SAXSdb — 1m5k

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

PROTEIN (U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A)

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Monomer	Protein 1 RNA 2	RNA INHIBITOR SUBSTRATE × 1 RNA HAIRPIN RIBOZYME × 1 CALCIUM ION × 16 CHLORIDE ION × 2 water × 3	Consistent with all polymers
2	Protein–RNA	Monomer	Protein 1 RNA 2	RNA INHIBITOR SUBSTRATE × 1 RNA HAIRPIN RIBOZYME × 1 CALCIUM ION × 17 water × 3	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SNRPA_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–100； UniProt 1–100 Author chain F； PDBConstruct 1–100； UniProt 1–100

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	1m5k
Deposition date deposition_date	2002-07-09
Structure title title	Crystal structure of a hairpin ribozyme in the catalytically-active conformation
Keywords keywords	HAIRPIN RIBOZYME, CATALYTIC RNA, U1A RNA BINDING PROTEIN DOCKED CONFORMATION, SUBSTRATE INHIBITOR STRAND, TRANSLATION-RNA COMPLEX; TRANSLATION/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.

1m5k__assembly_1__model_1

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

Download this curve (.dat)

1m5k__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1m5k__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.98 Å
Rg (electron density)	31.83 Å
Total Rg	31.70 Å
Atom count	3186
Residues	202
Excluded volume	48606 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1m5k__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1m5k__assembly_2__model_1`	trimeric （3）	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 (6)

Entity 1 Entity 1 polymer

Description description	RNA INHIBITOR SUBSTRATE
Molecular weight formula_weight	6739.9 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	A,D
Atom count atom_count	6474

GGCCACCUGACAGUCCUCUCC

Entity 2 Entity 2 polymer

Description description	RNA HAIRPIN RIBOZYME
Molecular weight formula_weight	29969.8 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	B,E

GGAGAGAGAAGUCAACCAGAGAAACACACCAACCCAUUGCACUCCGGGUUGGUGGUAUAUUACCUGGUACGGGGGAAACUUCGUGGUGGCCG

Entity 3 Entity 3 polymer

Description description	PROTEIN (U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A)
Molecular weight formula_weight	11498.5 kDa
Mutation mutation	Y31H,Q36R
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,F

MAVPETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGT

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 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	33

Entity 5 Entity 5 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	103

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1m5kc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.7 — RNA-binding domain, RBD, aka RNA recognition motif (RRM)
Family Family family	d.58.7.1 — Canonical RBD

Domain ID domain_id	d1m5kf_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.7 — RNA-binding domain, RBD, aka RNA recognition motif (RRM)
Family Family family	d.58.7.1 — Canonical RBD

CATH v4.4 (2 domains)

Domain ID domain_id	1m5kC00
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	1m5kF00
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	256.300 Å
Unit-cell length b length_b	44.100 Å
Unit-cell length c length_c	102.400 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	109.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	61.070 Å
R factor r_factor	0.2300
R_work r_work	0.2290
R_free r_free	0.2840

Crystal structure of a hairpin ribozyme in the catalytically-active conformation

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

PROTEIN (U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A)

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

1m5k__assembly_1__model_1

1m5k__assembly_1__model_1 | I(q)

1m5k__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (2)

Crystal structure of a hairpin ribozyme in the catalytically-active conformation

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

PROTEIN (U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A)

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

1m5k__assembly_1__model_1

1m5k__assembly_1__model_1 | I(q)

1m5k__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (2)