8y9y

Structure of the SecA-SecY complex with the substrate FtsQ-LacY(+1C)

Method: ELECTRON MICROSCOPY

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

Protein translocase subunit SecA

Bacillus subtilis subsp. subtilis str. 168

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 4	Protein translocase subunit SecY × 1 （A4IJK8） Protein translocase subunit SecE × 1 （A4IJH4） Substrate FtsQ-LacY(+1C) × 1 （P02920,P06136） MAGNESIUM ION × 1 BERYLLIUM TRIFLUORIDE ION × 1 ADENOSINE-5'-DIPHOSPHATE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SECA_BACSU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–778； UniProt 1–778

Protein translocase subunit SecY

Geobacillus thermodenitrificans NG80-2

UniProt A4IJK8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 4	Protein translocase subunit SecA × 1 （P28366） Protein translocase subunit SecE × 1 （A4IJH4） Substrate FtsQ-LacY(+1C) × 1 （P02920,P06136） MAGNESIUM ION × 1 BERYLLIUM TRIFLUORIDE ION × 1 ADENOSINE-5'-DIPHOSPHATE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A4IJK8_GEOTN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain Y； PDBConstruct 1–430； UniProt 1–430

Protein translocase subunit SecE

Geobacillus thermodenitrificans NG80-2

UniProt A4IJH4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 4	Protein translocase subunit SecA × 1 （P28366） Protein translocase subunit SecY × 1 （A4IJK8） Substrate FtsQ-LacY(+1C) × 1 （P02920,P06136） MAGNESIUM ION × 1 BERYLLIUM TRIFLUORIDE ION × 1 ADENOSINE-5'-DIPHOSPHATE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A4IJH4_GEOTN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain E； PDBConstruct 1–60； UniProt 1–60

Substrate FtsQ-LacY(+1C)

Escherichia coli K-12

UniProt P02920

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 4	Protein translocase subunit SecA × 1 （P28366） Protein translocase subunit SecY × 1 （A4IJK8） Protein translocase subunit SecE × 1 （A4IJH4） MAGNESIUM ION × 1 BERYLLIUM TRIFLUORIDE ION × 1 ADENOSINE-5'-DIPHOSPHATE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LACY_ECOLI
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain B； PDBConstruct 35–54； UniProt 315–334

Substrate FtsQ-LacY(+1C)

Escherichia coli K-12

UniProt P06136

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 4	Protein translocase subunit SecA × 1 （P28366） Protein translocase subunit SecY × 1 （A4IJK8） Protein translocase subunit SecE × 1 （A4IJH4） MAGNESIUM ION × 1 BERYLLIUM TRIFLUORIDE ION × 1 ADENOSINE-5'-DIPHOSPHATE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	FTSQ_ECOLI
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain B； PDBConstruct 1–25； UniProt 23–47

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	8y9y
Deposition date deposition_date	2024-02-07
Structure title title	Structure of the SecA-SecY complex with the substrate FtsQ-LacY(+1C)
Keywords keywords	Protein translocation, Membrane protein insertion, Protein chaperone, PROTEIN TRANSPORT; 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.

8y9y__assembly_1__model_1

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

Download this curve (.dat)

8y9y__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8y9y__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	36.52 Å
Rg (electron density)	36.10 Å
Total Rg	36.59 Å
Atom count	10207
Residues	1284
Excluded volume	183700 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8y9y__assembly_1__model_1`	tetrameric （4）	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	Protein translocase subunit SecA
Molecular weight formula_weight	88673.9 kDa
EC 编号 ec_number	7.4.2.8
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	10207

