SAXSdb — 5cxt

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

RNA-binding protein 39

Mus musculus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Splicing factor U2AF 65 kDa subunit × 1 （P26369） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Splicing factor U2AF 65 kDa subunit × 1 （P26369） water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Splicing factor U2AF 65 kDa subunit × 1 （P26369） water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Splicing factor U2AF 65 kDa subunit × 1 （P26369） water × 2	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 2	Splicing factor U2AF 65 kDa subunit × 1 （P26369） water × 2	Consistent with protein count
6	Protein heterocomplex	Heteromer	Protein 2	Splicing factor U2AF 65 kDa subunit × 1 （P26369） water × 2	Consistent with protein count
7	Protein heterocomplex	Heteromer	Protein 2	Splicing factor U2AF 65 kDa subunit × 1 （P26369） water × 2	Consistent with protein count
8	Protein heterocomplex	Heteromer	Protein 2	Splicing factor U2AF 65 kDa subunit × 1 （P26369） water × 2	Consistent with protein count
9	Protein heterocomplex	Heteromer	Protein 2	Splicing factor U2AF 65 kDa subunit × 1 （P26369） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RBM39_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–114； UniProt 418–530 Author chain C； PDBConstruct 2–114； UniProt 418–530 Author chain E； PDBConstruct 2–114； UniProt 418–530 Author chain G； PDBConstruct 2–114； UniProt 418–530 Author chain I； PDBConstruct 2–114； UniProt 418–530 Author chain K； PDBConstruct 2–114； UniProt 418–530 Author chain M； PDBConstruct 2–114； UniProt 418–530 Author chain O； PDBConstruct 2–114； UniProt 418–530 Author chain Q； PDBConstruct 2–114； UniProt 418–530

Splicing factor U2AF 65 kDa subunit

Mus musculus

UniProt P26369

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	RNA-binding protein 39 × 1 （Q8VH51） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	RNA-binding protein 39 × 1 （Q8VH51） water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	RNA-binding protein 39 × 1 （Q8VH51） water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	RNA-binding protein 39 × 1 （Q8VH51） water × 2	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 2	RNA-binding protein 39 × 1 （Q8VH51） water × 2	Consistent with protein count
6	Protein heterocomplex	Heteromer	Protein 2	RNA-binding protein 39 × 1 （Q8VH51） water × 2	Consistent with protein count
7	Protein heterocomplex	Heteromer	Protein 2	RNA-binding protein 39 × 1 （Q8VH51） water × 2	Consistent with protein count
8	Protein heterocomplex	Heteromer	Protein 2	RNA-binding protein 39 × 1 （Q8VH51） water × 2	Consistent with protein count
9	Protein heterocomplex	Heteromer	Protein 2	RNA-binding protein 39 × 1 （Q8VH51） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	U2AF2_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 2–29； UniProt 85–112 Author chain D； PDBConstruct 2–29； UniProt 85–112 Author chain F； PDBConstruct 2–29； UniProt 85–112 Author chain H； PDBConstruct 2–29； UniProt 85–112 Author chain J； PDBConstruct 2–29； UniProt 85–112 Author chain L； PDBConstruct 2–29； UniProt 85–112 Author chain N； PDBConstruct 2–29； UniProt 85–112 Author chain P； PDBConstruct 2–29； UniProt 85–112 Author chain R； PDBConstruct 2–29； UniProt 85–112

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	5cxt
Deposition date deposition_date	2015-07-29
Structure title title	Crystal structure of a RNA-binding protein 39 (RBM39) in complex with fragment of splicing factor (U2AF) from Unknown at 2.20 A resolution
Keywords keywords	;RBM39linker (PF15519), RNA recognition motif (PF13893), Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-BIOLOGY, RNA BINDING PROTEIN, Partnership for T-Cell Biology, TCELL ;; RNA BINDING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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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.

5cxt__assembly_1__model_1

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

Download this curve (.dat)

5cxt__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5cxt__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	14.74 Å
Rg (electron density)	13.62 Å
Total Rg	14.91 Å
Atom count	940
Residues	120
Excluded volume	16759 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5cxt__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5cxt__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`5cxt__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`5cxt__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`5cxt__assembly_5__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`5cxt__assembly_6__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`5cxt__assembly_7__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
8	1	`5cxt__assembly_8__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
9	1	`5cxt__assembly_9__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	RNA-binding protein 39
Molecular weight formula_weight	12622.3 kDa
Mutation mutation	N468Y
Source method src_method	man
Copy count entity_count	9

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G,I,K,M,O,Q
Atom count atom_count	9144

GVQPLATQCFQLSNMFNPQTEEEVGWDTEIKDDVIEECNKHGGVIHIYVDKYSAQGNVYVKCPSIAAAIAAVNALHGRWFAGKMITAAYVPLPTYHNLFPDSMTATQLLVPSRR

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 polymer

Description description	Splicing factor U2AF 65 kDa subunit
Molecular weight formula_weight	3439.1 kDa
Source method src_method	man
Copy count entity_count	9

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,F,H,J,L,N,P,R

GKKKVRKYWDVPPPGFEHITPMQYKAMQA

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 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	518

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6. Fold Classification (SCOP + CATH) 9 domains

CATH v4.4 (9 domains)

Domain ID domain_id	5cxtA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	330 — RRM (RNA recognition motif) domain

Domain ID domain_id	5cxtC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	330 — RRM (RNA recognition motif) domain

Domain ID domain_id	5cxtE00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	330 — RRM (RNA recognition motif) domain

Domain ID domain_id	5cxtG00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	330 — RRM (RNA recognition motif) domain

Domain ID domain_id	5cxtI00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	330 — RRM (RNA recognition motif) domain

Domain ID domain_id	5cxtK00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	330 — RRM (RNA recognition motif) domain

Domain ID domain_id	5cxtM00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	330 — RRM (RNA recognition motif) domain

Domain ID domain_id	5cxtO00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	330 — RRM (RNA recognition motif) domain

Domain ID domain_id	5cxtQ00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	330 — RRM (RNA recognition motif) domain

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Unit-cell length a length_a	127.283 Å
Unit-cell length b length_b	127.283 Å
Unit-cell length c length_c	78.864 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	27

Space group space_group	P 32
Space-group number int_tables_number	145
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	39.432 Å
R factor r_factor	0.1751
R_work r_work	0.1744
R_free r_free	0.1897

Crystal structure of a RNA-binding protein 39 (RBM39) in complex with fragment of splicing factor (U2AF) from Unknown at 2.20 A resolution

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

RNA-binding protein 39

State in the Current Structure

Other States of the Same Protein in the Database

Splicing factor U2AF 65 kDa subunit

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

5cxt__assembly_1__model_1

5cxt__assembly_1__model_1 | I(q)

5cxt__assembly_1__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 9 domains

CATH v4.4 (9 domains)

7. Citations (1)

Crystal structure of a RNA-binding protein 39 (RBM39) in complex with fragment of splicing factor (U2AF) from Unknown at 2.20 A resolution

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

RNA-binding protein 39

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Splicing factor U2AF 65 kDa subunit

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

5cxt__assembly_1__model_1

5cxt__assembly_1__model_1 | I(q)

5cxt__assembly_1__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 9 domains

CATH v4.4 (9 domains)

7. Citations (1)