2ipc

Crystal structure of the translocation ATPase SecA from Thermus thermophilus reveals a parallel, head-to-head dimer

Method: X-RAY DIFFRACTION

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

Preprotein translocase SecA subunit

Thermus thermophilus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5SIW3_THET8
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–997； UniProt 1–997 Author chain B； PDBConstruct 1–997； UniProt 1–997 Author chain C； PDBConstruct 1–997； UniProt 1–997 Author chain D； PDBConstruct 1–997； UniProt 1–997

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	2ipc
Deposition date deposition_date	2006-10-12
Structure title title	Crystal structure of the translocation ATPase SecA from Thermus thermophilus reveals a parallel, head-to-head dimer
Keywords keywords	;nucleotide binding fold, ATPase, parallel dimer, Structural Genomics, RIKEN Structural Genomics/Proteomics Initiative, RSGI, TRANSPORT PROTEIN ;; TRANSPORT PROTEIN
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.

2ipc__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2ipc__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2ipc__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	44.90 Å
Rg (electron density)	44.72 Å
Total Rg	44.99 Å
Atom count	15066
Residues	1873
Excluded volume	268440 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2ipc__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2ipc__assembly_2__model_1`	dimeric （2）	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 (2)

Entity 1 Entity 1 polymer

Description description	Preprotein translocase SecA subunit
Molecular weight formula_weight	114132.2 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	31502

MLGLLRRLFDNNEREIARYYKQVVEPVNRLEAEVEKLPDLAAAYRELKEKHEKGASLDELLPMAFALTRESAKRYLGMRHFDVQLIGGAVLHEGKIAEMKTGEGKTLVATLAVALNALTGKGVHVVTVNDYLARRDAEWMGPVYRGLGLSVGVIQHASTPAERRKAYLADVTYVTNSELGFDYLRDNMAISPDQLVLRHDHPLHYAIIDEVDSILIDEARTPLIISGPAEKATDLYYKMAEIAKKLERGLPAEPGVRKEPTGDYTVEEKNRSVHLTLQGIAKAEKLLGIEGLFSPENMELAHMLIQAIRAKELYHRDRDYIVQDGQVIIVDEFTGRLMPGRRYGEGLHQAIEAKEGVRIERENQTLATITYQNFFRLYEKRAGMTGTAKTEEKEFQEIYGMDVVVVPTNRPVIRKDFPDVVYRTEKGKFYAVVEEIAEKYERGQPVLVGTISIEKSERLSQMLKEPRLYLPRLEMRLELFKKASQKQQGPEWERLRKLLERPAQLKDEDLAPFEGLIPPKGNLRTAWEGLKRAVHTLAVLRQGIPHQVLNAKHHAREAEIVAQAGRSKTVTIATNMAGRGTDIKLGGNPEYLAAALLEKEGFDRYEWKVELFIKKMVAGKEEEARALAQELGIREELLERIREIREECKQDEERVRALGGLFIIGTERHESRRIDNQLRGRAGRQGDPGGSRFYVSFDDDLMRLFASDRVIAMLDRMGFDDSEPIEHPMVTRSIERAQKRVEDRNFAIRKQLLQFDDVLSRQREVIYAQRRLILLGKDEEVKEAAIGMVEETVASLAENFLNPEVHPEDWDLEGLKATLLDTAPQLQDFPFAELRALKAEEAVERLVEAALKAYEAREAELSPPLMRAVERFVILNVVDNAWKEHLHNLDVLRQGIFLRGYGQKDPFQEYKIEATRLFNEMVAFIKSEVAKFLFRLKVEAEPVRPVREAPYVPVPEAKPEPSEVFGVERKRATPPPQPGLSRAERRRLMRQEKKRKK

Source Source

Source organism organism	Thermus thermophilus
NCBI taxonomy ID ncbi_taxonomy_id	300852
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1370

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6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id	2ipcA01
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	2ipcA02
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	2ipcA04
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3060 — Helical scaffold and wing domains of SecA
Homologous superfamily homologous superfamily	10 — Helical scaffold and wing domains of SecA

Domain ID domain_id	2ipcB01
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	2ipcB02
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	2ipcB04
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3060 — Helical scaffold and wing domains of SecA
Homologous superfamily homologous superfamily	10 — Helical scaffold and wing domains of SecA

Domain ID domain_id	2ipcC01
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	2ipcC02
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	2ipcC04
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3060 — Helical scaffold and wing domains of SecA
Homologous superfamily homologous superfamily	10 — Helical scaffold and wing domains of SecA

Domain ID domain_id	2ipcD01
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	2ipcD02
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	2ipcD04
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3060 — Helical scaffold and wing domains of SecA
Homologous superfamily homologous superfamily	10 — Helical scaffold and wing domains of SecA

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Unit-cell length a length_a	168.623 Å
Unit-cell length b length_b	168.623 Å
Unit-cell length c length_c	149.758 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 32
Space-group number int_tables_number	145
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	0.2213
R_work r_work	0.2213
R_free r_free	0.2545

Crystal structure of the translocation ATPase SecA from Thermus thermophilus reveals a parallel, head-to-head dimer

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

Preprotein translocase SecA subunit

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2ipc__assembly_2__model_1

2ipc__assembly_2__model_1 | I(q)

2ipc__assembly_2__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)

Crystal structure of the translocation ATPase SecA from Thermus thermophilus reveals a parallel, head-to-head dimer

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

Preprotein translocase SecA 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

2ipc__assembly_2__model_1

2ipc__assembly_2__model_1 | I(q)

2ipc__assembly_2__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)