3d8a

Co-crystal structure of TraM-TraD complex.

Method: X-RAY DIFFRACTION

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

Relaxosome protein TraM

Escherichia coli (strain K12)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	Protein traD × 4 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 8	Protein traD × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TRAM1_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–70； UniProt 58–127 Author chain B； PDBConstruct 1–70； UniProt 58–127 Author chain C； PDBConstruct 1–70； UniProt 58–127 Author chain D； PDBConstruct 1–70； UniProt 58–127 Author chain E； PDBConstruct 1–70； UniProt 58–127 Author chain F； PDBConstruct 1–70； UniProt 58–127 Author chain G； PDBConstruct 1–70； UniProt 58–127 Author chain H； PDBConstruct 1–70； UniProt 58–127

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	3d8a
Deposition date deposition_date	2008-05-22
Structure title title	Co-crystal structure of TraM-TraD complex.
Keywords keywords	;TraM tetramerization domain, TraD C-terminal peptide, protein complex, Conjugation, DNA-binding, ATP-binding, Inner membrane, Membrane, Nucleotide-binding, Transmembrane, DNA BINDING PROTEIN ;; DNA BINDING 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.

3d8a__assembly_1__model_1

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

Download this curve (.dat)

3d8a__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3d8a__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.28 Å
Rg (electron density)	17.91 Å
Total Rg	18.78 Å
Atom count	2224
Residues	280
Excluded volume	39573 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3d8a__assembly_1__model_1`	octameric （8）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3d8a__assembly_2__model_1`	octameric （8）	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	Relaxosome protein TraM
Molecular weight formula_weight	7980.9 kDa
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	4468

ESAFNQTEFNKLLLECVVKTQSSVAKILGIESLSPHVSGNSKFEYANMVEDIREKVSSEMERFFPKNDDE

Source Source

Source organism organism	Escherichia coli (strain K12)
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Protein traD
Molecular weight formula_weight	1079.0 kDa
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	S,T,U,V,W,X,Y,Z

GEDVEPGDDF

Source Source

Source organism organism	Escherichia coli K12
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	12

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d3d8aa_
Class class	a — All alpha proteins
Fold Fold fold	a.241 — TraM-like
Superfamily Superfamily superfamily	a.241.1 — TraM-like
Family Family family	a.241.1.1 — TraM-like

Domain ID domain_id	d3d8ab_
Class class	a — All alpha proteins
Fold Fold fold	a.241 — TraM-like
Superfamily Superfamily superfamily	a.241.1 — TraM-like
Family Family family	a.241.1.1 — TraM-like

Domain ID domain_id	d3d8ac_
Class class	a — All alpha proteins
Fold Fold fold	a.241 — TraM-like
Superfamily Superfamily superfamily	a.241.1 — TraM-like
Family Family family	a.241.1.1 — TraM-like

Domain ID domain_id	d3d8ad_
Class class	a — All alpha proteins
Fold Fold fold	a.241 — TraM-like
Superfamily Superfamily superfamily	a.241.1 — TraM-like
Family Family family	a.241.1.1 — TraM-like

Domain ID domain_id	d3d8ae_
Class class	a — All alpha proteins
Fold Fold fold	a.241 — TraM-like
Superfamily Superfamily superfamily	a.241.1 — TraM-like
Family Family family	a.241.1.1 — TraM-like

Domain ID domain_id	d3d8af_
Class class	a — All alpha proteins
Fold Fold fold	a.241 — TraM-like
Superfamily Superfamily superfamily	a.241.1 — TraM-like
Family Family family	a.241.1.1 — TraM-like

Domain ID domain_id	d3d8ag_
Class class	a — All alpha proteins
Fold Fold fold	a.241 — TraM-like
Superfamily Superfamily superfamily	a.241.1 — TraM-like
Family Family family	a.241.1.1 — TraM-like

Domain ID domain_id	d3d8ah_
Class class	a — All alpha proteins
Fold Fold fold	a.241 — TraM-like
Superfamily Superfamily superfamily	a.241.1 — TraM-like
Family Family family	a.241.1.1 — TraM-like

CATH v4.4 (8 domains)

Domain ID domain_id	3d8aA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	2320 —

Domain ID domain_id	3d8aB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	2320 —

Domain ID domain_id	3d8aC00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	2320 —

Domain ID domain_id	3d8aD00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	2320 —

Domain ID domain_id	3d8aE00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	2320 —

Domain ID domain_id	3d8aF00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	2320 —

Domain ID domain_id	3d8aG00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	2320 —

Domain ID domain_id	3d8aH00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	2320 —

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Unit-cell length a length_a	142.246 Å
Unit-cell length b length_b	142.246 Å
Unit-cell length c length_c	70.950 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	72

Space group space_group	H 3
Space-group number int_tables_number	146
Crystal system crystal_system	—

Resolution resolution	2.550 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	0.2197
R_work r_work	0.2177
R_free r_free	0.2575

Co-crystal structure of TraM-TraD complex.

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

Relaxosome protein TraM

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

3d8a__assembly_1__model_1

3d8a__assembly_1__model_1 | I(q)

3d8a__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 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Co-crystal structure of TraM-TraD complex.

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

Relaxosome protein TraM

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

3d8a__assembly_1__model_1

3d8a__assembly_1__model_1 | I(q)

3d8a__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 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)