SAXSdb — 9xbl

▼

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

Eukaryotic peptide chain release factor GTP-binding subunit

Saccharomyces cerevisiae

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 homooligomer Homooligomer Protein × 5 PDB declaration: pentameric（5） Consistent with protein copy count	Chain A； UniProt 1–253 Chain B； UniProt 1–253 Chain C； UniProt 1–253 Chain D； UniProt 1–253 Chain E； UniProt 1–253	Not recorded	No other associated polymer	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.40 Å

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 9XBL	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1YJO Structure of NNQQNY from yeast prion Sup35 with zinc acetate Deposited 2005-01-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 8–13（6 aa） Fragment：prion determining domain of Sup35	Not recorded	ZN ZINC ION × 2 ACY ACETIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；293 K；ZINC SULFATE, SODIUM ACETATE, HEPES, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 7.00	Resolution 1.30 Å R-free 0.152
1YJP Structure of GNNQQNY from yeast prion Sup35 Deposited 2005-01-15	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 7–13（7 aa） Fragment：prion determining domain of Sup35	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；water, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.80 Å R-free 0.190
4CRN Cryo-EM of a pretermination complex with eRF1 and eRF3 Deposited 2014-02-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain P 256–685（430 aa）	Not recorded	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；LIQUID ETHANE, VITROBOT MARK 4	Resolution 9.10 Å
5K2E Structure of NNQQNY from yeast prion Sup35 with zinc acetate determined by MicroED Deposited 2016-05-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 18 PDB declaration: octadecameric	Chain A 8–13（6 aa） Fragment：UNP residues 8-13	Not recorded	ZN ZINC ION × 18 ACY ACETIC ACID × 18	ELECTRON CRYSTALLOGRAPHY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE；Plunged into liquid ethane (FEI VITROBOT MARK IV) X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；273 K；1.0 M sodium acetate, 0.1 M HEPES, pH 7.0, 0.01 M zinc sulfate	Resolution 1.00 Å R-free 0.194
5K2F Structure of NNQQNY from yeast prion Sup35 with cadmium acetate determined by MicroED Deposited 2016-05-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 18 PDB declaration: octadecameric	Chain A 8–13（6 aa） Fragment：UNP residues 8-13	Not recorded	CD CADMIUM ION × 18 ACT ACETATE ION × 18	ELECTRON CRYSTALLOGRAPHY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE；Plunged into liquid ethane (FEI VITROBOT MARK IV) X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；273 K；1.0 M sodium acetate, 0.1 M HEPES, pH 7.0, 0.01 M cadmium sulfate	Resolution 1.00 Å R-free 0.241
5K2G Structure of GNNQQNY from yeast prion Sup35 in space group P21 determined by MicroED Deposited 2016-05-18	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 18 PDB declaration: octadecameric	Chain A 7–13（7 aa） Fragment：UNP residues 7-13	Not recorded	No recorded non-water small molecule	ELECTRON CRYSTALLOGRAPHY cryo-EM buffer pH 7；water cryo-EM vitrification conditions Cryogen ETHANE；Plunged into liquid ethane (FEI VITROBOT MARK IV) X-ray crystallization conditions BATCH；pH 7；273 K；water	Resolution 1.10 Å R-free 0.224
5K2H Structure of GNNQQNY from yeast prion Sup35 in space group P212121 determined by MicroED Deposited 2016-05-18	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 18 PDB declaration: octadecameric	Chain A 7–13（7 aa） Fragment：UNP residues 7-13	Not recorded	No recorded non-water small molecule	ELECTRON CRYSTALLOGRAPHY cryo-EM buffer pH 7；water cryo-EM vitrification conditions Cryogen ETHANE；Plunged into liquid ethane (FEI VITROBOT MARK IV) X-ray crystallization conditions BATCH；pH 7；273 K；water	Resolution 1.05 Å R-free 0.186
9XBK Cryo-EM structure of Sup35NM S17R fibril formed at 4 degrees (S17R4N) Deposited 2025-10-24	Different mutation/modification	Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 1–253（253 aa） Chain B 1–253（253 aa） Chain C 1–253（253 aa） Chain D 1–253（253 aa） Chain E 1–253（253 aa）	Mutation：S17R Mutation：S17R Mutation：S17R Mutation：S17R Mutation：S17R	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.40 Å
9XBM Cryo-EM structure of Sup35NM S17R fibril formed at 37 degrees (S17R37C) Deposited 2025-10-24	Parsed fields agree	Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 1–253（253 aa） Chain B 1–253（253 aa） Chain C 1–253（253 aa） Chain D 1–253（253 aa） Chain E 1–253（253 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.40 Å
9XBN Cryo-EM structure of Sup35NM fibril formed at 4 degrees (Sc4) Deposited 2025-10-24	Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 1–253（253 aa） Chain B 1–253（253 aa） Chain C 1–253（253 aa） Chain D 1–253（253 aa） Chain E 1–253（253 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
9XBO Cryo-EM structure of Sup35NM fibril formed at 37 degrees (Sc37) Deposited 2025-10-24	Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 1–253（253 aa） Chain B 1–253（253 aa） Chain C 1–253（253 aa） Chain D 1–253（253 aa） Chain E 1–253（253 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
9XBP Cryo-EM structure of Sup35NM S17R fibril formed at 4 degrees (S17R4C) Deposited 2025-10-24	Different mutation/modification Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 1–253（253 aa） Chain B 1–253（253 aa） Chain C 1–253（253 aa） Chain D 1–253（253 aa） Chain E 1–253（253 aa）	Mutation：S17R Mutation：S17R Mutation：S17R Mutation：S17R Mutation：S17R	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.20 Å

