1jk9

Heterodimer between H48F-ySOD1 and yCCS

Method: X-RAY DIFFRACTION

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

superoxide dismutase

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	copper chaperone for superoxide dismutase × 1 （P40202） ZINC ION × 2 SULFATE ION × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	copper chaperone for superoxide dismutase × 1 （P40202） ZINC ION × 2 SULFATE ION × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	copper chaperone for superoxide dismutase × 2 （P40202） ZINC ION × 4 SULFATE ION × 2 water × 4	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 4	copper chaperone for superoxide dismutase × 2 （P40202） ZINC ION × 4 SULFATE ION × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SODC_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–153； UniProt 1–153 Author chain C； PDBConstruct 1–153； UniProt 1–153

copper chaperone for superoxide dismutase

Saccharomyces cerevisiae

UniProt P40202

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	superoxide dismutase × 1 （P00445） ZINC ION × 2 SULFATE ION × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	superoxide dismutase × 1 （P00445） ZINC ION × 2 SULFATE ION × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	superoxide dismutase × 2 （P00445） ZINC ION × 4 SULFATE ION × 2 water × 4	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 4	superoxide dismutase × 2 （P00445） ZINC ION × 4 SULFATE ION × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CCS1_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–249； UniProt 1–249 Author chain D； PDBConstruct 1–249； UniProt 1–249

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	1jk9
Deposition date deposition_date	2001-07-11
Structure title title	Heterodimer between H48F-ySOD1 and yCCS
Keywords keywords	;protein-protein complex, heterodimer, metallochaperone, chaperone, copper, Amyotrophic Lateral Sclerosis, Lou Gehrig's Disease, OXIDOREDUCTASE ;; OXIDOREDUCTASE
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.

1jk9__assembly_1__model_1

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

Download this curve (.dat)

1jk9__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1jk9__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.13 Å
Rg (electron density)	22.00 Å
Total Rg	22.94 Å
Atom count	2984
Residues	396
Excluded volume	52633 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1jk9__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1jk9__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1jk9__assembly_3__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1jk9__assembly_4__model_1`	tetrameric （4）	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 (5)

Entity 1 Entity 1 polymer

Description description	superoxide dismutase
Molecular weight formula_weight	15752.4 kDa
EC 编号 ec_number	1.15.1.1
Mutation mutation	H48F
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	5979

VQAVAVLKGDAGVSGVVKFEQASESEPTTVSYEIAGNSPNAERGFHIFEFGDATNGCVSAGPHFNPFKKTHGAPTDEVRHVGDMGNVKTDENGVAKGSFKDSLIKLIGPTSVVGRSVVIHAGQDDLGKGDTEESLKTGNAGPRPACGVIGLTN

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 BL21(DE3)

Entity 2 Entity 2 polymer

Description description	copper chaperone for superoxide dismutase
Molecular weight formula_weight	27361.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MTTNDTYEATYAIPMHCENCVNDIKACLKNVPGINSLNFDIEQQIMSVESSVAPSTIINTLRNCGKDAIIRGAGKPNSSAVAILETFQKYTIDQKKDTAVRGLARIVQVGENKTLFDITVNGVPEAGNYHASIHEKGDVSKGVESTGKVWHKFDEPIECFNESDLGKNLYSGKTFLSAPLPTWQLIGRSFVISKSLNHPENEPSSVKDYSFLGVIARSAGVWENNKQVCACTGKTVWEERKDALANNIK

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 BL21(DE3)

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	4

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	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	11

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1jk9a_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.8 — Cu,Zn superoxide dismutase-like
Family Family family	b.1.8.1 — Cu,Zn superoxide dismutase-like

Domain ID domain_id	d1jk9b1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.8 — Cu,Zn superoxide dismutase-like
Family Family family	b.1.8.1 — Cu,Zn superoxide dismutase-like

Domain ID domain_id	d1jk9b2
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	d1jk9c_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.8 — Cu,Zn superoxide dismutase-like
Family Family family	b.1.8.1 — Cu,Zn superoxide dismutase-like

Domain ID domain_id	d1jk9d1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.8 — Cu,Zn superoxide dismutase-like
Family Family family	b.1.8.1 — Cu,Zn superoxide dismutase-like

Domain ID domain_id	d1jk9d2
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 (6 domains)

Domain ID domain_id	1jk9A00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	200 — Superoxide dismutase, copper/zinc binding domain

Domain ID domain_id	1jk9B01
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	1jk9B02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	200 — Superoxide dismutase, copper/zinc binding domain

Domain ID domain_id	1jk9C00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	200 — Superoxide dismutase, copper/zinc binding domain

Domain ID domain_id	1jk9D01
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	1jk9D02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	200 — Superoxide dismutase, copper/zinc binding domain

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Unit-cell length a length_a	104.090 Å
Unit-cell length b length_b	104.090 Å
Unit-cell length c length_c	233.710 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	12

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	12.000 Å
R factor r_factor	0.2170
R_work r_work	0.2170
R_free r_free	0.2600

Heterodimer between H48F-ySOD1 and yCCS

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

superoxide dismutase

State in the Current Structure

Other States of the Same Protein in the Database

copper chaperone for superoxide dismutase

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

1jk9__assembly_1__model_1

1jk9__assembly_1__model_1 | I(q)

1jk9__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 (5)

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 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Heterodimer between H48F-ySOD1 and yCCS

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

superoxide dismutase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

copper chaperone for superoxide dismutase

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

1jk9__assembly_1__model_1

1jk9__assembly_1__model_1 | I(q)

1jk9__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 (5)

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 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)