SAXSdb — 5e4w

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

Thioredoxin-1

Escherichia coli O157:H7

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Signal recognition particle 43 kDa protein, chloroplastic × 1 （O22265） Inner membrane protein ALBINO3, chloroplastic × 1 （Q8LBP4） GLYCEROL × 1 CALCIUM ION × 1 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	Signal recognition particle 43 kDa protein, chloroplastic × 2 （O22265） Inner membrane protein ALBINO3, chloroplastic × 2 （Q8LBP4） GLYCEROL × 2 CALCIUM ION × 2 water × 6	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 3	Signal recognition particle 43 kDa protein, chloroplastic × 1 （O22265） Inner membrane protein ALBINO3, chloroplastic × 1 （Q8LBP4） GLYCEROL × 1 CALCIUM ION × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	THIO_ECO57
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–107； UniProt 3–109 Author chain B； PDBConstruct 1–107； UniProt 3–109

Signal recognition particle 43 kDa protein, chloroplastic

Arabidopsis thaliana

UniProt O22265

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Thioredoxin-1 × 1 （P0AA27） Inner membrane protein ALBINO3, chloroplastic × 1 （Q8LBP4） GLYCEROL × 1 CALCIUM ION × 1 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	Thioredoxin-1 × 2 （P0AA27） Inner membrane protein ALBINO3, chloroplastic × 2 （Q8LBP4） GLYCEROL × 2 CALCIUM ION × 2 water × 6	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 3	Thioredoxin-1 × 1 （P0AA27） Inner membrane protein ALBINO3, chloroplastic × 1 （Q8LBP4） GLYCEROL × 1 CALCIUM ION × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SR43C_ARATH
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–105； UniProt 265–369 Author chain D； PDBConstruct 1–105； UniProt 265–369

Inner membrane protein ALBINO3, chloroplastic

Arabidopsis thaliana

UniProt Q8LBP4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Thioredoxin-1 × 1 （P0AA27） Signal recognition particle 43 kDa protein, chloroplastic × 1 （O22265） GLYCEROL × 1 CALCIUM ION × 1 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	Thioredoxin-1 × 2 （P0AA27） Signal recognition particle 43 kDa protein, chloroplastic × 2 （O22265） GLYCEROL × 2 CALCIUM ION × 2 water × 6	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 3	Thioredoxin-1 × 1 （P0AA27） Signal recognition particle 43 kDa protein, chloroplastic × 1 （O22265） GLYCEROL × 1 CALCIUM ION × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ALB3_ARATH
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain E； PDBConstruct 1–9； UniProt 453–461 Author chain F； PDBConstruct 1–9； UniProt 453–461

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	5e4w
Deposition date deposition_date	2015-10-07
Structure title title	Crystal structure of cpSRP43 chromodomains 2 and 3 in complex with the Alb3 tail
Keywords keywords	Signal recognition particle, chromodomain, membrane insertase Alb3, chloroplast, signaling protein, 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.

5e4w__assembly_1__model_1

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

Download this curve (.dat)

5e4w__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5e4w__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.02 Å
Rg (electron density)	22.37 Å
Total Rg	23.11 Å
Atom count	1752
Residues	222
Excluded volume	31240 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5e4w__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5e4w__assembly_2__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`5e4w__assembly_3__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 (6)

Entity 1 Entity 1 polymer

Description description	Thioredoxin-1
Molecular weight formula_weight	11744.4 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	3545

DKIIHLTDDSFDTDVLKADGAILVDFWAEWCGPCKMIAPILDEIADEYQGKLTVAKLNIDQNPGTAPKYGIRGIPTLLLFKNGEVAATKVGALSKGQLKEFLDANLAGS

Source Source

Source organism organism	Escherichia coli O157:H7
NCBI taxonomy ID ncbi_taxonomy_id	83334
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Signal recognition particle 43 kDa protein, chloroplastic
Molecular weight formula_weight	12032.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

QVFEYAEVDEIVEKRGKGKDVEYLVRWKDGGDCEWVKGVHVAEDVAKDYEDGLEYAVAESVIGKRVGDDGKTIEYLVKWTDMSDATWEPQDNVDSTLVLLYQQQQ

Source Source

Source organism organism	Arabidopsis thaliana
Common name common_name	Mouse-ear cress
NCBI taxonomy ID ncbi_taxonomy_id	3702
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Inner membrane protein ALBINO3, chloroplastic
Molecular weight formula_weight	1152.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

SKRSKRKRT

Source Source

Source organism organism	Arabidopsis thaliana
Common name common_name	Mouse-ear cress
NCBI taxonomy ID ncbi_taxonomy_id	3702
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	41

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d5e4wa1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.47 — Thioredoxin fold
Superfamily Superfamily superfamily	c.47.1 — Thioredoxin-like
Family Family family	c.47.1.1 — Thioltransferase

Domain ID domain_id	d5e4wa2
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

Domain ID domain_id	d5e4wb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.47 — Thioredoxin fold
Superfamily Superfamily superfamily	c.47.1 — Thioredoxin-like
Family Family family	c.47.1.1 — Thioltransferase

Domain ID domain_id	d5e4wb2
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 (4 domains)

Domain ID domain_id	5e4wA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	30 — Glutaredoxin
Homologous superfamily homologous superfamily	10 — Glutaredoxin

Domain ID domain_id	5e4wB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	30 — Glutaredoxin
Homologous superfamily homologous superfamily	10 — Glutaredoxin

Domain ID domain_id	5e4wC02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	5e4wD02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	40 —

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Unit-cell length a length_a	79.592 Å
Unit-cell length b length_b	163.668 Å
Unit-cell length c length_c	37.430 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 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	45.000 Å
R factor r_factor	0.2517
R_work r_work	0.2495
R_free r_free	0.2915

Crystal structure of cpSRP43 chromodomains 2 and 3 in complex with the Alb3 tail

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

Thioredoxin-1

State in the Current Structure

Other States of the Same Protein in the Database

Signal recognition particle 43 kDa protein, chloroplastic

State in the Current Structure

Other States of the Same Protein in the Database

Inner membrane protein ALBINO3, chloroplastic

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

5e4w__assembly_1__model_1

5e4w__assembly_1__model_1 | I(q)

5e4w__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 (6)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of cpSRP43 chromodomains 2 and 3 in complex with the Alb3 tail

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

Thioredoxin-1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Signal recognition particle 43 kDa protein, chloroplastic

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Inner membrane protein ALBINO3, chloroplastic

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

5e4w__assembly_1__model_1

5e4w__assembly_1__model_1 | I(q)

5e4w__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 (6)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)