3din

Crystal structure of the protein-translocation complex formed by the SecY channel and the SecA ATPase

Method: X-RAY DIFFRACTION

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

Protein translocase subunit secA

Thermotoga maritima MSB8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Preprotein translocase subunit SecY × 1 （Q9X1I9） Preprotein translocase subunit secE × 1 （P35874） Preprotein translocase subunit SecG × 1 （B1L914） MAGNESIUM ION × 1 ADENOSINE-5'-DIPHOSPHATE × 1 BERYLLIUM TRIFLUORIDE ION × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Preprotein translocase subunit SecY × 1 （Q9X1I9） Preprotein translocase subunit secE × 1 （P35874） Preprotein translocase subunit SecG × 1 （B1L914） MAGNESIUM ION × 1 ADENOSINE-5'-DIPHOSPHATE × 1 BERYLLIUM TRIFLUORIDE ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SECA_THEMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–871； UniProt 1–871 Author chain B； PDBConstruct 1–871； UniProt 1–871

Preprotein translocase subunit SecY

Thermotoga maritima MSB8

UniProt Q9X1I9

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Protein translocase subunit secA × 1 （Q9X1R4） Preprotein translocase subunit secE × 1 （P35874） Preprotein translocase subunit SecG × 1 （B1L914） MAGNESIUM ION × 1 ADENOSINE-5'-DIPHOSPHATE × 1 BERYLLIUM TRIFLUORIDE ION × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Protein translocase subunit secA × 1 （Q9X1R4） Preprotein translocase subunit secE × 1 （P35874） Preprotein translocase subunit SecG × 1 （B1L914） MAGNESIUM ION × 1 ADENOSINE-5'-DIPHOSPHATE × 1 BERYLLIUM TRIFLUORIDE ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9X1I9_THEMA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–431； UniProt 1–431 Author chain F； PDBConstruct 1–431； UniProt 1–431

Preprotein translocase subunit secE

Thermotoga maritima MSB8

UniProt P35874

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Protein translocase subunit secA × 1 （Q9X1R4） Preprotein translocase subunit SecY × 1 （Q9X1I9） Preprotein translocase subunit SecG × 1 （B1L914） MAGNESIUM ION × 1 ADENOSINE-5'-DIPHOSPHATE × 1 BERYLLIUM TRIFLUORIDE ION × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Protein translocase subunit secA × 1 （Q9X1R4） Preprotein translocase subunit SecY × 1 （Q9X1I9） Preprotein translocase subunit SecG × 1 （B1L914） MAGNESIUM ION × 1 ADENOSINE-5'-DIPHOSPHATE × 1 BERYLLIUM TRIFLUORIDE ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SECE_THEMA
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain D； PDBConstruct 1–65； UniProt 1–65 Author chain G； PDBConstruct 1–65； UniProt 1–65

Preprotein translocase subunit SecG

Thermotoga sp.

UniProt B1L914

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Protein translocase subunit secA × 1 （Q9X1R4） Preprotein translocase subunit SecY × 1 （Q9X1I9） Preprotein translocase subunit secE × 1 （P35874） MAGNESIUM ION × 1 ADENOSINE-5'-DIPHOSPHATE × 1 BERYLLIUM TRIFLUORIDE ION × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Protein translocase subunit secA × 1 （Q9X1R4） Preprotein translocase subunit SecY × 1 （Q9X1I9） Preprotein translocase subunit secE × 1 （P35874） MAGNESIUM ION × 1 ADENOSINE-5'-DIPHOSPHATE × 1 BERYLLIUM TRIFLUORIDE ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	B1L914_THESQ
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain E； PDBConstruct 1–76； UniProt 1–76 Author chain H； PDBConstruct 1–76； UniProt 1–76

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	3din
Deposition date deposition_date	2008-06-20
Structure title title	Crystal structure of the protein-translocation complex formed by the SecY channel and the SecA ATPase
Keywords keywords	;protein translocation, membrane protein, ATPase, ATP-binding, Inner membrane, Nucleotide-binding, Protein transport, Transport, Transmembrane ;; MEMBRANE PROTEIN, PROTEIN TRANSPORT
Experimental Method method	X-RAY DIFFRACTION

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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.

