SAXSdb — 2zjs

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

Preprotein translocase SecY subunit

Thermus thermophilus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Preprotein translocase SecE subunit × 1 （Q8KZP4） ZINC ION × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	Preprotein translocase SecE subunit × 1 （Q8KZP4） Fab56 (heavy chain) × 1 Fab56 (light chain) × 1 ZINC ION × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 4	Preprotein translocase SecE subunit × 2 （Q8KZP4） ZINC ION × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8KZP3_THETH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain Y； PDBConstruct 1–434； UniProt 1–434

Preprotein translocase SecE subunit

Thermus thermophilus

UniProt Q8KZP4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Preprotein translocase SecY subunit × 1 （Q8KZP3） ZINC ION × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	Preprotein translocase SecY subunit × 1 （Q8KZP3） Fab56 (heavy chain) × 1 Fab56 (light chain) × 1 ZINC ION × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 4	Preprotein translocase SecY subunit × 2 （Q8KZP3） ZINC ION × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8KZP4_THETH
Isoform	—
PDB entities	2
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	2zjs
Deposition date deposition_date	2008-03-08
Structure title title	Crystal Structure of SecYE translocon from Thermus thermophilus with a Fab fragment
Keywords keywords	;Translocon, Sec, Protein-conducting-channel, Membrane, Protein transport, Translocation, Transmembrane, Transport, PROTEIN TRANSPORT-IMMUNE SYSTEM COMPLEX ;; PROTEIN TRANSPORT/IMMUNE SYSTEM
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.

2zjs__assembly_1__model_1

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

Download this curve (.dat)

2zjs__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2zjs__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.36 Å
Rg (electron density)	24.13 Å
Total Rg	25.04 Å
Atom count	3597
Residues	461
Excluded volume	66014 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2zjs__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2zjs__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2zjs__assembly_3__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2zjs__assembly_4__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`2zjs__assembly_5__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 (5)

Entity 1 Entity 1 polymer

Description description	Preprotein translocase SecY subunit
Molecular weight formula_weight	47643.1 kDa
Mutation mutation	L2V, R252G
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Y
Atom count atom_count	6932

MVKAFWSALQIPELRQRVLFTLLVLAAYRLGAFIPTPGVDLDKIQEFLRTAQGGVFGIINLFSGGNFERFSIFALGIMPYITAAIIMQILVTVVPALEKLSKEGEEGRRIINQYTRIGGIALGAFQGFFLATAFLGAEGGRFLLPGWSPGPFFWFVVVVTQVAGIALLLWMAERITEYGIGNGTSLIIFAGIVVEWLPQILRTIGLIRTGEVNLVAFLFFLAFIVLAFAGMAAVQQAERRIPVQYARKVVGGRVYGGQATYIPIKLNAAGVIPIIFAAAILQIPIFLAAPFQDNPVLQGIANFFNPTRPSGLFIEVLLVILFTYVYTAVQFDPKRIAESLREYGGFIPGIRPGEPTVKFLEHIVSRLTLWGALFLGLVTLLPQIIQNLTGIHSIAFSGIGLLIVVGVALDTLRQVESQLMLRSYEGFLSRGRLR

Source Source

Source organism organism	Thermus thermophilus
NCBI taxonomy ID ncbi_taxonomy_id	274
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Preprotein translocase SecE subunit
Molecular weight formula_weight	7072.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

MFARLIRYFQEARAELARVTWPTREQVVEGTQAILLFTLAFMVILGLYDTVFRFLIGLLR

Source Source

Source organism organism	Thermus thermophilus
NCBI taxonomy ID ncbi_taxonomy_id	274
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Fab56 (heavy chain)
Molecular weight formula_weight	23781.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

QVQLQQSGAELMKPGASVKISCKATGYTFSSYWIAWVKQRPGHGLEWIGEILPGSGSTNYNEKFKGKATFTADTSSNTAYMQLSSLTSEDSAVYYCARSPYYYGNWDYWGQGTTLTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDC

Source Source

Source organism organism	Mus musculus
Common name common_name	mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090

Entity 4 Entity 4 polymer

Description description	Fab56 (light chain)
Molecular weight formula_weight	23736.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

DIQMTQTTSSLSASLGDRVTISCRASQDISNYLNWYQQKPDGTVKLLIYYTSRLHSGVPSRFSGSGSGTDYSLTISNLEQEDIATYFCQQGNTLPWTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Source Source

Source organism organism	Mus musculus
Common name common_name	mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090

Entity 5 Entity 5 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2zjsh1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d2zjsh2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (6 domains)

Domain ID domain_id	2zjsE00
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	1030 — Preprotein translocase secy subunit

Domain ID domain_id	2zjsH01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2zjsH02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2zjsL01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2zjsL02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2zjsY00
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

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Unit-cell length a length_a	189.096 Å
Unit-cell length b length_b	103.073 Å
Unit-cell length c length_c	78.005 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	105.18 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	3.200 Å
Low-resolution limit resolution_low	48.430 Å
R factor r_factor	0.2460
R_work r_work	0.2442
R_free r_free	0.2798

Crystal Structure of SecYE translocon from Thermus thermophilus with a Fab fragment

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

2zjs__assembly_1__model_1

2zjs__assembly_1__model_1 | I(q)

2zjs__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 (5)

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

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (2 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Crystal Structure of SecYE translocon from Thermus thermophilus with a Fab fragment

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

2zjs__assembly_1__model_1

2zjs__assembly_1__model_1 | I(q)

2zjs__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 (5)

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

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (2 domains)

CATH v4.4 (6 domains)

7. Citations (1)