SAXSdb — 9jsv

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

M-alpha

OrganismNot specified

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 × 8 PDB declaration: octameric（8） Consistent with protein copy count	Chain A； UniProt 149–182 Chain B； UniProt 149–182 Chain C； UniProt 149–182 Chain D； UniProt 149–182 Chain E； UniProt 149–182 Chain F； UniProt 149–182 Chain G； UniProt 149–182 Chain H； UniProt 149–182	Not recorded	No other associated polymer	ELECTRON MICROSCOPY cryo-EM buffer：pH 4.4 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 1.79 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 9JSV	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1TVB Crystal structure of Melanoma Antigen gp100(209-217) Bound to Human Class I MHC HLA-A2 Deposited 2004-06-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 209–217（9 aa） Fragment：residues 209-217	Not recorded	GOL GLYCEROL × 9	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；PEG 3350, MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.80 Å R-free 0.216
1TVB Crystal structure of Melanoma Antigen gp100(209-217) Bound to Human Class I MHC HLA-A2 Deposited 2004-06-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 209–217（9 aa） Fragment：residues 209-217	Not recorded	GOL GLYCEROL × 13	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；PEG 3350, MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.80 Å R-free 0.216
1TVH Crystal structure of Modified Melanoma Antigen gp100(209-T2M) Bound to Human Class I MHC HLA-A2 Deposited 2004-06-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 209–217（9 aa） Fragment：residues 209-217	Not recorded	GOL GLYCEROL × 13	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；PEG 3350, MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.80 Å R-free 0.247
1TVH Crystal structure of Modified Melanoma Antigen gp100(209-T2M) Bound to Human Class I MHC HLA-A2 Deposited 2004-06-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 209–217（9 aa） Fragment：residues 209-217	Not recorded	GOL GLYCEROL × 15	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；PEG 3350, MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.80 Å R-free 0.247
3CC5 H-2Db complex with human gp100 Deposited 2008-02-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 25–33（9 aa） Fragment：Extracellular part, UNP residues 25-33	Not recorded	SO4 SULFATE ION × 2 GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；10% PEG 6000, 0.1M Ammonium sulfate, 0.1M Tris, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.91 Å R-free 0.268
3CC5 H-2Db complex with human gp100 Deposited 2008-02-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 25–33（9 aa） Fragment：Extracellular part, UNP residues 25-33	Not recorded	SO4 SULFATE ION × 1 GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；10% PEG 6000, 0.1M Ammonium sulfate, 0.1M Tris, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.91 Å R-free 0.268
4IS6 Crystal structure of HLA-DR4 bound to GP100 peptide Deposited 2013-01-16	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 44–59（16 aa） Fragment：UNP residues 44-59	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；PEG8000, magnesium chloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.50 Å R-free 0.298
6VM7 SILv44 T cell receptor bound to HLA-A2 presenting gp100 peptide (ITDQVPFSV) Deposited 2020-01-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain C 209–217（9 aa） Fragment：epitope (UNP residues 209-217)	Not recorded	GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；296 K；16% v/v PEG3350, 280 mM ammonium citrate dibasic	Resolution 2.41 Å R-free 0.241
6VM8 SILv44 T cell receptor bound to HLA-A2 presenting gp100T2M peptide (IMDQVPFSV) Deposited 2020-01-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain C 209–217（9 aa） Fragment：epitope (UNP residues 209-217)	Mutation：T210M	FLC CITRATE ANION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；296 K；20% v/v PEG3350, 236 mM ammonium citrate dibasic	Resolution 2.41 Å R-free 0.221
6VM9 T4H2 T cell receptor bound to HLA-A2 presenting gp100T2M peptide (IMDQVPFSV) Deposited 2020-01-27	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain C 209–217（9 aa） Fragment：epitope (UNP residues 209-217)	Mutation：T210M	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；296 K；18% v/v PEG10000, 16% v/v glycerol, 250 mM Tris pH 8.5, 60 mM sodium chloride, seeded with crushed crystals	Resolution 2.90 Å R-free 0.250
6VMA T4H2 T cell receptor bound to HLA-A2 presenting gp100 peptide (ITDQVPFSV) Deposited 2020-01-27	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain C 209–217（9 aa） Fragment：epitope (UNP residues 209-217)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；296 K；18% v/v PEG10000, 16% v/v glycerol, 100 mM Tris pH 8.5, 100 mM sodium chloride	Resolution 2.75 Å R-free 0.219
6VMC T4H2 T cell receptor bound to HLA-A2 presenting gp100T2L peptide (ILDQVPFSV) Deposited 2020-01-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain C 209–217（9 aa） Fragment：epitope (UNP residues 209-217)	Mutation：T210L	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；296 K；18% v/v PEG10000, 16% v/v glycerol, 250 mM Tris pH 8.5, 60 mM sodium chloride	Resolution 2.85 Å R-free 0.238
7PHR Structure of a fully assembled T-cell receptor engaging a tumor-associated peptide-MHC I Deposited 2021-08-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 11 PDB declaration: undecameric	Chain P 280–288（9 aa）	Mutation：A9V	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.08 Å
9JST Wild-type native PMEL amyloid - polymorph 1 Deposited 2024-10-01	Different construct	Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 148–182（35 aa） Chain B 148–182（35 aa） Chain C 148–182（35 aa） Chain D 148–182（35 aa） Chain E 148–182（35 aa） Chain F 148–182（35 aa） Chain G 148–182（35 aa） Chain H 148–182（35 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 4.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 1.79 Å
9JSU Wild-type native PMEL amyloid - polymorph 2 Deposited 2024-10-01	Different construct	Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 151–183（33 aa） Chain B 151–183（33 aa） Chain C 151–183（33 aa） Chain D 151–183（33 aa） Chain E 151–183（33 aa） Chain F 151–183（33 aa） Chain G 151–183（33 aa） Chain H 151–183（33 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 4.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 1.79 Å
9JSW Wild-type PMEL CAF amyloid -in vitro polymerized Deposited 2024-10-01	Different construct Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 148–182（35 aa） Chain B 148–182（35 aa） Chain C 148–182（35 aa） Chain D 148–182（35 aa） Chain E 148–182（35 aa） Chain F 148–182（35 aa） Chain G 148–182（35 aa） Chain H 148–182（35 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 4.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 1.94 Å
9JSX G175S PMEL CAF amyloid - in vitro polymerized Deposited 2024-10-01	Parsed fields agree	Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 149–182（34 aa） Chain B 149–182（34 aa） Chain C 149–182（34 aa） Chain D 149–182（34 aa） Chain E 149–182（34 aa） Chain F 149–182（34 aa） Chain G 149–182（34 aa） Chain H 149–182（34 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 4.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 1.79 Å
9LIP The cryo-EM structure of the native PMEL fibril lamella Deposited 2025-01-14	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 48 PDB declaration: 48-meric	Chain A 66–89（24 aa） Chain B 148–222（75 aa） Chain C 231–298（68 aa） Chain D 475–491（17 aa） Chain E 66–89（24 aa） Chain F 148–222（75 aa） Chain G 231–298（68 aa） Chain H 475–491（17 aa） Chain I 66–89（24 aa） Chain J 148–222（75 aa） Chain K 231–298（68 aa） Chain L 475–491（17 aa） Chain M 66–89（24 aa） Chain N 148–222（75 aa） Chain O 231–298（68 aa） Chain P 475–491（17 aa） Chain Q 66–89（24 aa） Chain R 148–222（75 aa） Chain S 231–298（68 aa） Chain T 475–491（17 aa） Chain U 66–89（24 aa） Chain V 148–222（75 aa） Chain W 231–298（68 aa） Chain X 475–491（17 aa） Chain Y 66–89（24 aa） Chain Z 148–222（75 aa） Chain a 231–298（68 aa） Chain b 475–491（17 aa） Chain c 66–89（24 aa） Chain d 148–222（75 aa） Chain e 231–298（68 aa） Chain f 475–491（17 aa） Chain g 66–89（24 aa） Chain h 148–222（75 aa） Chain i 231–298（68 aa） Chain j 475–491（17 aa） Chain k 66–89（24 aa） Chain l 148–222（75 aa） Chain m 231–298（68 aa） Chain n 475–491（17 aa） Chain o 66–89（24 aa） Chain p 148–222（75 aa） Chain q 231–298（68 aa） Chain r 475–491（17 aa） Chain s 66–89（24 aa） Chain t 148–222（75 aa） Chain u 231–298（68 aa） Chain v 475–491（17 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.48 Å

