2puk

Crystal structure of the binary complex between ferredoxin: thioredoxin reductase and thioredoxin m

Method: X-RAY DIFFRACTION

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

Ferredoxin-thioredoxin reductase, catalytic chain

Synechocystis sp.

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Ferredoxin-thioredoxin reductase, variable chain × 1 （Q55781） Thioredoxin M-type, chloroplast (TRX-M) × 1 （P07591） IRON/SULFUR CLUSTER × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Ferredoxin-thioredoxin reductase, variable chain × 1 （Q55781） Thioredoxin M-type, chloroplast (TRX-M) × 1 （P07591） IRON/SULFUR CLUSTER × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q55389_SYNY3
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–109； UniProt 9–116 Author chain E； PDBConstruct 2–109； UniProt 9–116

Ferredoxin-thioredoxin reductase, variable chain

Synechocystis sp.

UniProt Q55781

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Ferredoxin-thioredoxin reductase, catalytic chain × 1 （Q55389） Thioredoxin M-type, chloroplast (TRX-M) × 1 （P07591） IRON/SULFUR CLUSTER × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Ferredoxin-thioredoxin reductase, catalytic chain × 1 （Q55389） Thioredoxin M-type, chloroplast (TRX-M) × 1 （P07591） IRON/SULFUR CLUSTER × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	FTRV_SYNY3
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–73； UniProt 1–73 Author chain F； PDBConstruct 1–73； UniProt 1–73

Thioredoxin M-type, chloroplast (TRX-M)

Spinacia oleracea

UniProt P07591

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Ferredoxin-thioredoxin reductase, catalytic chain × 1 （Q55389） Ferredoxin-thioredoxin reductase, variable chain × 1 （Q55781） IRON/SULFUR CLUSTER × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Ferredoxin-thioredoxin reductase, catalytic chain × 1 （Q55389） Ferredoxin-thioredoxin reductase, variable chain × 1 （Q55781） IRON/SULFUR CLUSTER × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TRXM_SPIOL
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–106； UniProt 75–180 Author chain G； PDBConstruct 1–106； UniProt 75–180

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	2puk
Deposition date deposition_date	2007-05-09
Structure title title	Crystal structure of the binary complex between ferredoxin: thioredoxin reductase and thioredoxin m
Keywords keywords	Thioredoxin, protein-protein complex, redox, iron-sulfur, ELECTRON TRANSPORT; ELECTRON 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.

2puk__assembly_1__model_1

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

Download this curve (.dat)

2puk__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2puk__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.14 Å
Rg (electron density)	20.35 Å
Total Rg	20.99 Å
Atom count	2288
Residues	287
Excluded volume	40856 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2puk__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2puk__assembly_2__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 (4)

Entity 1 Entity 1 polymer

Description description	Ferredoxin-thioredoxin reductase, catalytic chain
Molecular weight formula_weight	12453.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,E
Atom count atom_count	4578

NNKTLAAMKNFAEQYAKRTDTYFCSDLSVTAVVIEGLARHKEELGSPLCPCRHYEDKEAEVKNTFWNCPCVPMRERKECHCMLFLTPDNDFAGDAQDIPMETLEEVKAS

Source Source

Source organism organism	Synechocystis sp.
NCBI taxonomy ID ncbi_taxonomy_id	1143
Host organism host_organism	Escherichia coli BL21

Entity 2 Entity 2 polymer

Description description	Ferredoxin-thioredoxin reductase, variable chain
Molecular weight formula_weight	8326.5 kDa
Mutation mutation	C40S
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MNVGDRVRVTSSVVVYHHPEHKKTAFDLQGMEGEVAAVLTEWQGRPISANLPVLVKFEQRFKAHFRPDEVTLI

Source Source

Source organism organism	Synechocystis sp.
NCBI taxonomy ID ncbi_taxonomy_id	1143
Host organism host_organism	Escherichia coli BL21

Entity 3 Entity 3 polymer

Description description	Thioredoxin M-type, chloroplast (TRX-M)
Molecular weight formula_weight	11864.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