MLGILNKMFDPTKRTLNRYEKIANDIDAIRGDYENLSDDALKHKTIEFKERLEKGATTDDLLVEAFAVVREASRRVTGMFPFKVQLMGGVALHDGNIAEMKTGEGKTLTSTLPVYLNALTGKGVHVVTVNEYLASRDAEQMGKIFEFLGLTVGLNLNSMSKDEKREAYAADITYSTNNELGFDYLRDNMVLYKEQMVQRPLHFAVIDEVDSILIDEARTPLIISGQAAKSTKLYVQANAFVRTLKAEKDYTYDIKTKAVQLTEEGMTKAEKAFGIDNLFDVKHVALNHHINQALKAHVAMQKDVDYVVEDGQVVIVDSFTGRLMKGRRYSEGLHQAIEAKEGLEIQNESMTLATITFQNYFRMYEKLAGMTGTAKTEEEEFRNIYNMQVVTIPTNRPVVRDDRPDLIYRTMEGKFKAVAEDVAQRYMTGQPVLVGTVAVETSELISKLLKNKGIPHQVLNAKNHEREAQIIEEAGQKGAVTIATNMAGRGTDIKLGEGVKELGGLAVVGTERHESRRIDNQLRGRSGRQGDPGITQFYLSMEDELMRRFGAERTMAMLDRFGMDDSTPIQSKMVSRAVESSQKRVEGNNFDSRKQLLQYDDVLRQQREVIYKQRFEVIDSENLREIVENMIKSSLERAIAAYTPREELPEEWKLDGLVDLINTTYLDEGALEKSDIFGKEPDEMLELIMDRIITKYNEKEEQFGKEQMREFEKVIVLRAVDSKWMDHIDAMDQLRQGIHLRAYAQTNPLREYQMEGFAMFEHMIESIEDEVAKFVMKA

Source Source

Source organism organism	Bacillus subtilis subsp. subtilis str. 168
NCBI taxonomy ID ncbi_taxonomy_id	224308
Host organism host_organism	Escherichia coli K-12

Entity 2 Entity 2 polymer

Description description	Protein translocase subunit SecY
Molecular weight formula_weight	47512.1 kDa
Mutation mutation	G60C, Q202T, F211T, R213N
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Y

MFRTISNFMRVSDIRNKIIFTLLMLIVFRIGTFIPVPSVNTDVLKLQDQLNAFGVLNIFCGGALQNFSIFAMGVMPYITASIIVQLLQMDVVPKFAEWSKQGEMGRRKLAQFTRYFTIVLGFIQALGMSYGFNNLAGGMLIQNPGIGTYLLIAVVLTAGTAFLMWLGEQITAKGVGNGISIIIFAGIVSGIPTILNQIYAQTFENVGEDLTLNIVRLLLVALAVVAVIVGVIYIQQAFRKIPIQYAKRLEGRNPVGGHSTHLPLKVNPAGVIPVIFAVSFLIAPPTIASFFGTNDVTLWIRRTFDYTHPVGMTIYVVLIIAFTYFYAFVQVNPEQMADNLKKQGGYIPGIRPGKNTQEYVTRILYRLTLVGSLFLAFIAVLPVFFVNFANLPPSAQIGGTSLLIVVGVALETMKQLESQLVKRHYRGFIK

Source Source

Source organism organism	Geobacillus thermodenitrificans NG80-2
NCBI taxonomy ID ncbi_taxonomy_id	420246
Host organism host_organism	Escherichia coli K-12

Entity 3 Entity 3 polymer

Description description	Protein translocase subunit SecE
Molecular weight formula_weight	8249.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

MQRVTNFFKEVVRELKKVSWPNRKELVNYTAVVLATVAFFTVFFAVIDLGISQLIRLVFEGGHHHHHHHH

Source Source

Source organism organism	Geobacillus thermodenitrificans NG80-2
NCBI taxonomy ID ncbi_taxonomy_id	420246
Host organism host_organism	Escherichia coli K-12

Entity 4 Entity 4 polymer

Description description	Substrate FtsQ-LacY(+1C)
Molecular weight formula_weight	7793.0 kDa
Mutation mutation	T1M,R2A,L3K,A4K,G5T,C53A
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MAKKTILFLLTVLTTVLVSGWVVLGCQYEDGSSGVVILKTLHMFEVPFLLVGAFSISGDGDSPHSYHSGDGDK

Source Source

Source organism organism	Escherichia coli K-12
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli K-12

Entity 5 Entity 5 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	BERYLLIUM TRIFLUORIDE ION
Molecular weight formula_weight	66.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	1

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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	—

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

Resolution resolution	3.29 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	212292

Structure of the SecA-SecY complex with the substrate FtsQ-LacY(+1C)

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

Protein translocase subunit SecA

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 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

Protein 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

Substrate FtsQ-LacY(+1C)

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Substrate FtsQ-LacY(+1C)

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

8y9y__assembly_1__model_1

8y9y__assembly_1__model_1 | I(q)

8y9y__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 (7)

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

Source Source

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

7. Citations (1)