2d1p

crystal structure of heterohexameric TusBCD proteins, which are crucial for the tRNA modification

Method: X-RAY DIFFRACTION

▼

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

Hypothetical UPF0163 protein yheN

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Hypothetical UPF0116 protein yheM × 2 （P45531） Hypothetical protein yheL × 2 （P45530） water × 6	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	Hypothetical UPF0116 protein yheM × 2 （P45531） Hypothetical protein yheL × 2 （P45530） SULFATE ION × 1 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YHEN_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 13–140； UniProt 1–128 Author chain D； PDBConstruct 13–140； UniProt 1–128 Author chain G； PDBConstruct 13–140； UniProt 1–128

Hypothetical UPF0116 protein yheM

Escherichia coli

UniProt P45531

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Hypothetical UPF0163 protein yheN × 2 （P45532） Hypothetical protein yheL × 2 （P45530） water × 6	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	Hypothetical UPF0163 protein yheN × 2 （P45532） Hypothetical protein yheL × 2 （P45530） SULFATE ION × 1 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YHEM_ECOLI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–119； UniProt 1–119 Author chain E； PDBConstruct 1–119； UniProt 1–119 Author chain H； PDBConstruct 1–119； UniProt 1–119

Hypothetical protein yheL

Escherichia coli

UniProt P45530

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Hypothetical UPF0163 protein yheN × 2 （P45532） Hypothetical UPF0116 protein yheM × 2 （P45531） water × 6	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	Hypothetical UPF0163 protein yheN × 2 （P45532） Hypothetical UPF0116 protein yheM × 2 （P45531） SULFATE ION × 1 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YHEL_ECOLI
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–95； UniProt 1–95 Author chain F； PDBConstruct 1–95； UniProt 1–95 Author chain I； PDBConstruct 1–95； UniProt 1–95

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	2d1p
Deposition date deposition_date	2005-08-30
Structure title title	crystal structure of heterohexameric TusBCD proteins, which are crucial for the tRNA modification
Keywords keywords	tRNA modification, sulfur transfer, Structural genomics, TRANSLATION; TRANSLATION
Experimental Method method	X-RAY DIFFRACTION

▼

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.

2d1p__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2d1p__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2d1p__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	25.09 Å
Rg (electron density)	23.72 Å
Total Rg	24.68 Å
Atom count	5283
Residues	686
Excluded volume	94040 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2d1p__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2d1p__assembly_2__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Hypothetical UPF0163 protein yheN
Molecular weight formula_weight	15055.7 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D,G
Atom count atom_count	8214

MRGSHHHHHHGSMRFAIVVTGPAYGTQQASSAFQFAQALIADGHELSSVFFYREGVYNANQLTSPASDEFDLVRAWQQLNAQHGVALNICVAAALRRGVVDETEAGRLGLASSNLQQGFTLSGLGALAEASLTCDRVVQF

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Hypothetical UPF0116 protein yheM
Molecular weight formula_weight	13057.0 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,E,H

MKRIAFVFSTAPHGTAAGREGLDALLATSALTDDLAVFFIADGVFQLLPGQKPDAVLARDYIATFKLLGLYDIEQCWVCAASLRERGLDPQTPFVVEATPLEADALRRELANYDVILRF

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Hypothetical protein yheL
Molecular weight formula_weight	10729.3 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,F,I

MLHTLHRSPWLTDFAALLRLLSEGDELLLLQDGVTAAVDGNRYLESLRNAPIKVYALNEDLIARGLTGQISNDIILIDYTDFVRLTVKHPSQMAW

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	284

▼

6. Fold Classification (SCOP + CATH) 21 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d2d1pa1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.114 — DsrEFH-like
Superfamily Superfamily superfamily	c.114.1 — DsrEFH-like
Family Family family	c.114.1.1 — DsrEF-like

Domain ID domain_id	d2d1pa2
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	d2d1pb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.114 — DsrEFH-like
Superfamily Superfamily superfamily	c.114.1 — DsrEFH-like
Family Family family	c.114.1.1 — DsrEF-like

Domain ID domain_id	d2d1pc1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.114 — DsrEFH-like
Superfamily Superfamily superfamily	c.114.1 — DsrEFH-like
Family Family family	c.114.1.2 — DsrH-like

