SAXSdb — 2hrk

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

Glutamyl-tRNA synthetase, cytoplasmic

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	GU4 nucleic-binding protein 1 × 1 （P46672） CHLORIDE ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SYEC_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–207； UniProt 1–207

GU4 nucleic-binding protein 1

Saccharomyces cerevisiae

UniProt P46672

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Glutamyl-tRNA synthetase, cytoplasmic × 1 （P46655） CHLORIDE ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	G4P1_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–122； UniProt 1–122

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	2hrk
Deposition date deposition_date	2006-07-20
Structure title title	Structural basis of yeast aminoacyl-tRNA synthetase complex formation revealed by crystal structures of two binary sub-complexes
Keywords keywords	protein complex protein interaction GST-fold, ligase-RNA Binding Protein COMPLEX; ligase/RNA 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.

2hrk__assembly_1__model_1

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

Download this curve (.dat)

2hrk__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2hrk__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.77 Å
Rg (electron density)	20.83 Å
Total Rg	21.87 Å
Atom count	2315
Residues	298
Excluded volume	41629 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2hrk__assembly_1__model_1`	dimeric （2）	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	Glutamyl-tRNA synthetase, cytoplasmic
Molecular weight formula_weight	22765.4 kDa
EC 编号 ec_number	6.1.1.17
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2589

MTKLFSKVKESIEGIKMPSTLTINGKAPIVAYAELIAARIVNALAPNSIAIKLVDDKKAPAAKLDDATEDVFNKITSKFAAIFDNGDKEQVAKWVNLAQKELVIKNFAKLSQSLETLDSQLNLRTFILGGLKYSAADVACWGALRSNGMCGSIIKNKVDVNVSRWYTLLEMDPIFGEAHDFLSKSLLELKKSANVGKKKETHKANFE

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	GU4 nucleic-binding protein 1
Molecular weight formula_weight	14002.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MSDLVTKFESLIISKYPVSFTKEQSAQAAQWESVLKSGQIQPHLDQLNLVLRDNTFIVSTLYPTSTDVHVFEVALPLIKDLVASSKDVKSTYTTYRHILRWIDYMQNLLEVSSTDKLEINHD

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	274

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2hrkb_
Class class	a — All alpha proteins
Fold Fold fold	a.45 — GST C-terminal domain-like
Superfamily Superfamily superfamily	a.45.1 — GST C-terminal domain-like
Family Family family	a.45.1.2 — Arc1p N-terminal domain-like

CATH v4.4 (3 domains)

Domain ID domain_id	2hrkA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	30 — Glutaredoxin
Homologous superfamily homologous superfamily	70 —

Domain ID domain_id	2hrkA02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1050 — Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2hrkB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1050 — Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2
Homologous superfamily homologous superfamily	10 —

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Unit-cell length a length_a	40.320 Å
Unit-cell length b length_b	86.310 Å
Unit-cell length c length_c	47.120 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	99.37 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	2.050 Å
Low-resolution limit resolution_low	45.000 Å
R factor r_factor	0.1939
R_work r_work	0.1906
R_free r_free	0.2555

Structural basis of yeast aminoacyl-tRNA synthetase complex formation revealed by crystal structures of two binary sub-complexes

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

Glutamyl-tRNA synthetase, cytoplasmic

State in the Current Structure

Other States of the Same Protein in the Database

GU4 nucleic-binding protein 1

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

2hrk__assembly_1__model_1

2hrk__assembly_1__model_1 | I(q)

2hrk__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 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (1 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Structural basis of yeast aminoacyl-tRNA synthetase complex formation revealed by crystal structures of two binary sub-complexes

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

Glutamyl-tRNA synthetase, cytoplasmic

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

GU4 nucleic-binding protein 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2hrk__assembly_1__model_1

2hrk__assembly_1__model_1 | I(q)

2hrk__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 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (1 domains)

CATH v4.4 (3 domains)

7. Citations (1)