jia__assembly_8__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
9	1	`5jia__assembly_9__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
10	1	`5jia__assembly_10__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
11	1	`5jia__assembly_11__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
12	1	`5jia__assembly_12__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
13	1	`5jia__assembly_13__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
14	1	`5jia__assembly_14__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
15	1	`5jia__assembly_15__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
16	1	`5jia__assembly_16__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Ran-binding protein 10
Molecular weight formula_weight	23273.0 kDa
Source method src_method	man
Copy count entity_count	16

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P
Atom count atom_count	27983

SPGEQELSRRLQRLYPAVNQHETPLPRSWSPKDKYNYIGLSQGNLRVHYKGHGKNHKDAASVRATHPIPAACGIYYFEVKIVSKGRDGYMGIGLSAQGVNMNRLPGWDKHSYGYHGDDGHSFCSSGTGQPYGPTFTTGDVIGCCVNLINGTCFYTKNGHSLGIAFTDLPANLYPTVGLQTPGEIVDANFGQQPFLFDIEDYMREWRAKVQ

Source Source

Source organism organism	Mus musculus
Common name common_name	Mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	IMIDAZOLE
Molecular weight formula_weight	69.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	2321

▼

6. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

Domain ID domain_id	5jiaA00
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	5jiaB00
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	5jiaC00
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	5jiaD00
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	5jiaE00
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	5jiaF00
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	5jiaG00
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	5jiaH00
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	5jiaI00
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	5jiaJ00
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	5jiaK00
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	5jiaL00
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	5jiaM00
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	5jiaN00
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	5jiaO00
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	5jiaP00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	920 — SPRY domain

▶

Unit-cell length a length_a	146.340 Å
Unit-cell length b length_b	79.240 Å
Unit-cell length c length_c	157.630 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	97.91 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	32

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	41.250 Å
R factor r_factor	0.1840
R_work r_work	0.1840
R_free r_free	0.2270

The Crystal Structure Of IUS-SPRY Domain From RanBP10

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

Ran-binding protein 10

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5jia__assembly_4__model_1

5jia__assembly_4__model_1 | I(q)

5jia__assembly_4__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

7. Citations (1)

The Crystal Structure Of IUS-SPRY Domain From RanBP10

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

Ran-binding protein 10

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5jia__assembly_4__model_1

5jia__assembly_4__model_1 | I(q)

5jia__assembly_4__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

7. Citations (1)