SAXSdb — 7d8r

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

Microphthalmia-associated transcription factor,Methionyl-tRNA synthetase beta subunit

Aquifex aeolicus VF5

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Homooligomer	Protein 2	water × 2	Consistent with protein count
2	Insufficient information	Homooligomer	Protein 2	water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O66738_AQUAE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 75–178； UniProt 8–111 Author chain B； PDBConstruct 75–178； UniProt 8–111 Author chain C； PDBConstruct 75–178； UniProt 8–111 Author chain D； PDBConstruct 75–178； UniProt 8–111

Microphthalmia-associated transcription factor,Methionyl-tRNA synthetase beta subunit

Aquifex aeolicus VF5

UniProt O75030

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Homooligomer	Protein 2	water × 2	Consistent with protein count
2	Insufficient information	Homooligomer	Protein 2	water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MITF_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–74； UniProt 324–395 Author chain B； PDBConstruct 3–74； UniProt 324–395 Author chain C； PDBConstruct 3–74； UniProt 324–395 Author chain D； PDBConstruct 3–74； UniProt 324–395

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	7d8r
Deposition date deposition_date	2020-10-09
Structure title title	MITF HLHLZ structure
Keywords keywords	TRANSCRIPTION FACTOR, TRANSCRIPTION; TRANSCRIPTION
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.

7d8r__assembly_1__model_1

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

Download this curve (.dat)

7d8r__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7d8r__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	36.89 Å
Rg (electron density)	36.98 Å
Total Rg	37.06 Å
Atom count	2389
Residues	342
Excluded volume	42608 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7d8r__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`7d8r__assembly_2__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)

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	7d8rA01
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	280 — MYOD Basic-Helix-Loop-Helix Domain, subunit B
Homologous superfamily homologous superfamily	10 — Helix-loop-helix DNA-binding domain

Domain ID domain_id	7d8rA02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

Domain ID domain_id	7d8rB01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

Domain ID domain_id	7d8rC01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

Domain ID domain_id	7d8rD01
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	280 — MYOD Basic-Helix-Loop-Helix Domain, subunit B
Homologous superfamily homologous superfamily	10 — Helix-loop-helix DNA-binding domain

Domain ID domain_id	7d8rD02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

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Unit-cell length a length_a	41.910 Å
Unit-cell length b length_b	78.120 Å
Unit-cell length c length_c	80.590 Å
Unit-cell angle α angle_alpha	93.18 °
Unit-cell angle β angle_beta	105.03 °
Unit-cell angle γ angle_gamma	105.62 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	38.693 Å
R factor r_factor	0.2866
R_work r_work	0.2847
R_free r_free	0.3182

Description description	Microphthalmia-associated transcription factor,Methionyl-tRNA synthetase beta subunit
Molecular weight formula_weight	20600.9 kDa
Source method src_method	man
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	4798

MITF HLHLZ structure

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

Microphthalmia-associated transcription factor,Methionyl-tRNA synthetase beta subunit

State in the Current Structure

Other States of the Same Protein in the Database

Microphthalmia-associated transcription factor,Methionyl-tRNA synthetase beta subunit

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

7d8r__assembly_1__model_1

7d8r__assembly_1__model_1 | I(q)

7d8r__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)

Source organism organism	Aquifex aeolicus VF5
NCBI taxonomy ID ncbi_taxonomy_id	224324
Host organism host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	38

MITF HLHLZ structure

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

Microphthalmia-associated transcription factor,Methionyl-tRNA synthetase beta subunit

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Microphthalmia-associated transcription factor,Methionyl-tRNA synthetase beta subunit

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

7d8r__assembly_1__model_1

7d8r__assembly_1__model_1 | I(q)

7d8r__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)