3din__assembly_1__model_1

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

Download this curve (.dat)

3din__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3din__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	36.56 Å
Rg (electron density)	36.24 Å
Total Rg	36.71 Å
Atom count	10684
Residues	1333
Excluded volume	193150 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3din__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3din__assembly_2__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	100643.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	21368

MILFDKNKRILKKYAKMVSKINQIESDLRSKKNSELIRLSMVLKEKVNSFEDADEHLFEAFALVREAARRTLGMRPFDVQVMGGIALHEGKVAEMKTGEGKTLAATMPIYLNALIGKGVHLVTVNDYLARRDALWMGPVYLFLGLRVGVINSLGKSYEVVWKNPDLARKAIEENWSVWPDGFNGEVLKEESMNKEAVEAFQVELKEITRKEAYLCDVTYGTNNEFGFDYLRDNLVLDYNDKVQRGHFYAIVDEADSVLIDEARTPLIISGPSKESPSVYRRFAQIAKKFVKDKDFTVDEKARTIILTEEGVAKAEKIIGVENLYDPGNVSLLYHLINALKALHLFKKDVDYVVMNGEVIIVDEFTGRLLPGRRYSGGLHQAIEAKEGVPIKEESITYATITFQNYFRMYEKLAGMTGTAKTEESEFVQVYGMEVVVIPTHKPMIRKDHDDLVFRTQKEKYEKIVEEIEKRYKKGQPVLVGTTSIEKSELLSSMLKKKGIPHQVLNAKYHEKEAEIVAKAGQKGMVTIATNMAGRGTDIKLGPGVAELGGLCIIGTERHESRRIDNQLRGRAGRQGDPGESIFFLSLEDDLLRIFGSEQIGKVMNILKIEEGQPIQHPMLSKLIENIQKKVEGINFSIRKTLMEMDDVLDKQRRAVYSLRDQILLEKDYDEYLKDIFEDVVSTRVEEFCSGKNWDIESLKNSLSFFPAGLFDLDEKQFSSSEELHDYLFNRLWEEYQRKKQEIGEDYRKVIRFLMLRIIDDHWRRYLEEVEHVKEAVQLRSYGQKDPIVEFKKETYYMFDEMMRRINDTIANYVLRVVKVSEKDEKEAKEELGKIRLVHEEFNLVNRAMRRATEKKKKKDGLHSFGRIRVKR

Source Source

Source organism organism	Thermotoga maritima MSB8
NCBI taxonomy ID ncbi_taxonomy_id	243274
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Preprotein translocase subunit SecY
Molecular weight formula_weight	48217.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,F

MWQAFKNAFKIPELRDRIIFTFLALIVFRMGIYIPVPGLNLEAWGEIFRRIAETAGVAGILSFYDVFTGGALSRFSVFTMSVTPYITASIILQLLASVMPSLKEMLREGEEGRKKFAKYTRRLTLLIGGFQAFFVSFSLARSNPDMVAPGVNVLQFTVLSTMSMLAGTMFLLWLGERITEKGIGNGISILIFAGIVARYPSYIRQAYLGGLNLLEWIFLIAVALITIFGIILVQQAERRITIQYARRVTGRRVYGGASTYLPIKVNQGGVIPIIFASAIVSIPSAIASITNNETLKNLFRAGGFLYLLIYGLLVFFFTYFYSVVIFDPREISENIRKYGGYIPGLRPGRSTEQYLHRVLNRVTFIGAVFLVVIALLPYLVQGAIKVNVWIGGTSALIAVGVALDIIQQMETHMVMRHYEGFIKKGKIRGRR

Source Source

Source organism organism	Thermotoga maritima MSB8
NCBI taxonomy ID ncbi_taxonomy_id	243274
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Preprotein translocase subunit secE
Molecular weight formula_weight	7322.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,G

MEKLRKFFREVIAEAKKISWPSRKELLTSFGVVLVILAVTSVYFFVLDFIFSGVVSAIFKALGIG

Source Source

Source organism organism	Thermotoga maritima MSB8
NCBI taxonomy ID ncbi_taxonomy_id	243274
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	Preprotein translocase subunit SecG
Molecular weight formula_weight	8251.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,H