EVQDVNDSSWKEFVLESEVPVMVDFWAPWCGPSKLIAPVIDELAKEYSGKIAVYKLNTDEAPGIATQYNIRSIPTVLFFKNGERKESIIGAVPKSTLTDSIEKYLS

Source Source

Source organism organism	Spinacia oleracea
Common name common_name	spinach
NCBI taxonomy ID ncbi_taxonomy_id	3562
Host organism host_organism	Escherichia coli BL21

Entity 4 Entity 4 non-polymer

Description description	IRON/SULFUR CLUSTER
Molecular weight formula_weight	351.6 kDa
Source method src_method	syn
Copy count entity_count	2

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6. Fold Classification (SCOP + CATH) 13 domains

SCOP 2.08 (7 domains)

Domain ID domain_id	d2puka_
Class class	g — Small proteins
Fold Fold fold	g.36 — Ferredoxin thioredoxin reductase (FTR), catalytic beta chain
Superfamily Superfamily superfamily	g.36.1 — Ferredoxin thioredoxin reductase (FTR), catalytic beta chain
Family Family family	g.36.1.1 — Ferredoxin thioredoxin reductase (FTR), catalytic beta chain

Domain ID domain_id	d2pukb_
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.4 — Electron transport accessory proteins
Family Family family	b.34.4.3 — Ferredoxin thioredoxin reductase (FTR), alpha (variable) chain

Domain ID domain_id	d2pukc_
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	d2puke2
Class class	g — Small proteins
Fold Fold fold	g.36 — Ferredoxin thioredoxin reductase (FTR), catalytic beta chain
Superfamily Superfamily superfamily	g.36.1 — Ferredoxin thioredoxin reductase (FTR), catalytic beta chain
Family Family family	g.36.1.1 — Ferredoxin thioredoxin reductase (FTR), catalytic beta chain

Domain ID domain_id	d2puke3
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	d2pukf_
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.4 — Electron transport accessory proteins
Family Family family	b.34.4.3 — Ferredoxin thioredoxin reductase (FTR), alpha (variable) chain

Domain ID domain_id	d2pukg_
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

CATH v4.4 (6 domains)

Domain ID domain_id	2pukA00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	460 — Ferredoxin Thioredoxin Reductase
Homologous superfamily homologous superfamily	10 — Ferredoxin thioredoxin reductase catalytic beta subunit

Domain ID domain_id	2pukB00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	2pukC00
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	2pukE00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	460 — Ferredoxin Thioredoxin Reductase
Homologous superfamily homologous superfamily	10 — Ferredoxin thioredoxin reductase catalytic beta subunit

Domain ID domain_id	2pukF00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	2pukG00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	30 — Glutaredoxin
Homologous superfamily homologous superfamily	10 — Glutaredoxin

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Unit-cell length a length_a	53.952 Å
Unit-cell length b length_b	42.223 Å
Unit-cell length c length_c	145.344 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.29 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2370
R_work r_work	0.2350
R_free r_free	0.2840

Crystal structure of the binary complex between ferredoxin: thioredoxin reductase and thioredoxin m

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

Ferredoxin-thioredoxin reductase, catalytic chain

State in the Current Structure

Other States of the Same Protein in the Database

Ferredoxin-thioredoxin reductase, variable chain

State in the Current Structure

Other States of the Same Protein in the Database

Thioredoxin M-type, chloroplast (TRX-M)

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

2puk__assembly_1__model_1

2puk__assembly_1__model_1 | I(q)

2puk__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 (4)

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

6. Fold Classification (SCOP + CATH) 13 domains

SCOP 2.08 (7 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Crystal structure of the binary complex between ferredoxin: thioredoxin reductase and thioredoxin m

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

Ferredoxin-thioredoxin reductase, catalytic chain

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Ferredoxin-thioredoxin reductase, variable chain

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Thioredoxin M-type, chloroplast (TRX-M)

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

2puk__assembly_1__model_1

2puk__assembly_1__model_1 | I(q)

2puk__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 (4)

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

6. Fold Classification (SCOP + CATH) 13 domains

SCOP 2.08 (7 domains)

CATH v4.4 (6 domains)

7. Citations (1)