1zho

The structure of a ribosomal protein L1 in complex with mRNA

Method: X-RAY DIFFRACTION

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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	mRNA × 1 POTASSIUM ION × 1 water × 2	Consistent with all polymers
2	Protein–RNA	Monomer	Protein 1 RNA 1	mRNA × 1 POTASSIUM ION × 1 water × 2	Consistent with all polymers
3	Protein–RNA	Monomer	Protein 1 RNA 1	mRNA × 1 POTASSIUM ION × 1 water × 2	Consistent with all polymers
4	Protein–RNA	Monomer	Protein 1 RNA 1	mRNA × 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	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–228； UniProt 1–228 Author chain C； PDBConstruct 1–228； UniProt 1–228 Author chain E； PDBConstruct 1–228； UniProt 1–228 Author chain G； PDBConstruct 1–228； UniProt 1–228

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	1zho
Deposition date deposition_date	2005-04-26
Structure title title	The structure of a ribosomal protein L1 in complex with mRNA
Keywords keywords	;RIBOSOME, RIBOSOMAL PROTEIN, MRNA-PROTEIN COMPLEX, L1, REGULATION OF GENE EXPRESSION, RNA-PROTEIN INTERACTION, STRUCTURAL PROTEIN-RNA COMPLEX ;; STRUCTURAL 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.

1zho__assembly_1__model_1

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

Download this curve (.dat)

1zho__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1zho__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.26 Å
Rg (electron density)	20.71 Å
Total Rg	21.44 Å
Atom count	2559
Residues	263
Excluded volume	42786 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1zho__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1zho__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1zho__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1zho__assembly_4__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	mRNA
Molecular weight formula_weight	12270.4 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	B,D,F,H
Atom count atom_count	10515

GGGAGUGAAGGAGGCUUCGGCCGCGAAACUUCACUCCC

Entity 2 Entity 2 polymer

Description description	50S ribosomal protein L1
Molecular weight formula_weight	24877.2 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G

PKHGKRYRALLEKVDPNKIYTIDEAAHLVKELATAKFDETVEVHAKLGIDPRRSDQNVRGTVSLPHGLGKQVRVLAIAKGEKIKEAEEAGADYVGGEEIIQKILDGWMDFDAVVATPDVMGAVGSKLGRILGPRGLLPNPKAGTVGFNIGEIIREIKAGRIEFRNDKTGAIHAPVGKASFPPEKLADNIRAFIRALEAHKPEGAKGTFLRSVYVTTTMGPSVRINPHS

Source Source

Source organism organism	Thermus thermophilus
NCBI taxonomy ID ncbi_taxonomy_id	274
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	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	279

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1zhoa1
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.24 — Ribosomal protein L1
Superfamily Superfamily superfamily	e.24.1 — Ribosomal protein L1
Family Family family	e.24.1.1 — Ribosomal protein L1

Domain ID domain_id	d1zhoc1
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.24 — Ribosomal protein L1
Superfamily Superfamily superfamily	e.24.1 — Ribosomal protein L1
Family Family family	e.24.1.1 — Ribosomal protein L1

Domain ID domain_id	d1zhoe1
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.24 — Ribosomal protein L1
Superfamily Superfamily superfamily	e.24.1 — Ribosomal protein L1
Family Family family	e.24.1.1 — Ribosomal protein L1

Domain ID domain_id	d1zhog1
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.24 — Ribosomal protein L1
Superfamily Superfamily superfamily	e.24.1 — Ribosomal protein L1
Family Family family	e.24.1.1 — Ribosomal protein L1

CATH v4.4 (8 domains)

Domain ID domain_id	1zhoA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	190 — Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase
Homologous superfamily homologous superfamily	20 — Ribosomal protein L1/L10, rRNA-binding domain

Domain ID domain_id	1zhoA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	790 — Ribosomal protein L1/L10, domain II

Domain ID domain_id	1zhoC01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	190 — Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase
Homologous superfamily homologous superfamily	20 — Ribosomal protein L1/L10, rRNA-binding domain

Domain ID domain_id	1zhoC02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	790 — Ribosomal protein L1/L10, domain II

Domain ID domain_id	1zhoE01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	190 — Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase
Homologous superfamily homologous superfamily	20 — Ribosomal protein L1/L10, rRNA-binding domain

Domain ID domain_id	1zhoE02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	790 — Ribosomal protein L1/L10, domain II

Domain ID domain_id	1zhoG01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	190 — Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase
Homologous superfamily homologous superfamily	20 — Ribosomal protein L1/L10, rRNA-binding domain

Domain ID domain_id	1zhoG02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	790 — Ribosomal protein L1/L10, domain II

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Unit-cell length a length_a	71.600 Å
Unit-cell length b length_b	101.900 Å
Unit-cell length c length_c	119.600 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	93.66 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	37.060 Å
R factor r_factor	0.2180
R_work r_work	0.2180
R_free r_free	0.2810

The structure of a ribosomal protein L1 in complex with mRNA

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

1zho__assembly_1__model_1

1zho__assembly_1__model_1 | I(q)

1zho__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

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) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)

The structure of a ribosomal protein L1 in complex with mRNA

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

1zho__assembly_1__model_1

1zho__assembly_1__model_1 | I(q)

1zho__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

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) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)