Domain ID domain_id	d2d1pd2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.114 — DsrEFH-like
Superfamily Superfamily superfamily	c.114.1 — DsrEFH-like
Family Family family	c.114.1.1 — DsrEF-like

Domain ID domain_id	d2d1pd3
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	d2d1pe_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.114 — DsrEFH-like
Superfamily Superfamily superfamily	c.114.1 — DsrEFH-like
Family Family family	c.114.1.1 — DsrEF-like

Domain ID domain_id	d2d1pf_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.114 — DsrEFH-like
Superfamily Superfamily superfamily	c.114.1 — DsrEFH-like
Family Family family	c.114.1.2 — DsrH-like

Domain ID domain_id	d2d1pg2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.114 — DsrEFH-like
Superfamily Superfamily superfamily	c.114.1 — DsrEFH-like
Family Family family	c.114.1.1 — DsrEF-like

Domain ID domain_id	d2d1pg3
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	d2d1ph_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.114 — DsrEFH-like
Superfamily Superfamily superfamily	c.114.1 — DsrEFH-like
Family Family family	c.114.1.1 — DsrEF-like

Domain ID domain_id	d2d1pi_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.114 — DsrEFH-like
Superfamily Superfamily superfamily	c.114.1 — DsrEFH-like
Family Family family	c.114.1.2 — DsrH-like

CATH v4.4 (9 domains)

Domain ID domain_id	2d1pA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1260 — Hypothetical Protein Ychn; Chain: A,
Homologous superfamily homologous superfamily	10 — DsrEFH-like

Domain ID domain_id	2d1pB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1260 — Hypothetical Protein Ychn; Chain: A,
Homologous superfamily homologous superfamily	10 — DsrEFH-like

Domain ID domain_id	2d1pC00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1260 — Hypothetical Protein Ychn; Chain: A,
Homologous superfamily homologous superfamily	10 — DsrEFH-like

Domain ID domain_id	2d1pD00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1260 — Hypothetical Protein Ychn; Chain: A,
Homologous superfamily homologous superfamily	10 — DsrEFH-like

Domain ID domain_id	2d1pE00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1260 — Hypothetical Protein Ychn; Chain: A,
Homologous superfamily homologous superfamily	10 — DsrEFH-like

Domain ID domain_id	2d1pF00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1260 — Hypothetical Protein Ychn; Chain: A,
Homologous superfamily homologous superfamily	10 — DsrEFH-like

Domain ID domain_id	2d1pG00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1260 — Hypothetical Protein Ychn; Chain: A,
Homologous superfamily homologous superfamily	10 — DsrEFH-like

Domain ID domain_id	2d1pH00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1260 — Hypothetical Protein Ychn; Chain: A,
Homologous superfamily homologous superfamily	10 — DsrEFH-like

Domain ID domain_id	2d1pI00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1260 — Hypothetical Protein Ychn; Chain: A,
Homologous superfamily homologous superfamily	10 — DsrEFH-like

▶

Unit-cell length a length_a	141.392 Å
Unit-cell length b length_b	141.392 Å
Unit-cell length c length_c	135.686 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	24

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	2.150 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2094
R_work r_work	0.2094
R_free r_free	0.2423

crystal structure of heterohexameric TusBCD proteins, which are crucial for the tRNA modification

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

Hypothetical UPF0163 protein yheN

State in the Current Structure

Other States of the Same Protein in the Database

Hypothetical UPF0116 protein yheM

State in the Current Structure

Other States of the Same Protein in the Database

Hypothetical protein yheL

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

2d1p__assembly_2__model_1

2d1p__assembly_2__model_1 | I(q)

2d1p__assembly_2__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 (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 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 21 domains

SCOP 2.08 (12 domains)

CATH v4.4 (9 domains)

7. Citations (1)

crystal structure of heterohexameric TusBCD proteins, which are crucial for the tRNA modification

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

Hypothetical UPF0163 protein yheN

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Hypothetical UPF0116 protein yheM

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Hypothetical protein yheL

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

2d1p__assembly_2__model_1

2d1p__assembly_2__model_1 | I(q)

2d1p__assembly_2__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 (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 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 21 domains

SCOP 2.08 (12 domains)

CATH v4.4 (9 domains)

7. Citations (1)