MKTFFLIVHTIISVALIYMVQVQMSKFSELGGAFGSGGLHTVFGRRKGLDTGGKITLVLSVLFFVSCVVTAFVLTR

Source Source

Source organism organism	Thermotoga sp.
NCBI taxonomy ID ncbi_taxonomy_id	126740
Host organism host_organism	Escherichia coli

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	2

Entity 6 Entity 6 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	BERYLLIUM TRIFLUORIDE ION
Molecular weight formula_weight	66.0 kDa
Source method src_method	syn
Copy count entity_count	2

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6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (14 domains)

Domain ID domain_id	d3dina1
Class class	a — All alpha proteins
Fold Fold fold	a.162 — Pre-protein crosslinking domain of SecA
Superfamily Superfamily superfamily	a.162.1 — Pre-protein crosslinking domain of SecA
Family Family family	a.162.1.1 — Pre-protein crosslinking domain of SecA

Domain ID domain_id	d3dina2
Class class	a — All alpha proteins
Fold Fold fold	a.172 — Helical scaffold and wing domains of SecA
Superfamily Superfamily superfamily	a.172.1 — Helical scaffold and wing domains of SecA
Family Family family	a.172.1.1 — Helical scaffold and wing domains of SecA

Domain ID domain_id	d3dina3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.19 — Tandem AAA-ATPase domain

Domain ID domain_id	d3dina4
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.19 — Tandem AAA-ATPase domain

Domain ID domain_id	d3dinb1
Class class	a — All alpha proteins
Fold Fold fold	a.162 — Pre-protein crosslinking domain of SecA
Superfamily Superfamily superfamily	a.162.1 — Pre-protein crosslinking domain of SecA
Family Family family	a.162.1.1 — Pre-protein crosslinking domain of SecA

Domain ID domain_id	d3dinb2
Class class	a — All alpha proteins
Fold Fold fold	a.172 — Helical scaffold and wing domains of SecA
Superfamily Superfamily superfamily	a.172.1 — Helical scaffold and wing domains of SecA
Family Family family	a.172.1.1 — Helical scaffold and wing domains of SecA

Domain ID domain_id	d3dinb3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.19 — Tandem AAA-ATPase domain

Domain ID domain_id	d3dinb4
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.19 — Tandem AAA-ATPase domain

Domain ID domain_id	d3dinc_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.41 — Preprotein translocase SecY subunit
Superfamily Superfamily superfamily	f.41.1 — Preprotein translocase SecY subunit
Family Family family	f.41.1.1 — Preprotein translocase SecY subunit

Domain ID domain_id	d3dind_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.23 — Single transmembrane helix
Superfamily Superfamily superfamily	f.23.28 — Preprotein translocase SecE subunit
Family Family family	f.23.28.1 — Preprotein translocase SecE subunit

Domain ID domain_id	d3dine_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.17 — Transmembrane helix hairpin
Superfamily Superfamily superfamily	f.17.6 — Sec-beta or SecG subunit of protein translocation channel
Family Family family	f.17.6.2 — SecG subunit

Domain ID domain_id	d3dinf_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.41 — Preprotein translocase SecY subunit
Superfamily Superfamily superfamily	f.41.1 — Preprotein translocase SecY subunit
Family Family family	f.41.1.1 — Preprotein translocase SecY subunit

Domain ID domain_id	d3ding_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.23 — Single transmembrane helix
Superfamily Superfamily superfamily	f.23.28 — Preprotein translocase SecE subunit
Family Family family	f.23.28.1 — Preprotein translocase SecE subunit

Domain ID domain_id	d3dinh_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.17 — Transmembrane helix hairpin
Superfamily Superfamily superfamily	f.17.6 — Sec-beta or SecG subunit of protein translocation channel
Family Family family	f.17.6.2 — SecG subunit

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Unit-cell length a length_a	101.616 Å
Unit-cell length b length_b	156.003 Å
Unit-cell length c length_c	358.155 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	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	4.500 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	0.2790
R_work r_work	0.2790
R_free r_free	0.3030

Crystal structure of the protein-translocation complex formed by the SecY channel and the SecA ATPase

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

Preprotein 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

Preprotein translocase subunit 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3din__assembly_1__model_1

3din__assembly_1__model_1 | I(q)

3din__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

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

6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (14 domains)

7. Citations (1)