3j45

Structure of a non-translocating SecY protein channel with the 70S ribosome

Method: ELECTRON MICROSCOPY

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

Protein translocase subunit SecY

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 6 RNA 5	Preprotein translocase subunit SecE × 1 （P0AG96） Protein-export membrane protein SecG × 1 （P0AG99） 50S ribosomal protein L23 × 1 （P0ADZ0） 50S ribosomal protein L24 × 1 （P60624） 50S ribosomal protein L29 × 1 （P0A7M6） 23S ribosomal RNA × 1 23S ribosomal RNA × 1 23S ribosomal RNA × 1 23S ribosomal RNA × 1 23S ribosomal RNA × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SECY_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain y； PDBConstruct 2–436； UniProt 6–440

Preprotein translocase subunit SecE

Escherichia coli

UniProt P0AG96

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 6 RNA 5	Protein translocase subunit SecY × 1 （P0AGA2） Protein-export membrane protein SecG × 1 （P0AG99） 50S ribosomal protein L23 × 1 （P0ADZ0） 50S ribosomal protein L24 × 1 （P60624） 50S ribosomal protein L29 × 1 （P0A7M6） 23S ribosomal RNA × 1 23S ribosomal RNA × 1 23S ribosomal RNA × 1 23S ribosomal RNA × 1 23S ribosomal RNA × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SECE_ECOLI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain E； PDBConstruct 2–55； UniProt 74–127

Protein-export membrane protein SecG

Escherichia coli

UniProt P0AG99

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 6 RNA 5	Protein translocase subunit SecY × 1 （P0AGA2） Preprotein translocase subunit SecE × 1 （P0AG96） 50S ribosomal protein L23 × 1 （P0ADZ0） 50S ribosomal protein L24 × 1 （P60624） 50S ribosomal protein L29 × 1 （P0A7M6） 23S ribosomal RNA × 1 23S ribosomal RNA × 1 23S ribosomal RNA × 1 23S ribosomal RNA × 1 23S ribosomal RNA × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SECG_ECOLI
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain G； PDBConstruct 1–65； UniProt 9–73

50S ribosomal protein L23

OrganismNot specified

UniProt P0ADZ0

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 6 RNA 5	Protein translocase subunit SecY × 1 （P0AGA2） Preprotein translocase subunit SecE × 1 （P0AG96） Protein-export membrane protein SecG × 1 （P0AG99） 50S ribosomal protein L24 × 1 （P60624） 50S ribosomal protein L29 × 1 （P0A7M6） 23S ribosomal RNA × 1 23S ribosomal RNA × 1 23S ribosomal RNA × 1 23S ribosomal RNA × 1 23S ribosomal RNA × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RL23_ECOLI
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain T； PDBConstruct 1–100； UniProt 1–100

50S ribosomal protein L24

OrganismNot specified

UniProt P60624

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 6 RNA 5	Protein translocase subunit SecY × 1 （P0AGA2） Preprotein translocase subunit SecE × 1 （P0AG96） Protein-export membrane protein SecG × 1 （P0AG99） 50S ribosomal protein L23 × 1 （P0ADZ0） 50S ribosomal protein L29 × 1 （P0A7M6） 23S ribosomal RNA × 1 23S ribosomal RNA × 1 23S ribosomal RNA × 1 23S ribosomal RNA × 1 23S ribosomal RNA × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RL24_ECOLI
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain U； PDBConstruct 1–103； UniProt 2–104

50S ribosomal protein L29

OrganismNot specified

UniProt P0A7M6

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 6 RNA 5	Protein translocase subunit SecY × 1 （P0AGA2） Preprotein translocase subunit SecE × 1 （P0AG96） Protein-export membrane protein SecG × 1 （P0AG99） 50S ribosomal protein L23 × 1 （P0ADZ0） 50S ribosomal protein L24 × 1 （P60624） 23S ribosomal RNA × 1 23S ribosomal RNA × 1 23S ribosomal RNA × 1 23S ribosomal RNA × 1 23S ribosomal RNA × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RL29_ECOLI
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain Y； PDBConstruct 1–63； UniProt 1–63

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	3j45
Deposition date deposition_date	2013-06-18
Structure title title	Structure of a non-translocating SecY protein channel with the 70S ribosome
Keywords keywords	70S, SECYEG, protein translocation channel, RIBOSOME-PROTEIN TRANSPORT complex; RIBOSOME/PROTEIN TRANSPORT
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.

