1m8v

Structure of Pyrococcus abyssii Sm Protein in Complex with a Uridine Heptamer

Method: X-RAY DIFFRACTION

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

PUTATIVE SNRNP SM-LIKE PROTEIN

Pyrococcus abyssi

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Homooligomer	Protein 14 RNA 7	5'-R(PUPUPUPUPUPUP*U)-3' × 7 CALCIUM ION × 7 URIDINE-5'-MONOPHOSPHATE × 14 water × 21	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RUXX_PYRAB
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 3–77； UniProt 1–75 Author chain B； PDBConstruct 3–77； UniProt 1–75 Author chain C； PDBConstruct 3–77； UniProt 1–75 Author chain D； PDBConstruct 3–77； UniProt 1–75 Author chain E； PDBConstruct 3–77； UniProt 1–75 Author chain F； PDBConstruct 3–77； UniProt 1–75 Author chain G； PDBConstruct 3–77； UniProt 1–75 Author chain H； PDBConstruct 3–77； UniProt 1–75 Author chain I； PDBConstruct 3–77； UniProt 1–75 Author chain J； PDBConstruct 3–77； UniProt 1–75 Author chain K； PDBConstruct 3–77； UniProt 1–75 Author chain L； PDBConstruct 3–77； UniProt 1–75 Author chain M； PDBConstruct 3–77； UniProt 1–75 Author chain N； PDBConstruct 3–77； UniProt 1–75

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	1m8v
Deposition date deposition_date	2002-07-26
Structure title title	Structure of Pyrococcus abyssii Sm Protein in Complex with a Uridine Heptamer
Keywords keywords	Protein-RNA complex, Sm protein, RNA BINDING PROTEIN-RNA COMPLEX; RNA BINDING PROTEIN/RNA
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.

1m8v__assembly_1__model_1

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

Download this curve (.dat)

1m8v__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1m8v__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.47 Å
Rg (electron density)	31.01 Å
Total Rg	31.55 Å
Atom count	9022
Residues	1036
Excluded volume	159730 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1m8v__assembly_1__model_1`	21-meric （21）	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 (5)

Entity 1 Entity 1 polymer

Description description	5'-R(PUPUPUPUPUPUP*U)-3'
Molecular weight formula_weight	2098.2 kDa
Source method src_method	syn
Copy count entity_count	7

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	O,P,Q,R,S,T,U
Atom count atom_count	9227

UUUUUUU

Entity 2 Entity 2 polymer

Description description	PUTATIVE SNRNP SM-LIKE PROTEIN
Molecular weight formula_weight	8630.0 kDa
Source method src_method	man
Copy count entity_count	14

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

GAMAERPLDVIHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQDGEVVKRYGKIVIRGDNVLAISPTEE

Source Source

Source organism organism	Pyrococcus abyssi
NCBI taxonomy ID ncbi_taxonomy_id	29292
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 4 Entity 4 non-polymer

Description description	URIDINE-5'-MONOPHOSPHATE
Molecular weight formula_weight	324.2 kDa
Source method src_method	syn
Copy count entity_count	14

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	205

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6. Fold Classification (SCOP + CATH) 29 domains

SCOP 2.08 (15 domains)

Domain ID domain_id	d1m8va1
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	d1m8va2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1m8vb_
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	d1m8vc_
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	d1m8vd_
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	d1m8ve_
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	d1m8vf_
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	d1m8vg_
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	d1m8vh_
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	d1m8vi_
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	d1m8vj_
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	d1m8vk_
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	d1m8vl_
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	d1m8vm_
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	d1m8vn_
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 (14 domains)

Domain ID domain_id	1m8vA00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	1m8vB00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	1m8vC00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	1m8vD00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	1m8vE00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	1m8vF00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	1m8vG00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	1m8vH00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	1m8vI00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	1m8vJ00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	1m8vK00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	1m8vL00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	1m8vM00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	1m8vN00
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	68.000 Å
Unit-cell length b length_b	68.000 Å
Unit-cell length c length_c	84.800 Å
Unit-cell angle α angle_alpha	105.00 °
Unit-cell angle β angle_beta	108.80 °
Unit-cell angle γ angle_gamma	100.00 °
Molecules per unit cell Z z_pdb	14

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

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	—
R_work r_work	0.2120
R_free r_free	0.2820

Structure of Pyrococcus abyssii Sm Protein in Complex with a Uridine Heptamer

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

PUTATIVE SNRNP SM-LIKE PROTEIN

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

1m8v__assembly_1__model_1

1m8v__assembly_1__model_1 | I(q)

1m8v__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 29 domains

SCOP 2.08 (15 domains)

CATH v4.4 (14 domains)

7. Citations (1)

Structure of Pyrococcus abyssii Sm Protein in Complex with a Uridine Heptamer

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

PUTATIVE SNRNP SM-LIKE 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

1m8v__assembly_1__model_1

1m8v__assembly_1__model_1 | I(q)

1m8v__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 29 domains

SCOP 2.08 (15 domains)

CATH v4.4 (14 domains)

7. Citations (1)