SAXSdb — 6qtb

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

Midasin,Midasin

Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Ribosome biogenesis protein YTM1 × 1 （G0SFB5） MAGNESIUM ION × 1 GLYCEROL × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Ribosome biogenesis protein YTM1 × 1 （G0SFB5） MAGNESIUM ION × 1 GLYCEROL × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	G0SHE6_CHATD
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–45； UniProt 4690–4733 Author chain A； PDBConstruct 49–272； UniProt 4774–4997 Author chain D； PDBConstruct 2–45； UniProt 4690–4733 Author chain D； PDBConstruct 49–272； UniProt 4774–4997

Ribosome biogenesis protein YTM1

Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)

UniProt G0SFB5

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Midasin,Midasin × 1 （G0SHE6） MAGNESIUM ION × 1 GLYCEROL × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Midasin,Midasin × 1 （G0SHE6） MAGNESIUM ION × 1 GLYCEROL × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YTM1_CHATD
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 11–101； UniProt 8–98 Author chain E； PDBConstruct 11–101； UniProt 8–98

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	6qtb
Deposition date deposition_date	2019-02-22
Structure title title	Crystal structure of Rea1-MIDAS/Ytm1-UBL complex from Chaetomium thermophilum
Keywords keywords	ribosome biogenesis, integrin, midas, RIBOSOME; RIBOSOME
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.

6qtb__assembly_1__model_1

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

Download this curve (.dat)

6qtb__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6qtb__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.92 Å
Rg (electron density)	21.84 Å
Total Rg	22.64 Å
Atom count	2701
Residues	341
Excluded volume	48185 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6qtb__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6qtb__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 (5)

Entity 1 Entity 1 polymer

Description description	Midasin,Midasin
Molecular weight formula_weight	31464.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D
Atom count atom_count	5794

MHISDEQLKRPLRDYGEALEMWSTFQTKTQALSQSLSSQLRLILTGSGIPSKRAYQILLCVDDSSSMSDDNRSTAGNLALESLVMVARALTVLEAGQIGVMGFGTDVFVAHALTDPPFTSQDAGARVLQQFTFRQDSTDMVLLLRRTIDHFREARLIQASSSRGGEDLWQLALILSDGLVQSRDHARLRPLLREAMEQRVMVVFIVMDDARSRKGHSVLELKEARFGPDGVPVIHRYLDSFPFPYYLIVHHLEDLPGALAALLRTWFAEVNSGSHHHHHH

Source Source

Source organism organism	Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
NCBI taxonomy ID ncbi_taxonomy_id	759272
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Ribosome biogenesis protein YTM1
Molecular weight formula_weight	11444.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MKHHHHHHPMAPAPVAQVKVIFTTTEPDLELPESKRQLLVPADIRRYGLSRILNSESMLDTGSIPFDFLINGSFLRSSLEDYLTSNGLSLETTLTLQYVRS

Source Source

Source organism organism	Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
NCBI taxonomy ID ncbi_taxonomy_id	759272
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	406

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Unit-cell length a length_a	75.553 Å
Unit-cell length b length_b	83.176 Å
Unit-cell length c length_c	77.686 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	117.72 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.890 Å
Low-resolution limit resolution_low	36.580 Å
R factor r_factor	0.1912
R_work r_work	0.1900
R_free r_free	0.2127

Crystal structure of Rea1-MIDAS/Ytm1-UBL complex from Chaetomium thermophilum

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

Midasin,Midasin

State in the Current Structure

Other States of the Same Protein in the Database

Ribosome biogenesis protein YTM1

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

6qtb__assembly_1__model_1

6qtb__assembly_1__model_1 | I(q)

6qtb__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

7. Citations (1)

Crystal structure of Rea1-MIDAS/Ytm1-UBL complex from Chaetomium thermophilum

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

Midasin,Midasin

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Ribosome biogenesis protein YTM1

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

6qtb__assembly_1__model_1

6qtb__assembly_1__model_1 | I(q)

6qtb__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

7. Citations (1)