5eul

Structure of the SecA-SecY complex with a translocating polypeptide substrate

Method: X-RAY DIFFRACTION

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

Protein translocase subunit SecA, Insertion Peptide Chimera

Bacillus subtilis

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 SecY × 1 （A4IJK8） Preprotein translocase SecE subunit × 1 （A4IJH4） AYC08 × 1 MAGNESIUM ION × 1 BERYLLIUM TRIFLUORIDE ION × 1 ADENOSINE-5'-DIPHOSPHATE × 1 HEXATANTALUM DODECABROMIDE × 18	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 1–742； UniProt 1–742 Author chain A； PDBConstruct 791–827； UniProt 744–780

Protein translocase subunit SecY

Geobacillus thermodenitrificans (strain NG80-2)

UniProt A4IJK8

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, Insertion Peptide Chimera × 1 （P28366） Preprotein translocase SecE subunit × 1 （A4IJH4） AYC08 × 1 MAGNESIUM ION × 1 BERYLLIUM TRIFLUORIDE ION × 1 ADENOSINE-5'-DIPHOSPHATE × 1 HEXATANTALUM DODECABROMIDE × 18	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 1–424； UniProt 1–430

Preprotein translocase SecE subunit

Geobacillus thermodenitrificans (strain NG80-2)

UniProt A4IJH4

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, Insertion Peptide Chimera × 1 （P28366） Protein translocase subunit SecY × 1 （A4IJK8） AYC08 × 1 MAGNESIUM ION × 1 BERYLLIUM TRIFLUORIDE ION × 1 ADENOSINE-5'-DIPHOSPHATE × 1 HEXATANTALUM DODECABROMIDE × 18	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

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	5eul
Deposition date deposition_date	2015-11-18
Structure title title	Structure of the SecA-SecY complex with a translocating polypeptide substrate
Keywords keywords	SecY, SecA, ATPase, channel, PROTEIN TRANSPORT; 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.

5eul__assembly_1__model_1

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

Download this curve (.dat)

5eul__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5eul__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	37.81 Å
Rg (electron density)	38.33 Å
Total Rg	38.19 Å
Atom count	10511
Residues	1297
Excluded volume	193520 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5eul__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 (8)

Entity 1 Entity 1 polymer

Description description	Protein translocase subunit SecA, Insertion Peptide Chimera
Molecular weight formula_weight	94360.2 kDa
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	10511

MLGILNKMFDPTKRTLNRYEKIANDIDAIRGDYENLSDDALKHKTIEFKERLEKGATTDDLLVEAFAVVREASRRVTGMFPFKVQLMGGVALHDGNIAEMKTGEGKTLTSTLPVYLNALTGKGVHVVTVNEYLASRDAEQMGKIFEFLGLTVGLNLNSMSKDEKREAYAADITYSTNNELGFDYLRDNMVLYKEQMVQRPLHFAVIDEVDSILIDEARTPLIISGQAAKSTKLYVQANAFVRTLKAEKDYTYDIKTKAVQLTEEGMTKAEKAFGIDNLFDVKHVALNHHINQALKAHVAMQKDVDYVVEDGQVVIVDSFTGRLMKGRRYSEGLHQAIEAKEGLEIQNESMTLATITFQNYFRMYEKLAGMTGTAKTEEEEFRNIYNMQVVTIPTNRPVVRDDRPDLIYRTMEGKFKAVAEDVAQRYMTGQPVLVGTVAVETSELISKLLKNKGIPHQVLNAKNHEREAQIIEEAGQKGAVTIATNMAGRGTDIKLGEGVKELGGLAVVGTERHESRRIDNQLRGRSGRQGDPGITQFYLSMEDELMRRFGAERTMAMLDRFGMDDSTPIQSKMVSRAVESSQKRVEGNNFDSRKQLLQYDDVLRQQREVIYKQRFEVIDSENLREIVENMIKSSLERAIAAYTPREELPEEWKLDGLVDLINTTYLDEGALEKSDIFGKEPDEMLELIMDRIITKYNEKEEQFGKEQMREFEKVIVLRAVDSKWMDHIDAMDQLRQGIHLRGSGGSGGKKTAIAIAVALAGFATVASYAQYEDGCSGELERQHTFAGGPGAQTNPLREYQMEGFAMFEHMIESIEDEVAKFVMKAEITSLEVLFQG

Source Source

Source organism organism	Bacillus subtilis
NCBI taxonomy ID ncbi_taxonomy_id	224308
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Protein translocase subunit SecY
Molecular weight formula_weight	46768.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Y

MFRTISNFMRVSDIRNKIIFTLLMLIVFRIGTFIPVPSVNTDVLKLQDQLNAFGVLNIFCGGALQNFSIFAMGVMPYITASIIVQLLQMDVVPKFAEWSKQGEMGRRKLAQFTRYFTIVLGFIQALGMSYGFNNLAGGMLIQNPGIGTYLLIAVVLTAGTAFLMWLGEQITAKGVGNGISIIIFAGIVSGIPTILNQIYAQTFGGLNIVRLLLVALAVVAVIVGVIYIQQAFRKIPIQYAKRLEGRNPVGGHSTHLPLKVNPAGVIPVIFAVSFLIAPPTIASFFGTNDVTLWIRRTFDYTHPVGMTIYVVLIIAFTYFYAFVQVNPEQMADNLKKQGGYIPGIRPGKNTQEYVTRILYRLTLVGSLFLAFIAVLPVFFVNFANLPPSAQIGGTSLLIVVGVALETMKQLESQLVKRHYRGFIK

Source Source

Source organism organism	Geobacillus thermodenitrificans (strain NG80-2)
NCBI taxonomy ID ncbi_taxonomy_id	420246
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Preprotein translocase SecE subunit
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 (strain NG80-2)
NCBI taxonomy ID ncbi_taxonomy_id	420246
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	AYC08
Molecular weight formula_weight	14475.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	V

QVQLVETGGGLVQPGGSLRLSCGASGSIFNMYAMGWYRQAPGKQREVVARIATDDSTMYPDSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCYYQRTVMSQPYWGQGTQVTVSSGGLPETGGHHHHHH

Source Source

Source organism organism	Vicugna pacos
NCBI taxonomy ID ncbi_taxonomy_id	30538
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	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

Entity 8 Entity 8 non-polymer

Description description	HEXATANTALUM DODECABROMIDE
Molecular weight formula_weight	2044.5 kDa
Source method src_method	syn
Copy count entity_count	18

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6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	5eulA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	5eulA02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1440 — Pre-protein croslinking domain of SecA
Homologous superfamily homologous superfamily	10 — SecA, preprotein cross-linking domain

Domain ID domain_id	5eulV00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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Unit-cell length a length_a	127.798 Å
Unit-cell length b length_b	127.798 Å
Unit-cell length c length_c	554.772 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 61 2 2
Space-group number int_tables_number	178
Crystal system crystal_system	—

Resolution resolution	3.700 Å
Low-resolution limit resolution_low	53.852 Å
R factor r_factor	0.2962
R_work r_work	0.2952
R_free r_free	0.3148

Structure of the SecA-SecY complex with a translocating polypeptide substrate

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

Protein translocase subunit SecA, Insertion Peptide Chimera

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

Preprotein translocase SecE subunit

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

5eul__assembly_1__model_1

5eul__assembly_1__model_1 | I(q)

5eul__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (8)

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

Entity 8 Entity 8 non-polymer

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)