SAXSdb — 5cxb

▼

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

Ribosome biogenesis protein YTM1

Chaetomium thermophilum

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–495	Not recorded	Ribosome biogenesis protein ERB1 × 1 （G0SCK6） EDO 1,2-ETHANEDIOL × 3 NA SODIUM ION × 1 GOL GLYCEROL × 2 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；20% PEG 8000, 0.1M Hepes pH 7.5	Resolution 2.10 Å R-free 0.213

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 5CXB	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5CXC Structure of Ytm1 bound to the C-terminal domain of Erb1 in P 65 2 2 space group Deposited 2015-07-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–495（495 aa） Fragment：UNP residues 433-801	Not recorded	CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.6；294 K；15% PEG 4000,0.1M Na citrate pH 5.6, 0.2M Ammonium sulfate	Resolution 3.10 Å R-free 0.239
5CYK Structure of Ytm1 bound to the C-terminal domain of Erb1-R486E Deposited 2015-07-30	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–495（495 aa）	Not recorded	CL CHLORIDE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；297 K；0.1M Hepes pH 7.5, 2M Ammonium Sulfate	Resolution 3.00 Å R-free 0.262
5EM2 Crystal structure of the Erb1-Ytm1 complex Deposited 2015-11-05	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–495（495 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 6 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291.15 K；20-28% ethylene glycol	Resolution 2.67 Å R-free 0.251
5EM2 Crystal structure of the Erb1-Ytm1 complex Deposited 2015-11-05	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–495（495 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291.15 K；20-28% ethylene glycol	Resolution 2.67 Å R-free 0.251
6QTB Crystal structure of Rea1-MIDAS/Ytm1-UBL complex from Chaetomium thermophilum Deposited 2019-02-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 8–98（91 aa）	Not recorded	MG MAGNESIUM ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；3 M NaCl and 0.1 M Tris (pH 8.5)	Resolution 1.89 Å R-free 0.213
6QTB Crystal structure of Rea1-MIDAS/Ytm1-UBL complex from Chaetomium thermophilum Deposited 2019-02-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 8–98（91 aa）	Not recorded	MG MAGNESIUM ION × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；3 M NaCl and 0.1 M Tris (pH 8.5)	Resolution 1.89 Å R-free 0.213
8I9X Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - Ytm1-1 Deposited 2023-02-07	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 58 PDB declaration: 60-meric	Chain CD 1–495（495 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
8I9Y Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - Ytm1-2 Deposited 2023-02-07	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 57 PDB declaration: 59-meric	Chain CD 1–495（495 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
8I9Z Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - State Spb4 Deposited 2023-02-07	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 58 PDB declaration: 60-meric	Chain CD 1–495（495 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å
8IA0 Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - State Puf6 Deposited 2023-02-07	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 62 PDB declaration: 64-meric	Chain CD 1–495（495 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å
8PV2 Chaetomium thermophilum pre-60S State 10 - pre-5S rotation with Ytm1-Erb1 Deposited 2023-07-17	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 57-meric	Chain CD 1–495（495 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 3 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.63 Å

9 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	G0SFB5_CHATD
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 20–514； UniProt 1–495

Ribosome biogenesis protein ERB1

Chaetomium thermophilum

UniProt G0SCK6

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 433–801	Not recorded	Ribosome biogenesis protein YTM1 × 1 （G0SFB5） EDO 1,2-ETHANEDIOL × 3 NA SODIUM ION × 1 GOL GLYCEROL × 2 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；20% PEG 8000, 0.1M Hepes pH 7.5	Resolution 2.10 Å R-free 0.213

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 5CXB	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5CXC Structure of Ytm1 bound to the C-terminal domain of Erb1 in P 65 2 2 space group Deposited 2015-07-28	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 433–801（369 aa）	Not recorded	CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.6；294 K；15% PEG 4000,0.1M Na citrate pH 5.6, 0.2M Ammonium sulfate	Resolution 3.10 Å R-free 0.239
5CYK Structure of Ytm1 bound to the C-terminal domain of Erb1-R486E Deposited 2015-07-30	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 433–801（369 aa） Fragment：UNP residues 433-801	Mutation：R486E	CL CHLORIDE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；297 K；0.1M Hepes pH 7.5, 2M Ammonium Sulfate	Resolution 3.00 Å R-free 0.262
5EM2 Crystal structure of the Erb1-Ytm1 complex Deposited 2015-11-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 423–801（379 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 6 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291.15 K；20-28% ethylene glycol	Resolution 2.67 Å R-free 0.251
5EM2 Crystal structure of the Erb1-Ytm1 complex Deposited 2015-11-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 423–801（379 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291.15 K；20-28% ethylene glycol	Resolution 2.67 Å R-free 0.251
8I9P Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - State Mak16 Deposited 2023-02-07	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 31 PDB declaration: 33-meric	Chain CC 1–801（801 aa）	Not recorded	ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
8I9R Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - State 5S RNP Deposited 2023-02-07	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric	Chain CC 1–801（801 aa）	Not recorded	ZN ZINC ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
8I9T Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - State Dbp10-1 Deposited 2023-02-07	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 55-meric	Chain CC 1–801（801 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
8I9V Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - State Dbp10-2 Deposited 2023-02-07	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 56-meric	Chain CC 1–801（801 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
8I9W Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - Dbp10-3 Deposited 2023-02-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 52-meric	Chain CC 1–801（801 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
8I9X Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - Ytm1-1 Deposited 2023-02-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 58 PDB declaration: 60-meric	Chain CC 1–801（801 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
8I9Y Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - Ytm1-2 Deposited 2023-02-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 57 PDB declaration: 59-meric	Chain CC 1–801（801 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
8I9Z Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - State Spb4 Deposited 2023-02-07	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 58 PDB declaration: 60-meric	Chain CC 1–801（801 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å
8IA0 Cryo-EM structure of a Chaetomium thermophilum pre-60S ribosomal subunit - State Puf6 Deposited 2023-02-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 62 PDB declaration: 64-meric	Chain CC 1–801（801 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å
8PV2 Chaetomium thermophilum pre-60S State 10 - pre-5S rotation with Ytm1-Erb1 Deposited 2023-07-17	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 57-meric	Chain CC 1–801（801 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 3 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.63 Å

