5vdf

Crystal Structure of Cu(I)-loaded yeast Atx1: Crystal Form II

Method: X-RAY DIFFRACTION

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

Metal homeostasis factor ATX1

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	COPPER (I) ION × 1 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	COPPER (I) ION × 1 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	COPPER (I) ION × 1 water × 2	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 2	COPPER (I) ION × 1 water × 2	Consistent with protein count
5	Protein homooligomer	Homooligomer	Protein 2	COPPER (I) ION × 1 water × 2	Consistent with protein count
6	Protein homooligomer	Homooligomer	Protein 2	COPPER (I) ION × 1 water × 2	Consistent with protein count
7	Protein homooligomer	Homooligomer	Protein 2	COPPER (I) ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ATX1_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–73； UniProt 1–73 Author chain B； PDBConstruct 1–73； UniProt 1–73 Author chain C； PDBConstruct 1–73； UniProt 1–73 Author chain D； PDBConstruct 1–73； UniProt 1–73 Author chain E； PDBConstruct 1–73； UniProt 1–73 Author chain F； PDBConstruct 1–73； UniProt 1–73 Author chain G； PDBConstruct 1–73； UniProt 1–73 Author chain H； PDBConstruct 1–73； UniProt 1–73

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	5vdf
Deposition date deposition_date	2017-04-02
Structure title title	Crystal Structure of Cu(I)-loaded yeast Atx1: Crystal Form II
Keywords keywords	Atx1, metallochaperone, copper transfer, metal-binding domain, ferredoxin-like fold, METAL BINDING PROTEIN; METAL 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.

5vdf__assembly_5__model_1

Assembly 5 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

5vdf__assembly_5__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5vdf__assembly_5__model_1 | P(r) · Pending

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

Rg（Guinier）	17.72 Å
Rg (electron density)	16.72 Å
Total Rg	17.96 Å
Atom count	1135
Residues	144
Excluded volume	20703 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5vdf__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5vdf__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`5vdf__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`5vdf__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`5vdf__assembly_5__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`5vdf__assembly_6__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`5vdf__assembly_7__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 (3)

Entity 1 Entity 1 polymer

Description description	Metal homeostasis factor ATX1
Molecular weight formula_weight	8232.6 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	4635

MAEIKHYQFNVVMTCSGCSGAVNKVLTKLEPDVSKIDISLEKQLVDVYTTLPYDFILEKIKKTGKEVRSGKQL

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	COPPER (I) ION
Molecular weight formula_weight	63.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	174

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d5vdfa_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.17 — HMA, heavy metal-associated domain
Family Family family	d.58.17.1 — HMA, heavy metal-associated domain

Domain ID domain_id	d5vdfb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.17 — HMA, heavy metal-associated domain
Family Family family	d.58.17.1 — HMA, heavy metal-associated domain

Domain ID domain_id	d5vdfc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.17 — HMA, heavy metal-associated domain
Family Family family	d.58.17.1 — HMA, heavy metal-associated domain

Domain ID domain_id	d5vdfd_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.17 — HMA, heavy metal-associated domain
Family Family family	d.58.17.1 — HMA, heavy metal-associated domain

Domain ID domain_id	d5vdfe_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.17 — HMA, heavy metal-associated domain
Family Family family	d.58.17.1 — HMA, heavy metal-associated domain

Domain ID domain_id	d5vdff_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.17 — HMA, heavy metal-associated domain
Family Family family	d.58.17.1 — HMA, heavy metal-associated domain

Domain ID domain_id	d5vdfg_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.17 — HMA, heavy metal-associated domain
Family Family family	d.58.17.1 — HMA, heavy metal-associated domain

Domain ID domain_id	d5vdfh_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.17 — HMA, heavy metal-associated domain
Family Family family	d.58.17.1 — HMA, heavy metal-associated domain

CATH v4.4 (8 domains)

Domain ID domain_id	5vdfA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	5vdfB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	5vdfC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	5vdfD00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	5vdfE00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	5vdfF00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	5vdfG00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	5vdfH00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	100 —

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Unit-cell length a length_a	46.148 Å
Unit-cell length b length_b	114.385 Å
Unit-cell length c length_c	58.135 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	92.32 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

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

Resolution resolution	1.930 Å
Low-resolution limit resolution_low	58.090 Å
R factor r_factor	0.1978
R_work r_work	0.1954
R_free r_free	0.2417

Crystal Structure of Cu(I)-loaded yeast Atx1: Crystal Form II

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

Metal homeostasis factor ATX1

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

5vdf__assembly_5__model_1

5vdf__assembly_5__model_1 | I(q)

5vdf__assembly_5__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 non-polymer

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)

Crystal Structure of Cu(I)-loaded yeast Atx1: Crystal Form II

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

Metal homeostasis factor ATX1

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

5vdf__assembly_5__model_1

5vdf__assembly_5__model_1 | I(q)

5vdf__assembly_5__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 non-polymer

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)