3deg

Complex of elongating Escherichia coli 70S ribosome and EF4(LepA)-GMPPNP

Method: ELECTRON MICROSCOPY

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

GTP-binding protein lepA

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 3 RNA 8	A/L-tRNA × 1 P-tRNA × 1 30S RNA helix 8 × 1 30S RNA helix 14 × 1 50S RNA helix 42-44 × 1 50S RNA helix 95 × 1 50S RNA helix 71 × 1 50S RNA helix 92 × 1 30S ribosomal protein S12 × 1 （P0A7S3） 50S ribosomal protein L11 × 1 （P0A7J7）	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LEPA_ECOLI
Isoform	—
PDB entities	9
Chains and sequence ranges	Author chain C； PDBConstruct 1–545； UniProt 1–545

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 8	A/L-tRNA × 1 P-tRNA × 1 30S RNA helix 8 × 1 30S RNA helix 14 × 1 50S RNA helix 42-44 × 1 50S RNA helix 95 × 1 50S RNA helix 71 × 1 50S RNA helix 92 × 1 GTP-binding protein lepA × 1 （P60785） 50S ribosomal protein L11 × 1 （P0A7J7）	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	10
Chains and sequence ranges	Author chain D； 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 8	A/L-tRNA × 1 P-tRNA × 1 30S RNA helix 8 × 1 30S RNA helix 14 × 1 50S RNA helix 42-44 × 1 50S RNA helix 95 × 1 50S RNA helix 71 × 1 50S RNA helix 92 × 1 GTP-binding protein lepA × 1 （P60785） 30S ribosomal protein S12 × 1 （P0A7S3）	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	11
Chains and sequence ranges	Author chain H； 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	3deg
Deposition date deposition_date	2008-06-10
Structure title title	Complex of elongating Escherichia coli 70S ribosome and EF4(LepA)-GMPPNP
Keywords keywords	;ribosome, translation, LepA, EF4, GTP-binding, Membrane, Nucleotide-binding, Antibiotic resistance, Ribonucleoprotein, Ribosomal protein, RNA-binding, rRNA-binding, tRNA-binding, Methylation ;; RIBOSOME
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.

3deg__assembly_1__model_1

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

Download this curve (.dat)

3deg__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3deg__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	47.92 Å
Rg (electron density)	46.51 Å
Total Rg	46.86 Å
Atom count	12950
Residues	1107
Excluded volume	206490 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3deg__assembly_1__model_1`	undecameric （11）	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 (11)

Entity 1 Entity 1 polymer

Description description	A/L-tRNA
Molecular weight formula_weight	24890.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	A
Atom count atom_count	12950

GCGGAUUUAGCUCAGUUGGGAGAGCGCCAGACUGAAGAUCUGGAGGUCCUGUGUUCGAUCCACAGAAUUCGCACCA

Entity 2 Entity 2 polymer

Description description	P-tRNA
Molecular weight formula_weight	24816.8 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	B

CGCGGGGUGGAGCAGCCUGGUAGCUCGUCGGGCUCAUAACCCGAAGGUCGUCGGUUCAAAUCCGGCCCCCGCAACCA

Entity 3 Entity 3 polymer

Description description	30S RNA helix 8
Molecular weight formula_weight	5161.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	E

CUACUGGAAACGGUAG

Entity 4 Entity 4 polymer

Description description	30S RNA helix 14
Molecular weight formula_weight	3827.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	F

CUCCUACGGGAG

Entity 5 Entity 5 polymer

Description description	50S RNA helix 42-44
Molecular weight formula_weight	22580.5 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	G

CCCAGACAGCCAGGAUGUUGGCUUAGAAGCAGCCAUCAUUUAAAGAAAGCGUAAUAGCUCACUGGUCGAG

Entity 6 Entity 6 polymer

Description description	50S RNA helix 95
Molecular weight formula_weight	9394.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	I

CUGCUCCUAGUACGAGAGGACCGGAGUGG

Entity 7 Entity 7 polymer

Description description	50S RNA helix 71
Molecular weight formula_weight	5765.5 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	J

UGUCGGGUAAGUUCCGAC

Entity 8 Entity 8 polymer

Description description	50S RNA helix 92
Molecular weight formula_weight	4745.8 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	K

AUGGCUGUUCGCCAU

Entity 9 Entity 9 polymer

Description description	GTP-binding protein lepA
Molecular weight formula_weight	60476.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MKNIRNFSIIAHIDHGKSTLSDRIIQICGGLSDREMEAQVLDSMDLERERGITIKAQSVTLDYKASDGETYQLNFIDTPGHVDFSYEVSRSLAACEGALLVVDAGQGVEAQTLANCYTAMEMDLEVVPVLNKIDLPAADPERVAEEIEDIVGIDATDAVRCSAKTGVGVQDVLERLVRDIPPPEGDPEGPLQALIIDSWFDNYLGVVSLIRIKNGTLRKGDKVKVMSTGQTYNADRLGIFTPKQVDRTELKCGEVGWLVCAIKDIHGAPVGDTLTLARNPAEKALPGFKKVKPQVYAGLFPVSSDDYEAFRDALGKLSLNDASLFYEPESSSALGFGFRCGFLGLLHMEIIQERLEREYDLDLITTAPTVVYEVETTSREVIYVDSPSKLPAVNNIYELREPIAECHMLLPQAYLGNVITLCVEKRGVQTNMVYHGNQVALTYEIPMAEVVLDFFDRLKSTSRGYASLDYNFKRFQASDMVRVDVLINGERVDALALITHRDNSQNRGRELVEKMKDLIPRQQFDIAIQAAIGTHIIARSTVKQL

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 10 Entity 10 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	D

ATVNQLVRKPRARKVAKSNVPALEACPQKRGVCTRVYTTTPKKPNSALRKVCRVRLTNGFEVTSYIGGEGHNLQEHSVILIRGGRVKDLPGVRYHTVRGALDCSGVKDRKQARSKYGVKRPKA

Entity 11 Entity 11 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	H

AKKVQAYVKLQVAAGMANPSPPVGPALGQQGVNIMEFCKAFNAKTDSIEKGLPIPVVITVYADRSFTFVTKTPPAAVLLKKAAGIKSGSGKPNKDKVGKISRAQLQEIAQTKAADMTGADIEAMTRSIEGTARSMGLVVED

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6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d3degd1
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
Family Family family	b.40.4.5 — Cold shock DNA-binding domain-like

Domain ID domain_id	d3degh1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.7 — Ribosomal protein L11, C-terminal domain
Family Family family	a.4.7.1 — Ribosomal protein L11, C-terminal domain

Domain ID domain_id	d3degh2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.47 — Ribosomal L11/L12e N-terminal domain
Superfamily Superfamily superfamily	d.47.1 — Ribosomal L11/L12e N-terminal domain
Family Family family	d.47.1.1 — Ribosomal L11/L12e N-terminal domain

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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	10.90 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	41294

Complex of elongating Escherichia coli 70S ribosome and EF4(LepA)-GMPPNP

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

GTP-binding protein lepA

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

3deg__assembly_1__model_1

3deg__assembly_1__model_1 | I(q)

3deg__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 (11)

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

Source Source

Entity 10 Entity 10 polymer

Polymer Polymer

Entity 11 Entity 11 polymer

Polymer Polymer

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (3 domains)

7. Citations (1)