12 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ERF3_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–253； UniProt 1–253 Author chain B； PDBConstruct 1–253； UniProt 1–253 Author chain C； PDBConstruct 1–253； UniProt 1–253 Author chain D； PDBConstruct 1–253； UniProt 1–253 Author chain E； PDBConstruct 1–253； UniProt 1–253

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	9xbl
Deposition date deposition_date	2025-10-24
最后修订 last_revision	2025-12-10
Structure title title	Cryo-EM structure of Sup35NM S17R fibril formed at 37 degrees (S17R37N)
Keywords keywords	Yeast, Sup35NM, Amyloid, PROTEIN FIBRIL; PROTEIN FIBRIL
Experimental Method method	ELECTRON MICROSCOPY

▼

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

Radius of gyration Rg (Guinier) rg_guinier	20.17 Å
Radius of gyration Rg (electron density) rg_electron	19.29 Å
Forward intensity I(0) i0	23799100.00
Molecular weight molecular_weight	32413.0 kDa
Excluded volume excluded_volume	38171 Å³
Envelope volume envelope_volume	44194 Å³
Hydration-shell volume shell_volume	19457 Å³
Envelope diameter envelope_diameter	69.3 Å
Shell Rg shell_rg	25.50 Å
Envelope Rg envelope_rg	19.50 Å
Shape Rg shape_rg	19.26 Å
Total Rg total_rg	20.07 Å
Total atoms total_atoms	2305
Residues n_residues	280
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	67.6 Å
Rg (real space) rg_real	20.13 Å
Rg uncertainty (real space) rg_real_error	0.39 Å
I(0) (real space) i0_real	2.3800e+07
I(0) uncertainty (real space) i0_real_error	2.9290e+05
Rg (reciprocal space) rg_reciprocal	20.14 Å
I(0) (reciprocal space) i0_reciprocal	23800000.0000
Solution quality estimate total_estimate	0.8865
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.2 Å
Skewness Skewness skewness	0.306
Kurtosis Kurtosis kurtosis	-0.347
Angular range angular_range	— – 0.3950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6219000.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.852; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.974

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (1)

▶

8. Citations (1)

▶

Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

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

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	2.40 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	120844

Description description	Eukaryotic peptide chain release factor GTP-binding subunit
Molecular weight formula_weight	29583.6 kDa
EC 编号 ec_number	3.6.5.-
Source method src_method	man
Copy count entity_count	5

Cryo-EM structure of Sup35NM S17R fibril formed at 37 degrees (S17R37N)

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

Eukaryotic peptide chain release factor GTP-binding subunit

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E
Atom count atom_count	2305

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;brewer's yeast ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli

fit	/app/data/saxs_computation/xb/9xbl/9xbl.fit
pddf	/app/data/pr_computation/xb/9xbl/9xbl.pr.out
profile	/app/data/saxs_computation/xb/9xbl/9xbl.dat