SAXSdb — 1b34

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

PROTEIN (SMALL NUCLEAR RIBONUCLEOPROTEIN SM D1)

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	PROTEIN (SMALL NUCLEAR RIBONUCLEOPROTEIN SM D2) × 1 （P62316） water × 2	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	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–119； UniProt 1–119

PROTEIN (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 2	PROTEIN (SMALL NUCLEAR RIBONUCLEOPROTEIN SM D1) × 1 （P62314） water × 2	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	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–118； UniProt 1–118

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	1b34
Deposition date deposition_date	1998-12-17
Structure title title	CRYSTAL STRUCTURE OF THE D1D2 SUB-COMPLEX FROM THE HUMAN SNRNP CORE DOMAIN
Keywords keywords	SNRNP, SPLICING, SPLICEOSOME, SM, CORE SNRNP DOMAIN, SYSTEMIC LUPUS ERYTHEMATOSUS, SLE, RNA BINDING PROTEIN; 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.

1b34__assembly_1__model_1

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

Download this curve (.dat)

1b34__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1b34__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	16.96 Å
Rg (electron density)	15.81 Å
Total Rg	17.00 Å
Atom count	1219
Residues	154
Excluded volume	22138 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1b34__assembly_1__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	PROTEIN (SMALL NUCLEAR RIBONUCLEOPROTEIN SM D1)
Molecular weight formula_weight	13310.7 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1239

MKLVRFLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRGNNIRYFILPDSLPLDTLLVDVEPKVKSKKREAVAGRGRGRGRGRGRGRGRGRGGPRR

Entity 2 Entity 2 polymer

Description description	PROTEIN (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 BL21(DE3)

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	20

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1b34a_
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	d1b34b_
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

CATH v4.4 (2 domains)

Domain ID domain_id	1b34A00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	1b34B00
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	75.300 Å
Unit-cell length b length_b	75.300 Å
Unit-cell length c length_c	91.990 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	6

Space group space_group	P 62
Space-group number int_tables_number	171
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	18.400 Å
R factor r_factor	—
R_work r_work	0.2490
R_free r_free	0.2860

CRYSTAL STRUCTURE OF THE D1D2 SUB-COMPLEX FROM THE HUMAN SNRNP CORE DOMAIN

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

PROTEIN (SMALL NUCLEAR RIBONUCLEOPROTEIN SM D1)

State in the Current Structure

Other States of the Same Protein in the Database

PROTEIN (SMALL NUCLEAR RIBONUCLEOPROTEIN SM D2)

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

1b34__assembly_1__model_1

1b34__assembly_1__model_1 | I(q)

1b34__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

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

CRYSTAL STRUCTURE OF THE D1D2 SUB-COMPLEX FROM THE HUMAN SNRNP CORE DOMAIN

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

PROTEIN (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

PROTEIN (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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1b34__assembly_1__model_1

1b34__assembly_1__model_1 | I(q)

1b34__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

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)