SAXSdb — 5xjr

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

Gem-associated protein 2

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	Small nuclear ribonucleoprotein Sm D1 × 1 （P62314） Small nuclear ribonucleoprotein Sm D2 × 1 （P62316） Small nuclear ribonucleoprotein E × 1 （P62304） Small nuclear ribonucleoprotein F × 1 （P62306） Small nuclear ribonucleoprotein G × 1 （P62308） Survival motor neuron protein × 1 （Q16637）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GEMI2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain 2； PDBConstruct 1–241； UniProt 40–280

Small nuclear ribonucleoprotein Sm D1

Homo sapiens

UniProt P62314

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	Gem-associated protein 2 × 1 （O14893） Small nuclear ribonucleoprotein Sm D2 × 1 （P62316） Small nuclear ribonucleoprotein E × 1 （P62304） Small nuclear ribonucleoprotein F × 1 （P62306） Small nuclear ribonucleoprotein G × 1 （P62308） Survival motor neuron protein × 1 （Q16637）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SMD1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–82； UniProt 1–82

Small nuclear ribonucleoprotein Sm D2

Homo sapiens

UniProt P62316

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	Gem-associated protein 2 × 1 （O14893） Small nuclear ribonucleoprotein Sm D1 × 1 （P62314） Small nuclear ribonucleoprotein E × 1 （P62304） Small nuclear ribonucleoprotein F × 1 （P62306） Small nuclear ribonucleoprotein G × 1 （P62308） Survival motor neuron protein × 1 （Q16637）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SMD2_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain B； PDBConstruct 1–118； UniProt 1–118

Small nuclear ribonucleoprotein E

Homo sapiens

UniProt P62304

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	Gem-associated protein 2 × 1 （O14893） Small nuclear ribonucleoprotein Sm D1 × 1 （P62314） Small nuclear ribonucleoprotein Sm D2 × 1 （P62316） Small nuclear ribonucleoprotein F × 1 （P62306） Small nuclear ribonucleoprotein G × 1 （P62308） Survival motor neuron protein × 1 （Q16637）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RUXE_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain E； PDBConstruct 1–92； UniProt 1–92

Small nuclear ribonucleoprotein F

Homo sapiens

UniProt P62306

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	Gem-associated protein 2 × 1 （O14893） Small nuclear ribonucleoprotein Sm D1 × 1 （P62314） Small nuclear ribonucleoprotein Sm D2 × 1 （P62316） Small nuclear ribonucleoprotein E × 1 （P62304） Small nuclear ribonucleoprotein G × 1 （P62308） Survival motor neuron protein × 1 （Q16637）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RUXF_HUMAN
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain F； PDBConstruct 1–86； UniProt 1–86

Small nuclear ribonucleoprotein G

Homo sapiens

UniProt P62308

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	Gem-associated protein 2 × 1 （O14893） Small nuclear ribonucleoprotein Sm D1 × 1 （P62314） Small nuclear ribonucleoprotein Sm D2 × 1 （P62316） Small nuclear ribonucleoprotein E × 1 （P62304） Small nuclear ribonucleoprotein F × 1 （P62306） Survival motor neuron protein × 1 （Q16637）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RUXG_HUMAN
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain G； PDBConstruct 1–76； UniProt 1–76

Survival motor neuron protein

Homo sapiens

UniProt Q16637

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 7	Gem-associated protein 2 × 1 （O14893） Small nuclear ribonucleoprotein Sm D1 × 1 （P62314） Small nuclear ribonucleoprotein Sm D2 × 1 （P62316） Small nuclear ribonucleoprotein E × 1 （P62304） Small nuclear ribonucleoprotein F × 1 （P62306） Small nuclear ribonucleoprotein G × 1 （P62308）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SMN_HUMAN
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain M； PDBConstruct 1–37； UniProt 26–62

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	5xjr
Deposition date deposition_date	2017-05-04
Structure title title	Crystal Structure of the Gemin2-binding domain of SMN, Gemin2dN39 in Complex with SmD1(1-82)/D2/F/E/G from Human
Keywords keywords	splicing; SPLICING
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.

