SAXSdb — 3ggz

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

Increased sodium tolerance protein 1

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	Vacuolar protein-sorting-associated protein 46 × 1 （P69771）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Vacuolar protein-sorting-associated protein 46 × 1 （P69771）	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Vacuolar protein-sorting-associated protein 46 × 1 （P69771）	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Vacuolar protein-sorting-associated protein 46 × 1 （P69771）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	IST1_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–193； UniProt 1–193 Author chain B； PDBConstruct 1–193； UniProt 1–193 Author chain C； PDBConstruct 1–193； UniProt 1–193 Author chain D； PDBConstruct 1–193； UniProt 1–193

Vacuolar protein-sorting-associated protein 46

Saccharomyces cerevisiae

UniProt P69771

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Increased sodium tolerance protein 1 × 1 （P53843）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Increased sodium tolerance protein 1 × 1 （P53843）	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Increased sodium tolerance protein 1 × 1 （P53843）	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Increased sodium tolerance protein 1 × 1 （P53843）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DID2_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain E； PDBConstruct 1–29； UniProt 176–204 Author chain F； PDBConstruct 1–29； UniProt 176–204 Author chain G； PDBConstruct 1–29； UniProt 176–204 Author chain H； PDBConstruct 1–29； UniProt 176–204

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	3ggz
Deposition date deposition_date	2009-03-02
Structure title title	Crystal Structure of S.cerevisiae Ist1 N-terminal domain in complex with Did2 MIM motif
Keywords keywords	novel MIM binding mode, Phosphoprotein, Coiled coil, Endosome, Membrane, Protein transport, Transport, ENDOCYTOSIS; PROTEIN TRANSPORT, ENDOCYTOSIS
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.

3ggz__assembly_4__model_1

Assembly 4 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3ggz__assembly_4__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3ggz__assembly_4__model_1 | P(r) · Pending

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

Rg（Guinier）	21.37 Å
Rg (electron density)	20.79 Å
Total Rg	21.56 Å
Atom count	1673
Residues	206
Excluded volume	30262 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3ggz__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3ggz__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3ggz__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3ggz__assembly_4__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 (2)

Entity 1 Entity 1 polymer

Description description	Increased sodium tolerance protein 1
Molecular weight formula_weight	22380.2 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	6595

MAPSMIPFTIKLKTCLKMCIQRLRYAQEKQQAIAKQSRRQVAQLLLTNKEQKAHYRVETLIHDDIHIELLEILELYCELLLARVQVINDISTEEQLVKEHMDDGINEAIRSLIYAILFVDEVKELSQLKDLMAWKINVEFVNGVIADHIDVPEKIIKKCSPSVPKEELVDLYLKEIAKTYDVPYSKLENSLSS

Source Source

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

Entity 2 Entity 2 polymer

Description description	Vacuolar protein-sorting-associated protein 46
Molecular weight formula_weight	3341.8 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

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

NVPEIKAKEVNVDDEKEDKLAQRLRALRG

Source Source

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

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3ggzA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1260 — Ferritin
Homologous superfamily homologous superfamily	60 — Vacuolar protein sorting-associated protein Ist1

Domain ID domain_id	3ggzB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1260 — Ferritin
Homologous superfamily homologous superfamily	60 — Vacuolar protein sorting-associated protein Ist1

Domain ID domain_id	3ggzC00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1260 — Ferritin
Homologous superfamily homologous superfamily	60 — Vacuolar protein sorting-associated protein Ist1

Domain ID domain_id	3ggzD00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1260 — Ferritin
Homologous superfamily homologous superfamily	60 — Vacuolar protein sorting-associated protein Ist1

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Unit-cell length a length_a	165.916 Å
Unit-cell length b length_b	165.916 Å
Unit-cell length c length_c	121.559 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	32

Space group space_group	P 42 2 2
Space-group number int_tables_number	93
Crystal system crystal_system	—

Resolution resolution	3.800 Å
Low-resolution limit resolution_low	49.030 Å
R factor r_factor	0.2890
R_work r_work	0.2890
R_free r_free	0.3070

Crystal Structure of S.cerevisiae Ist1 N-terminal domain in complex with Did2 MIM motif

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

Increased sodium tolerance protein 1

State in the Current Structure

Other States of the Same Protein in the Database

Vacuolar protein-sorting-associated protein 46

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

3ggz__assembly_4__model_1

3ggz__assembly_4__model_1 | I(q)

3ggz__assembly_4__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Crystal Structure of S.cerevisiae Ist1 N-terminal domain in complex with Did2 MIM motif

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

Increased sodium tolerance 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

Vacuolar protein-sorting-associated protein 46

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

3ggz__assembly_4__model_1

3ggz__assembly_4__model_1 | I(q)

3ggz__assembly_4__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)