SAXSdb — 1rh5

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

Preprotein translocase secY subunit

Methanocaldococcus jannaschii

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Preprotein translocase secE subunit × 1 （Q57817） SecBeta × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SECY_METJA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–436； UniProt 1–436

Preprotein translocase secE subunit

Methanocaldococcus jannaschii

UniProt Q57817

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Preprotein translocase secY subunit × 1 （Q60175） SecBeta × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SECE_METJA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–74； UniProt 1–74

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	1rh5
Deposition date deposition_date	2003-11-13
Structure title title	The structure of a protein conducting channel
Keywords keywords	Protein translocation, SecY, Membrane Protein, Protein Channels, 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.

1rh5__assembly_1__model_1

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

Download this curve (.dat)

1rh5__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1rh5__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.64 Å
Rg (electron density)	23.72 Å
Total Rg	24.76 Å
Atom count	3852
Residues	498
Excluded volume	71445 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1rh5__assembly_1__model_1`	trimeric （3）	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 (3)

Entity 1 Entity 1 polymer

Description description	Preprotein translocase secY subunit
Molecular weight formula_weight	47512.9 kDa
Mutation mutation	R422K, T423V
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	3852

MKKLIPILEKIPEVELPVKEITFKEKLKWTGIVLVLYFIMGCIDVYTAGAQIPAIFEFWQTITASRIGTLITLGIGPIVTAGIIMQLLVGSGIIQMDLSIPENRALFQGCQKLLSIIMCFVEAVLFVGAGAFGILTPLLAFLVIIQIAFGSIILIYLDEIVSKYGIGSGIGLFIAAGVSQTIFVGALGPEGYLWKFLNSLIQGVPNIEYIAPIIGTIIVFLMVVYAECMRVEIPLAHGRIKGAVGKYPIKFVYVSNIPVILAAALFANIQLWGLALYRMGIPILGHYEGGRAVDGIAYYLSTPYGLSSVISDPIHAIVYMIAMIITCVMFGIFWVETTGLDPKSMAKRIGSLGMAIKGFRKSEKAIEHRLKRYIPPLTVMSSAFVGFLATIANFIGALGGGTGVLLTVSIVYRMYEQLLRERTSELHPAIAKLLNK

Source Source

Source organism organism	Methanocaldococcus jannaschii
NCBI taxonomy ID ncbi_taxonomy_id	2190
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Preprotein translocase secE subunit
Molecular weight formula_weight	8451.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MKTDFNQKIEQLKEFIEECRRVWLVLKKPTKDEYLAVAKVTALGISLLGIIGYIIHVPATYIKGILKPPTTPRV

Source Source

Source organism organism	Methanocaldococcus jannaschii
NCBI taxonomy ID ncbi_taxonomy_id	2190
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	SecBeta
Molecular weight formula_weight	5967.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MSKREETGLATSAGLIRYMDETFSKIRVKPEHVIGVTVAFVIIEAILTYGRFL

Source Source

Source organism organism	Methanocaldococcus jannaschii
NCBI taxonomy ID ncbi_taxonomy_id	2190
Host organism host_organism	Escherichia coli

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6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1rh5a_
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	d1rh5b_
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	d1rh5c_
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.17.6.1 — Sec-beta subunit

CATH v4.4 (2 domains)

Domain ID domain_id	1rh5A00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3370 — Preprotein translocase SecY subunit
Homologous superfamily homologous superfamily	10 — SecY subunit domain

Domain ID domain_id	1rh5B00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	820 — Preprotein translocase SecE subunit

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Unit-cell length a length_a	102.930 Å
Unit-cell length b length_b	156.650 Å
Unit-cell length c length_c	69.800 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	4

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	3.200 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.2420
R_work r_work	0.2420
R_free r_free	0.2880

The structure of a protein conducting channel

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

Preprotein translocase secY subunit

State in the Current Structure

Other States of the Same Protein in the Database

Preprotein translocase secE 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

1rh5__assembly_1__model_1

1rh5__assembly_1__model_1 | I(q)

1rh5__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 (3)

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

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

CATH v4.4 (2 domains)

7. Citations (1)

The structure of a protein conducting channel

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

Preprotein translocase secY 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

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

1rh5__assembly_1__model_1

1rh5__assembly_1__model_1 | I(q)

1rh5__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 (3)

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

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

CATH v4.4 (2 domains)

7. Citations (1)