SAXSdb — 1nlt

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

Mitochondrial protein import protein MAS5

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	Seven residue peptide × 1 ZINC ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MAS5_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–248； UniProt 103–350

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	1nlt
Deposition date deposition_date	2003-01-07
Structure title title	The crystal structure of Hsp40 Ydj1
Keywords keywords	beta-strands, chaperone, heat shock, mitochondrion, PROTEIN TRANSPORT; PROTEIN TRANSPORT
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.

1nlt__assembly_1__model_1

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

Download this curve (.dat)

1nlt__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1nlt__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.01 Å
Rg (electron density)	30.50 Å
Total Rg	30.94 Å
Atom count	1815
Residues	235
Excluded volume	32515 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1nlt__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	Mitochondrial protein import protein MAS5
Molecular weight formula_weight	27388.6 kDa
Mutation mutation	no
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	1962

GAQRPRGPQRGKDIKHEISASLEELYKGRTAKLALNKQILCKECEGRGGKKGAVKKCTSCNGQGIKFVTRQMGPMIQRFQTECDVCHGTGDIIDPKDRCKSCNGKKVENERKILEVHVEPGMKDGQRIVFKGEADQAPDVIPGDVVFIVSERPHKSFKRDGDDLVYEAEIDLLTAIAGGEFALEHVSGDWLKVGIVPGEVIAPGMRKVIEGKGMPIPKYGGYGNLIIKFTIKDPENHFTSEENLKKLE

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	Seven residue peptide
Molecular weight formula_weight	867.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GWLYEIS

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	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	147

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1nlta1
Class class	b — All beta proteins
Fold Fold fold	b.4 — HSP40/DnaJ peptide-binding domain
Superfamily Superfamily superfamily	b.4.1 — HSP40/DnaJ peptide-binding domain
Family Family family	b.4.1.1 — HSP40/DnaJ peptide-binding domain

Domain ID domain_id	d1nlta2
Class class	b — All beta proteins
Fold Fold fold	b.4 — HSP40/DnaJ peptide-binding domain
Superfamily Superfamily superfamily	b.4.1 — HSP40/DnaJ peptide-binding domain
Family Family family	b.4.1.1 — HSP40/DnaJ peptide-binding domain

Domain ID domain_id	d1nlta3
Class class	g — Small proteins
Fold Fold fold	g.54 — DnaJ/Hsp40 cysteine-rich domain
Superfamily Superfamily superfamily	g.54.1 — DnaJ/Hsp40 cysteine-rich domain
Family Family family	g.54.1.1 — DnaJ/Hsp40 cysteine-rich domain

CATH v4.4 (3 domains)

Domain ID domain_id	1nltA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	260 — HSP40/DNAj peptide-binding domain
Homologous superfamily homologous superfamily	20 — Urease metallochaperone UreE, N-terminal domain

Domain ID domain_id	1nltA02
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	230 — Chaperone, DNAj Protein; Chain A
Homologous superfamily homologous superfamily	10 — Heat shock protein DnaJ, cysteine-rich domain

Domain ID domain_id	1nltA03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	260 — HSP40/DNAj peptide-binding domain
Homologous superfamily homologous superfamily	20 — Urease metallochaperone UreE, N-terminal domain

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Unit-cell length a length_a	55.025 Å
Unit-cell length b length_b	55.025 Å
Unit-cell length c length_c	161.870 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	6

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

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	27.500 Å
R factor r_factor	0.2690
R_work r_work	0.2690
R_free r_free	0.2960

The crystal structure of Hsp40 Ydj1

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

Mitochondrial protein import protein MAS5

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

1nlt__assembly_1__model_1

1nlt__assembly_1__model_1 | I(q)

1nlt__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)

The crystal structure of Hsp40 Ydj1

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

Mitochondrial protein import protein MAS5

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

1nlt__assembly_1__model_1

1nlt__assembly_1__model_1 | I(q)

1nlt__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)