15 other PDB entries and 18 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PMEL_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–34； UniProt 149–182 Author chain B； PDBConstruct 1–34； UniProt 149–182 Author chain C； PDBConstruct 1–34； UniProt 149–182 Author chain D； PDBConstruct 1–34； UniProt 149–182 Author chain E； PDBConstruct 1–34； UniProt 149–182 Author chain F； PDBConstruct 1–34； UniProt 149–182 Author chain G； PDBConstruct 1–34； UniProt 149–182 Author chain H； PDBConstruct 1–34； UniProt 149–182

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	9jsv
Deposition date deposition_date	2024-10-01
Structure title title	G175S mutant native PMEL amyloid
Keywords keywords	melanosome, melanoma, pigment, melanin, amyloid, glaucoma, STRUCTURAL PROTEIN; STRUCTURAL PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	23.73 Å
Radius of gyration Rg (electron density) rg_electron	23.33 Å
Forward intensity I(0) i0	13959900.00
Molecular weight molecular_weight	30147.0 kDa
Excluded volume excluded_volume	38522 Å³
Envelope volume envelope_volume	48423 Å³
Hydration-shell volume shell_volume	18598 Å³
Envelope diameter envelope_diameter	79.6 Å
Shell Rg shell_rg	28.66 Å
Envelope Rg envelope_rg	23.45 Å
Shape Rg shape_rg	23.40 Å
Total Rg total_rg	23.89 Å
Total atoms total_atoms	4248
Residues n_residues	272
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

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

Maximum dimension Dmax dmax	79.0 Å
Rg (real space) rg_real	23.87 Å
Rg uncertainty (real space) rg_real_error	0.81 Å
I(0) (real space) i0_real	1.3960e+07
I(0) uncertainty (real space) i0_real_error	2.2900e+05
Rg (reciprocal space) rg_reciprocal	23.84 Å
I(0) (reciprocal space) i0_reciprocal	13960000.0000
Solution quality estimate total_estimate	0.7973
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	25.9 Å
Skewness Skewness skewness	0.419
Kurtosis Kurtosis kurtosis	-0.436
Angular range angular_range	— – 0.3350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1541000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.846; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.828; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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8. Citations (1)

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Resolution resolution	1.79 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	576997

Description description	M-alpha
Molecular weight formula_weight	3786.3 kDa
Source method src_method	nat
Copy count entity_count	8

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,E,B,F,C,G,D,H
Atom count atom_count	4248

fit	/app/data/saxs_computation/js/9jsv/9jsv.fit
pddf	/app/data/pr_computation/js/9jsv/9jsv.pr.out
profile	/app/data/saxs_computation/js/9jsv/9jsv.dat

G175S mutant native PMEL amyloid

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

M-alpha

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)