8ya2

Structure of the SecA-SecY complex with the substrate FtsQ-LacY(+20C)

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 6	Protein translocase subunit SecY × 1 （A4IJK8） Protein translocase subunit SecE × 1 （A4IJH4） Cell division protein FtsQ,Lactose permease × 1 （P02920,P06136） Nanobody × 1 Green fluorescent protein × 1 （P42212） 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 6	Protein translocase subunit SecA × 1 （P28366） Protein translocase subunit SecE × 1 （A4IJH4） Cell division protein FtsQ,Lactose permease × 1 （P02920,P06136） Nanobody × 1 Green fluorescent protein × 1 （P42212） 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 6	Protein translocase subunit SecA × 1 （P28366） Protein translocase subunit SecY × 1 （A4IJK8） Cell division protein FtsQ,Lactose permease × 1 （P02920,P06136） Nanobody × 1 Green fluorescent protein × 1 （P42212） 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

Cell division protein FtsQ,Lactose permease

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 6	Protein translocase subunit SecA × 1 （P28366） Protein translocase subunit SecY × 1 （A4IJK8） Protein translocase subunit SecE × 1 （A4IJH4） Nanobody × 1 Green fluorescent protein × 1 （P42212） 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

Cell division protein FtsQ,Lactose permease

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 6	Protein translocase subunit SecA × 1 （P28366） Protein translocase subunit SecY × 1 （A4IJK8） Protein translocase subunit SecE × 1 （A4IJH4） Nanobody × 1 Green fluorescent protein × 1 （P42212） 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

Green fluorescent protein

Aequorea victoria

UniProt P42212

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 6	Protein translocase subunit SecA × 1 （P28366） Protein translocase subunit SecY × 1 （A4IJK8） Protein translocase subunit SecE × 1 （A4IJH4） Cell division protein FtsQ,Lactose permease × 1 （P02920,P06136） Nanobody × 1 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	GFP_AEQVI
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain G； PDBConstruct 1–225； UniProt 3–229

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	8ya2
Deposition date deposition_date	2024-02-07
Structure title title	Structure of the SecA-SecY complex with the substrate FtsQ-LacY(+20C)
Keywords keywords	Protein translocation, SecY, 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.

8ya2__assembly_1__model_1

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

Download this curve (.dat)

8ya2__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8ya2__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	41.59 Å
Rg (electron density)	41.41 Å
Total Rg	41.64 Å
Atom count	12899
Residues	1624
Excluded volume	231140 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8ya2__assembly_1__model_1`	hexameric （6）	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	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	12899

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	Cell division protein FtsQ,Lactose permease
Molecular weight formula_weight	8719.0 kDa
Mutation mutation	T1M,R2A,L3K,A4K,G5T,E45C,C53A
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MAKKTILFLLTVLTTVLVSGWVVLGAQYEDGSSGVVILKTLHMFCVPFLLVGAFSNADTSISGDGDSPHSYHSGDGDKLPEGV

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 polymer

Description description	Nanobody
Molecular weight formula_weight	12542.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

VALVESGGALVQPGGSLRLSCAASGFPVNRYSMRWYRQAPGKEREWVAGMSSAGDRSSYEDSVKGRFTISRDDARNTVYLQMNSLKPEDTAVYYCNVNVGFEYWGQGTQVTVSS

Source Source

Source organism organism	Lama glama
NCBI taxonomy ID ncbi_taxonomy_id	9844
Host organism host_organism	Escherichia coli K-12

Entity 6 Entity 6 polymer

Description description	Green fluorescent protein
Molecular weight formula_weight	25517.6 kDa
Mutation mutation	Q80R, F99S, M153T, V163A
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

KGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFXVQCFSRYPDHMKRHDFFKSAMPEGYVQERTISFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYITADKQKNGIKANFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGI

Source Source

Source organism organism	Aequorea victoria
NCBI taxonomy ID ncbi_taxonomy_id	6100
Host organism host_organism	Escherichia coli K-12

Entity 7 Entity 7 non-polymer

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

Entity 8 Entity 8 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 9 Entity 9 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	3.84 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	186802

Structure of the SecA-SecY complex with the substrate FtsQ-LacY(+20C)

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

Cell division protein FtsQ,Lactose permease

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Cell division protein FtsQ,Lactose permease

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Green fluorescent protein

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

8ya2__assembly_1__model_1

8ya2__assembly_1__model_1 | I(q)

8ya2__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

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 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 polymer

Polymer Polymer

Source Source

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer