3ep2

Model of Phe-tRNA(Phe) in the ribosomal pre-accommodated state revealed by cryo-EM

Method: ELECTRON MICROSCOPY

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

Elongation factor Tu

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 3 RNA 6	30S ribosomal protein S12 × 1 （P0A7S3） 50S ribosomal protein L11 × 1 （P0A7J7） tRNA × 1 Fragment h18 of the 16S rRNA × 1 Fragment h44 of the 16S rRNA × 1 Fragment H43-44 of the 23S rRNA × 1 Fragment H95 of the 23S rRNA × 1 Fragment H69 of the 23S rRNA × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	EFTU_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain X； PDBConstruct 1–393； UniProt 2–394

30S ribosomal protein S12

OrganismNot specified

UniProt P0A7S3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 3 RNA 6	Elongation factor Tu × 1 （P0A6N1） 50S ribosomal protein L11 × 1 （P0A7J7） tRNA × 1 Fragment h18 of the 16S rRNA × 1 Fragment h44 of the 16S rRNA × 1 Fragment H43-44 of the 23S rRNA × 1 Fragment H95 of the 23S rRNA × 1 Fragment H69 of the 23S rRNA × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RS12_ECOLI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain L； PDBConstruct 1–123； UniProt 2–124

50S ribosomal protein L11

OrganismNot specified

UniProt P0A7J7

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 3 RNA 6	Elongation factor Tu × 1 （P0A6N1） 30S ribosomal protein S12 × 1 （P0A7S3） tRNA × 1 Fragment h18 of the 16S rRNA × 1 Fragment h44 of the 16S rRNA × 1 Fragment H43-44 of the 23S rRNA × 1 Fragment H95 of the 23S rRNA × 1 Fragment H69 of the 23S rRNA × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RL11_ECOLI
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain I； PDBConstruct 1–141； UniProt 2–142

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	3ep2
Deposition date deposition_date	2008-09-29
Structure title title	Model of Phe-tRNA(Phe) in the ribosomal pre-accommodated state revealed by cryo-EM
Keywords keywords	;protein translation, ternary complex, A/T-tRNA, automated data collection, Antibiotic resistance, Elongation factor, GTP-binding, Membrane, Methylation, Nucleotide-binding, Phosphoprotein, Protein biosynthesis, Ribonucleoprotein, Ribosomal protein, RNA-binding, rRNA-binding, tRNA-binding, RIBOSOMAL PROTEIN-RNA COMPLEX ;; RIBOSOMAL PROTEIN/RNA
Experimental Method method	ELECTRON MICROSCOPY

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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.

3ep2__assembly_1__model_1

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

Download this curve (.dat)

3ep2__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3ep2__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	41.15 Å
Rg (electron density)	39.93 Å
Total Rg	39.98 Å
Atom count	187
Residues	187
Excluded volume	89113 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3ep2__assembly_1__model_1`	nonameric （9）	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 (9)

Entity 1 Entity 1 polymer

Description description	Elongation factor Tu
Molecular weight formula_weight	43239.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	X
Atom count atom_count	844

SKEKFERTKPHVNVGTIGHVDHGKTTLTAAITTVLAKTYGGAARAFDQIDNAPEEKARGITINTSHVEYDTPTRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHILLGRQVGVPYIIVFLNKCDMVDDEELLELVEMEVRELLSQYDFPGDDTPIVRGSALKALEGDAEWEAKILELAGFLDSYIPEPERAIDKPFLLPIEDVFSISGRGTVVTGRVERGIIKVGEEVEIVGIKETQKSTCTGVEMFRKLLDEGRAGENVGVLLRGIKREEIERGQVLAKPGTIKPHTKFESEVYILSKDEGGRHTPFFKGYRPQFYFRTTDVTGTIELPEGVEMVMPGDNIKMVVTLIHPIAMDDGLRFAIREGGRTVGAGVVAKVLS

Entity 2 Entity 2 polymer

Description description	30S ribosomal protein S12
Molecular weight formula_weight	13637.0 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

ATVNQLVRKPRARKVAKSNVPALEACPQKRGVCTRVYTTTPKKPNSALRKVCRVRLTNGFEVTSYIGGEGHNLQEHSVILIRGGRVKDLPGVRYHTVRGALDCSGVKDRKQARSKYGVKRPKA

Entity 3 Entity 3 polymer

Description description	50S ribosomal protein L11
Molecular weight formula_weight	14763.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I

AKKVQAYVKLQVAAGMANPSPPVGPALGQQGVNIMEFCKAFNAKTDSIEKGLPIPVVITVYADRSFTFVTKTPPAAVLLKKAAGIKSGSGKPNKDKVGKISRAQLQEIAQTKAADMTGADIEAMTRSIEGTARSMGLVVED

Entity 4 Entity 4 polymer

Description description	tRNA
Molecular weight formula_weight	23844.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	Y

CGGAUUUAGCUCAGUUGGGAGAGCGCCAGACUGAAGAUCUGGAGGUCCUGUGUUCGAUCCACAGAAUUCGCACC

Entity 5 Entity 5 polymer

Description description	Fragment h18 of the 16S rRNA
Molecular weight formula_weight	2871.8 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	A

CGCGGUAAU

Entity 6 Entity 6 polymer

Description description	Fragment h44 of the 16S rRNA
Molecular weight formula_weight	3601.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	C

GGGCGAAGUCG

Entity 7 Entity 7 polymer

Description description	Fragment H43-44 of the 23S rRNA
Molecular weight formula_weight	15504.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	B

AGGAUGUUGGCUUAGAAGCAGCCAUCAUUUAAAGAAAGCGUAAUAGCU

Entity 8 Entity 8 polymer

Description description	Fragment H95 of the 23S rRNA
Molecular weight formula_weight	9089.5 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	D

UGCUCCUAGUACGAGAGGACCGGAGUGG

Entity 9 Entity 9 polymer

Description description	Fragment H69 of the 23S rRNA
Molecular weight formula_weight	5427.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	E

GCCGUAACUAUAACGGU

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	1

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

Resolution resolution	9.00 Å
Resolution测定Method resolution_method	SINGLE PARTICLE
颗粒数 num_particles	75996

Model of Phe-tRNA(Phe) in the ribosomal pre-accommodated state revealed by cryo-EM

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

Elongation factor Tu

State in the Current Structure

Other States of the Same Protein in the Database

30S ribosomal protein S12

State in the Current Structure

Other States of the Same Protein in the Database

50S ribosomal protein L11

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

3ep2__assembly_1__model_1

3ep2__assembly_1__model_1 | I(q)

3ep2__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 polymer

Polymer Polymer

Entity 7 Entity 7 polymer

Polymer Polymer

Entity 8 Entity 8 polymer

Polymer Polymer

Entity 9 Entity 9 polymer

Polymer Polymer

7. Citations (2)

Model of Phe-tRNA(Phe) in the ribosomal pre-accommodated state revealed by cryo-EM

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

Elongation factor Tu

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

30S ribosomal protein S12

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

50S ribosomal protein L11

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

3ep2__assembly_1__model_1

3ep2__assembly_1__model_1 | I(q)

3ep2__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 polymer

Polymer Polymer

Entity 7 Entity 7 polymer

Polymer Polymer

Entity 8 Entity 8 polymer

Polymer Polymer

Entity 9 Entity 9 polymer

Polymer Polymer

7. Citations (2)