SAXSdb — 2pjp

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

Selenocysteine-specific elongation factor

Escherichia coli

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	SECIS RNA × 1 MAGNESIUM ION × 17 CHLORIDE ION × 2 CALCIUM ION × 4 SODIUM ION × 1 water × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SELB_ECOLI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–121； UniProt 487–607

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	2pjp
Deposition date deposition_date	2007-04-16
Structure title title	Structure of the mRNA-binding domain of elongation factor SelB from E.coli in complex with SECIS RNA
Keywords keywords	selb, protein-rna complex, elongation factor, secis, winged-helix, bulge, 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.

2pjp__assembly_1__model_1

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

Download this curve (.dat)

2pjp__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2pjp__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.09 Å
Rg (electron density)	18.29 Å
Total Rg	19.06 Å
Atom count	1497
Residues	144
Excluded volume	24852 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2pjp__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 (7)

Entity 1 Entity 1 polymer

Description description	SECIS RNA
Molecular weight formula_weight	7386.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	B
Atom count atom_count	1609

GGCGGUUGCAGGUCUGCACCGCC

Entity 2 Entity 2 polymer

Description description	Selenocysteine-specific elongation factor
Molecular weight formula_weight	14229.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

FSEEQQAIWQKAEPLFGDEPWWVRDLAKETGTDEQAMRLTLRQAAQQGIITAIVKDRYYRNDRIVEFANMIRDLDQECGSTCAADFRDRLGVGRKLAIQILEYFDRIGFTRRRGNDHLLRD

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli BL21

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	17

Entity 4 Entity 4 non-polymer

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

Entity 5 Entity 5 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	112

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	2pjpA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	2pjpA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

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Unit-cell length a length_a	103.498 Å
Unit-cell length b length_b	56.515 Å
Unit-cell length c length_c	48.414 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	95.60 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	51.500 Å
R factor r_factor	0.2040
R_work r_work	0.2000
R_free r_free	0.2510

Structure of the mRNA-binding domain of elongation factor SelB from E.coli in complex with SECIS RNA

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

Selenocysteine-specific elongation factor

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

2pjp__assembly_1__model_1

2pjp__assembly_1__model_1 | I(q)

2pjp__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 (7)

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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (2)

Structure of the mRNA-binding domain of elongation factor SelB from E.coli in complex with SECIS RNA

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

Selenocysteine-specific elongation factor

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

2pjp__assembly_1__model_1

2pjp__assembly_1__model_1 | I(q)

2pjp__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 (7)

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 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (2)