SAXSdb — 5cxc

▼

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

Ribosome biogenesis protein YTM1

Chaetomium thermophilum

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 ERB1 × 1 （G0SCK6） CHLORIDE ION × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	G0SFB5_CHATD
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 16–510； UniProt 1–495

Ribosome biogenesis protein ERB1

Chaetomium thermophilum

UniProt G0SCK6

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） CHLORIDE ION × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	G0SCK6_CHATD
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–369； UniProt 433–801

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	5cxc
Deposition date deposition_date	2015-07-28
Structure title title	Structure of Ytm1 bound to the C-terminal domain of Erb1 in P 65 2 2 space group
Keywords keywords	ribosome assembly, WD40, beta-propeller, ubiquitin-like domain, protein binding; PROTEIN BINDING
Experimental Method method	X-RAY DIFFRACTION

▼

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.

5cxc__assembly_1__model_1

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

Download this curve (.dat)

5cxc__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5cxc__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.26 Å
Rg (electron density)	29.78 Å
Total Rg	30.46 Å
Atom count	6162
Residues	800
Excluded volume	109190 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5cxc__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Ribosome biogenesis protein YTM1
Molecular weight formula_weight	54720.2 kDa
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	6170

MAHHHHHHSSGLEVLMDAPMEDAPAPVAQVKVIFTTTEPDLELPESKRQLLVPADIRRYGLSRILNSESMLDTGSIPFDFLINGSFLRSSLEDYLTSNGLSLETTLTLQYVRSLIPPVYEASFEHDDWVSAVDVLSATSPAGRWSSAANSSAAVQPGQERVLSASYDGLLRIWNASGSVIATSPSGSHGGHTASIKAAKFLTSDRLASAGMDRTVRVWKYTESDHFTGELKPTLELYGHTGSVDWLDVDGHSKHILTASADGAIGFWSASKASAPEPDASLLPGAHVSKRRKATSSVSTAQRGPLGLWSIHTAPATAAIFDPRDRTVAYSASQDHTVRTLDLTTGQVVSTLTLTHPLLSLSALTRAGTTSPLLAAGTSARHITMVDPRASSATTSVMTLRGHANKVVSLSPSPENEYSLVSGSHDGTCRVWDLRSVRPATKEEGSLGGVSEPVYVIERESWASKGKKKRPVAGDGCKVFSVVWDKLGIFSGGEDKKVQVNRGRNIVTEQK

Source Source

Source organism organism	Chaetomium thermophilum
NCBI taxonomy ID ncbi_taxonomy_id	209285
Host organism host_organism	Spodoptera frugiperda

Entity 2 Entity 2 polymer

Description description	Ribosome biogenesis protein ERB1
Molecular weight formula_weight	40919.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

PSPDELKPFPTVQQTIFRGHEGRVRSVAIDPTGVALATGGDDGTVRVWELLTGRQVWSVKLNGDEAVNTVRWRPTKDTFILAAAAGEDIFLMIPTHPSVTPALDQASRDILNAGFGHATNGKQQANLPPGKEPPGKWARPGTRLEDEGVLLRITVRSTIKAISWHRRGDHFATVSPSGQRSSVAIHTLSKHLTQIPFRKLNGLAQTASFHPLRPLFFVATQRSIRCYDLQKLELVKIVQPGAKWISSFDVHPGGDNLVVGSYDKRLLWHDLDLSNRPYKTMRFHTEAIRAVRFHKGGLPLFADASDDGSLQIFHGKVPNDQLENPTIVPVKMLKGHKVVNKLGVLDIDWHPREPWCVSAGADGTARLWM

Source Source

Source organism organism	Chaetomium thermophilum
NCBI taxonomy ID ncbi_taxonomy_id	209285
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

▼

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	5cxcA02
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

Domain ID domain_id	5cxcB00
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

▶

Unit-cell length a length_a	169.110 Å
Unit-cell length b length_b	169.110 Å
Unit-cell length c length_c	154.042 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 65 2 2
Space-group number int_tables_number	179
Crystal system crystal_system	—

Resolution resolution	3.100 Å
Low-resolution limit resolution_low	48.818 Å
R factor r_factor	0.1960
R_work r_work	0.1936
R_free r_free	0.2390

Structure of Ytm1 bound to the C-terminal domain of Erb1 in P 65 2 2 space group

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

Ribosome biogenesis protein YTM1

State in the Current Structure

Other States of the Same Protein in the Database

Ribosome biogenesis protein ERB1

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

5cxc__assembly_1__model_1

5cxc__assembly_1__model_1 | I(q)

5cxc__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Structure of Ytm1 bound to the C-terminal domain of Erb1 in P 65 2 2 space group

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

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

Ribosome biogenesis protein ERB1

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

5cxc__assembly_1__model_1

5cxc__assembly_1__model_1 | I(q)

5cxc__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)