13 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

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	5cxb
Deposition date deposition_date	2015-07-28
Structure title title	Structure of Ytm1 bound to the C-terminal domain of Erb1 in P21 21 2 space group
Keywords keywords	ribosome assembly, WD40, beta-propeller, ubiquitin-like domain, protein binding; PROTEIN BINDING
Experimental Method method	X-RAY DIFFRACTION

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	30.27 Å
Radius of gyration Rg (electron density) rg_electron	29.76 Å
Forward intensity I(0) i0	127459000.00
Molecular weight molecular_weight	89203.0 kDa
Excluded volume excluded_volume	111610 Å³
Envelope volume envelope_volume	137000 Å³
Hydration-shell volume shell_volume	38487 Å³
Envelope diameter envelope_diameter	107.6 Å
Shell Rg shell_rg	36.69 Å
Envelope Rg envelope_rg	30.06 Å
Shape Rg shape_rg	29.73 Å
Total Rg total_rg	30.46 Å
Total atoms total_atoms	6295
Residues n_residues	817
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	102.6 Å
Rg (real space) rg_real	30.29 Å
Rg uncertainty (real space) rg_real_error	0.91 Å
I(0) (real space) i0_real	1.2750e+08
I(0) uncertainty (real space) i0_real_error	2.2840e+06
Rg (reciprocal space) rg_reciprocal	30.29 Å
I(0) (reciprocal space) i0_reciprocal	127500000.0000
Solution quality estimate total_estimate	0.6892
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	33.5 Å
Skewness Skewness skewness	0.394
Kurtosis Kurtosis kurtosis	-0.269
Angular range angular_range	— – 0.2600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	28860000.0000
Real-space data points n_real_points	53
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.822; Stabil: 1.000; Sysdev: 0.193; Positv: 1.000; Valcen: 0.977; Smooth: 0.933

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Ribosome biogenesis protein YTM1
Molecular weight formula_weight	55149.7 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	6625

MAHHHHHHSSGLEVLFQGPMDAPMEDAPAPVAQVKVIFTTTEPDLELPESKRQLLVPADIRRYGLSRILNSESMLDTGSIPFDFLINGSFLRSSLEDYLTSNGLSLETTLTLQYVRSLIPPVYEASFEHDDWVSAVDVLSATSPAGRWSSAANSSAAVQPGQERVLSASYDGLLRIWNASGSVIATSPSGSHGGHTASIKAAKFLTSDRLASAGMDRTVRVWKYTESDHFTGELKPTLELYGHTGSVDWLDVDGHSKHILTASADGAIGFWSASKASAPEPDASLLPGAHVSKRRKATSSVSTAQRGPLGLWSIHTAPATAAIFDPRDRTVAYSASQDHTVRTLDLTTGQVVSTLTLTHPLLSLSALTRAGTTSPLLAAGTSARHITMVDPRASSATTSVMTLRGHANKVVSLSPSPENEYSLVSGSHDGTCRVWDLRSVRPATKEEGSLGGVSEPVYVIERESWASKGKKKRPVAGDGCKVFSVVWDKLGIFSGGEDKKVQVNRGRNIVTEQK

来源 Source

来源生物 organism	Chaetomium thermophilum
NCBI Class编号 ncbi_taxonomy_id	209285
宿主生物 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

来源 Source

来源生物 organism	Chaetomium thermophilum
NCBI Class编号 ncbi_taxonomy_id	209285
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	nat
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	326

▼

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	5cxbA02
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	5cxbB00
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

▶

8. Citations (1)

▶

Unit-cell length a length_a	86.443 Å
Unit-cell length b length_b	108.149 Å
Unit-cell length c length_c	108.618 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	4

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	48.533 Å
R factor r_factor	0.1648
R_work r_work	0.1639
R_free r_free	0.2132

fit	/app/data/saxs_computation/cx/5cxb/5cxb.fit
pddf	/app/data/pr_computation/cx/5cxb/5cxb.pr.out
profile	/app/data/saxs_computation/cx/5cxb/5cxb.dat

Structure of Ytm1 bound to the C-terminal domain of Erb1 in P21 21 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

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)