SAXSdb — 2vpl

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

50S RIBOSOMAL PROTEIN L1

THERMUS THERMOPHILUS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Monomer	Protein 1 RNA 1	FRAGMENT OF MRNA FOR L1-OPERON CONTAINING REGULATOR L1-BINDING SITE × 1 POTASSIUM ION × 1 water × 2	Consistent with all polymers
2	Protein–RNA	Monomer	Protein 1 RNA 1	FRAGMENT OF MRNA FOR L1-OPERON CONTAINING REGULATOR L1-BINDING SITE × 1 POTASSIUM ION × 1 water × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RL1_THETH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–67； UniProt 2–68 Author chain A； PDBConstruct 68–137； UniProt 160–229 Author chain C； PDBConstruct 1–67； UniProt 2–68 Author chain C； PDBConstruct 68–137； UniProt 160–229

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	2vpl
Deposition date deposition_date	2008-03-01
Structure title title	The structure of the complex between the first domain of L1 protein from Thermus thermophilus and mRNA from Methanococcus jannaschii
Keywords keywords	RIBOSOMAL PROTEIN, RNA-PROTEIN COMPLEX, TRANSLATION REGULATION, TRANSLATION, REPRESSOR, RNA-BINDING, TRNA-BINDING, RRNA-BINDING; TRANSLATION
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.

2vpl__assembly_1__model_1

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

Download this curve (.dat)

2vpl__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2vpl__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.22 Å
Rg (electron density)	20.29 Å
Total Rg	21.04 Å
Atom count	2102
Residues	185
Excluded volume	33597 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2vpl__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2vpl__assembly_2__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 (4)

Entity 1 Entity 1 polymer

Description description	50S RIBOSOMAL PROTEIN L1
Molecular weight formula_weight	15171.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	4507

PKHGKRYRALLEKVDPNKIYTIDEAAHLVKELATAKFDETVEVHAKLGIDPRRSDQNVRGTVSLPHGGRIEFRNDKTGAIHAPVGKASFPPEKLADNIRAFIRALEAHKPEGAKGTFLRSVYVTTTMGPSVRINPHS

Source Source

Source organism organism	THERMUS THERMOPHILUS
NCBI taxonomy ID ncbi_taxonomy_id	274
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	FRAGMENT OF MRNA FOR L1-OPERON CONTAINING REGULATOR L1-BINDING SITE
Molecular weight formula_weight	15522.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	B,D

GGAGUGAAGGAGGCUCGCGAACUCGCGAAGCCGAGAAACUUCACUCCC

Source Source

Source organism organism	METHANOCALDOCOCCUS JANNASCHII
NCBI taxonomy ID ncbi_taxonomy_id	2190
Host organism host_organism	ESCHERICHIA COLI

Entity 3 Entity 3 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	318

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	2vplA01
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	20 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	140 — 50S ribosomal protein L1; Chain A, Domain 1

Domain ID domain_id	2vplC01
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	20 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	140 — 50S ribosomal protein L1; Chain A, Domain 1

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Unit-cell length a length_a	76.100 Å
Unit-cell length b length_b	144.350 Å
Unit-cell length c length_c	56.160 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	8

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	0.2120
R_work r_work	0.2090
R_free r_free	0.2740

The structure of the complex between the first domain of L1 protein from Thermus thermophilus and mRNA from Methanococcus jannaschii

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

50S RIBOSOMAL PROTEIN L1

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

2vpl__assembly_1__model_1

2vpl__assembly_1__model_1 | I(q)

2vpl__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

The structure of the complex between the first domain of L1 protein from Thermus thermophilus and mRNA from Methanococcus jannaschii

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

50S RIBOSOMAL PROTEIN L1

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

2vpl__assembly_1__model_1

2vpl__assembly_1__model_1 | I(q)

2vpl__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)