3j45__assembly_1__model_1

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

Download this curve (.dat)

3j45__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3j45__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	75.68 Å
Rg (electron density)	75.75 Å
Total Rg	75.70 Å
Atom count	12465
Residues	1106
Excluded volume	202060 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3j45__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	Protein translocase subunit SecY
Molecular weight formula_weight	47643.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	y
Atom count atom_count	12465

XGLDFQSAKGGLGELKRRLLFVIGALIVFRIGSFIPIPGIDAAVLAKLLEQQRGTIIEMFNMFSGGALSRASIFALGIMPYISASIIIQLLTVVHPTLAEIKKEGESGRRKISQYTRYGTLVLAIFQSIGIATGLPNMPGMQGLVINPGFAFYFTAVVSLVTGTMFLMWLGEQITERGIGNGISIIIFAGIVAGLPPAIAHTIEQARQGDLHFLVLLLVAVLVFAVTFFVVFVERGQRRIVVNYAKRQQGRRVYAAQSTHLPLKVNMAGVIPAIFASSIILFPATIASWFGGGTGWNWLTTISLYLQPGQPLYVLLYASAIIFFCFFYTALVFNPRETADNLKKSGAFVPGIRPGEQTAKYIDKVMTRLTLVGALYITFICLIPEFMRDAMKVPFYFGGTSLLIVVVVIMDFMAQVQTLMMSSQYESALKKANLKGX

Source Source

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

Entity 2 Entity 2 polymer

Description description	Preprotein translocase subunit SecE
Molecular weight formula_weight	6123.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

XEARTEVRKVIWPTRQETLHTTLIVAAVTAVMSLILWGLDGILVRLVSFITGLRFX

Source Source

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

Entity 3 Entity 3 polymer

Description description	Protein-export membrane protein SecG
Molecular weight formula_weight	6542.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

FLIVAIGLVGLIMLQQGKGADMGASFGAGASATLFGSSGSGNFMTRMTALLATLFFIISLVLGNI

Source Source

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

Entity 4 Entity 4 polymer

Description description	50S ribosomal protein L23
Molecular weight formula_weight	11222.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	T

MIREERLLKVLRAPHVSEKASTAMEKSNTIVLKVAKDATKAEIKAAVQKLFEVEVEVVNTLVVKGKVKRHGQRIGRRSDWKKAYVTLKEGQNLDFVGGAE

Entity 5 Entity 5 polymer

Description description	50S ribosomal protein L24
Molecular weight formula_weight	11208.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	U

AAKIRRDDEVIVLTGKDKGKRGKVKNVLSSGKVIVEGINLVKKHQKPVPALNQPGGIVEKEAAIQVSNVAIFNAATGKADRVGFRFEDGKKVRFFKSNSETIK

Entity 6 Entity 6 polymer

Description description	50S ribosomal protein L29
Molecular weight formula_weight	7286.5 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Y

MKAKELREKSVEELNTELLNLLREQFNLRMQAASGQLQQSHLLKQVRRDVARVKTLLNEKAGA

Entity 7 Entity 7 polymer

Description description	23S ribosomal RNA
Molecular weight formula_weight	20350.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	1

AAGGACGUGCUAAUCUGCGAUAAGCGUCGGUAAGGUGAUAUGAACCGUUAUAACCGGCGAUUU

Entity 8 Entity 8 polymer

Description description	23S ribosomal RNA
Molecular weight formula_weight	11662.0 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	2

AAGGGUUCCUGUCCAACGUUAAUCGGGGCAGGGUGA

Entity 9 Entity 9 polymer

Description description	23S ribosomal RNA
Molecular weight formula_weight	5803.5 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	3

CGAGGCACUACGGUGCUG

Entity 10 Entity 10 polymer

Description description	23S ribosomal RNA
Molecular weight formula_weight	19776.8 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	4

CGGUGCCGGAAGGUUAAUUGAUGGGGUUAGCGCAAGCGAAGCUCUUGAUCGAAGCCCCGGU

Entity 11 Entity 11 polymer

Description description	23S ribosomal RNA
Molecular weight formula_weight	34811.5 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	5

UGAACAUUGAGCCUUGAUGUGUAGGAUAGGUGGGAGGCUUUGAAGUGUGGACGCCAGUCUGCAUGGAGCCGACCUUGAAAUACCACCCUUUAAUGUUUGAUGUUCUAA

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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	9.50 Å
Resolution测定Method resolution_method	projection matching
颗粒数 num_particles	39000

Structure of a non-translocating SecY protein channel with the 70S ribosome

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

Protein translocase subunit SecY

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Preprotein translocase subunit SecE

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Protein-export membrane protein SecG

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 L23

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 L24

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 L29

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

3j45__assembly_1__model_1

3j45__assembly_1__model_1 | I(q)

3j45__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

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

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