5xjr__assembly_1__model_1

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

Download this curve (.dat)

5xjr__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5xjr__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.77 Å
Rg (electron density)	29.18 Å
Total Rg	29.76 Å
Atom count	4890
Residues	612
Excluded volume	87826 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5xjr__assembly_1__model_1`	heptameric （7）	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 (7)

Entity 1 Entity 1 polymer

Description description	Gem-associated protein 2
Molecular weight formula_weight	27323.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	2
Atom count atom_count	4890

FDPSVPPRTPQEYLRRVQIEAAQCPDVVVAQIDPKKLKRKQSVNISLSGCQPAPEGYSPTLQWQQQQVAQFSTVRQNVNKHRSHWKSQQLDSNVTMPKSEDEEGWKKFCLGEKLCADGAVGPATNESPGIDYVQIGFPPLLSIVSRMNQATVTSVLEYLSNWFGERDFTPELGRWLYALLACLEKPLLPEAHSLIRQLARRCSEVRLLVDSKDDERVPALNLLICLVSRYFDQRDLADEPS

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Small nuclear ribonucleoprotein Sm D1
Molecular weight formula_weight	9301.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

MKLVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRGNNIRYFILPDSLPLDTLLVD

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Small nuclear ribonucleoprotein Sm D2
Molecular weight formula_weight	13551.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MSLLNKPKSEMTPEELQKREEEEFNTGPLSVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEVPKSGKGKKKSKPVNKDRYISKMFLRGDSVIVVLRNPLIAGK

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	Small nuclear ribonucleoprotein E
Molecular weight formula_weight	10817.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

MAYRGQGQKVQKVMVQPINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEIHSKTKSRKQLGRIMLKGDNITLLQSVSN

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 polymer

Description description	Small nuclear ribonucleoprotein F
Molecular weight formula_weight	9734.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

MSLPLNPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGHLGEVLIRCNNVLYIRGVEEEEEDGEMRE

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 6 Entity 6 polymer

Description description	Small nuclear ribonucleoprotein G
Molecular weight formula_weight	8508.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

MSKAHPPELKKFMDKKLSLKLNGGRHVQGILRGFDPFMNLVIDECVEMATSGQQNNIGMVVIRGNSIIMLEALERV

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 7 Entity 7 polymer

Description description	Survival motor neuron protein
Molecular weight formula_weight	4047.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M

GQSDDSDIWDDTALIKAYDKAVASFKHALKNGDICET

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

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6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d5xjra_
Class class	b — All beta proteins
Fold Fold fold	b.38 — Sm-like fold
Superfamily Superfamily superfamily	b.38.1 — Sm-like ribonucleoproteins
Family Family family	b.38.1.1 — Sm motif of small nuclear ribonucleoproteins, SNRNP

Domain ID domain_id	d5xjrb_
Class class	b — All beta proteins
Fold Fold fold	b.38 — Sm-like fold
Superfamily Superfamily superfamily	b.38.1 — Sm-like ribonucleoproteins
Family Family family	b.38.1.1 — Sm motif of small nuclear ribonucleoproteins, SNRNP

Domain ID domain_id	d5xjre_
Class class	b — All beta proteins
Fold Fold fold	b.38 — Sm-like fold
Superfamily Superfamily superfamily	b.38.1 — Sm-like ribonucleoproteins
Family Family family	b.38.1.0 — automated matches

Domain ID domain_id	d5xjrf_
Class class	b — All beta proteins
Fold Fold fold	b.38 — Sm-like fold
Superfamily Superfamily superfamily	b.38.1 — Sm-like ribonucleoproteins
Family Family family	b.38.1.0 — automated matches

Domain ID domain_id	d5xjrg_
Class class	b — All beta proteins
Fold Fold fold	b.38 — Sm-like fold
Superfamily Superfamily superfamily	b.38.1 — Sm-like ribonucleoproteins
Family Family family	b.38.1.0 — automated matches

CATH v4.4 (5 domains)

Domain ID domain_id	5xjrA00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	5xjrB00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	5xjrE00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	5xjrF00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	5xjrG00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	100 —

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Unit-cell length a length_a	82.960 Å
Unit-cell length b length_b	114.120 Å
Unit-cell length c length_c	130.140 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	3.120 Å
Low-resolution limit resolution_low	60.000 Å
R factor r_factor	0.1721
R_work r_work	0.1684
R_free r_free	0.2424

Crystal Structure of the Gemin2-binding domain of SMN, Gemin2dN39 in Complex with SmD1(1-82)/D2/F/E/G from Human

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

Gem-associated protein 2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Small nuclear ribonucleoprotein Sm D1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Small nuclear ribonucleoprotein Sm D2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Small nuclear ribonucleoprotein E

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Small nuclear ribonucleoprotein F

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Small nuclear ribonucleoprotein G

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Survival motor neuron protein

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

5xjr__assembly_1__model_1

5xjr__assembly_1__model_1 | I(q)

5xjr__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer