SAXSdb — 2ymt

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

AP-1 COMPLEX SUBUNIT GAMMA-LIKE 2

HOMO SAPIENS

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 665–785	Fragment：EAR DOMAIN, RESIDUES 665-785	PHAGE DISPLAY DERIVED GAMMA 2 ADAPTIN EAR DOMAIN BINDING PEPTIDE × 1 PDO 1,3-PROPANDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；100 MM MES/IMIDAZOLE PH 6.5, 0.02 M 1,6-HEXANEDIOL, 0.02 M 1-BUTANOL, 0.02 M (RS)-1,2- PROPANEDIOL, 0.02 M 2-PROPANOL, 0.02 M 1,4-BUTANEDIOL, 0.02 M 1,3-PROPANEDIOL, 10% (W/V) PEG 20000 AND 24% (V/V) PEG400 (USING A 2:1 RATIO OF PROTEIN TO MOTHER LIQUOR)	Resolution 1.80 Å R-free 0.242

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 2YMT	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2E9G Solution structure of the alpha adaptinC2 domain from human Adapter-related protein complex 1 gamma 2 subunit Deposited 2007-01-25	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 662–785（124 aa） Fragment：Alpha adaptinC2 domain, GAE	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；296 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient NMR sample composition 0.54mM alpha adaptinC2 domain U-15N,13C; 20mM d-Tris-HCl(pH 7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O, 90% H2O \| 90% H2O/10% D2O	Resolution not provided
3ZHF gamma 2 adaptin EAR domain crystal structure with preS1 site1 peptide NPDWDFN Deposited 2012-12-21	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 665–785（121 aa） Fragment：EAR DOMAIN, RESIDUES 665-785	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；100 MM MES/IMIDAZOLE PH 6.5, 0.02 M 1,6-HEXANEDIOL, 0.02 M 1-BUTANOL, 0.02 M (RS)-1, 2-PROPANEDIOL, 0.02 M 2-PROPANOL, 0.02 M 1,4-BUTANEDIOL, 0.02 M 1,3-PROPANEDIOL, 10% (W/V) PEG 20000 AND 24% (V/V) PEG400 (USING A 2:1 RATIO OF PROTEIN TO MOTHER LIQUOR), PEPTIDE WAS AT ABOUT 50 FOLD MOLAR EXCESS	Resolution 1.70 Å R-free 0.226
4BCX gamma 2 adaptin EAR domain crystal structure Deposited 2012-10-03	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 665–785（121 aa） Fragment：EAR DOMAIN, RESIDUES 665-785	Not recorded	IMD IMIDAZOLE × 1 PDO 1,3-PROPANDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；100 MM MES/IMIDAZOLE BUFFER PH 6.5, 0.03 M EACH OF DI-, TRI-, TETRA- AND PENTA-ETHYLENEGLYCOL, 10% (W/V) PEG 20000 AND 24% (V/V) PEG400 (USING A 2:1 RATIO OF PROTEIN TO MOTHER LIQUOR)	Resolution 2.00 Å R-free 0.268

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	AP1G2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–124； UniProt 665–785

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	2ymt
Deposition date deposition_date	2012-10-10
Structure title title	gamma 2 adaptin EAR domain crystal structure with phage peptide GEEWGPWV
Keywords keywords	PROTEIN TRANSPORT; PROTEIN TRANSPORT
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	16.52 Å
Radius of gyration Rg (electron density) rg_electron	15.06 Å
Forward intensity I(0) i0	3829450.00
Molecular weight molecular_weight	14483.0 kDa
Excluded volume excluded_volume	18419 Å³
Envelope volume envelope_volume	21027 Å³
Hydration-shell volume shell_volume	12280 Å³
Envelope diameter envelope_diameter	53.9 Å
Shell Rg shell_rg	20.33 Å
Envelope Rg envelope_rg	15.36 Å
Shape Rg shape_rg	15.07 Å
Total Rg total_rg	16.13 Å
Total atoms total_atoms	1026
Residues n_residues	128
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	55.4 Å
Rg (real space) rg_real	16.51 Å
Rg uncertainty (real space) rg_real_error	0.36 Å
I(0) (real space) i0_real	3.8290e+06
I(0) uncertainty (real space) i0_real_error	4.2430e+04
Rg (reciprocal space) rg_reciprocal	16.51 Å
I(0) (reciprocal space) i0_reciprocal	3829000.0000
Solution quality estimate total_estimate	0.8802
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	18.7 Å
Skewness Skewness skewness	0.328
Kurtosis Kurtosis kurtosis	-0.307
Angular range angular_range	— – 0.4800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	738900.0000
Real-space data points n_real_points	78
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.817; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.995

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	AP-1 COMPLEX SUBUNIT GAMMA-LIKE 2
Molecular weight formula_weight	13762.7 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	1172

GGSAPIPDLKVFEREGVQLNLSFIRPPENPALLLITITATNFSEGDVTHFICQAAVPKSLQLQLQAPSGNTVPARGGLPITQLFRILNPNKAPLRLKLRLTYDHFHQSVQEIFEVNNLPVESWQ

来源 Source

来源生物 organism	HOMO SAPIENS
通用名 common_name	HUMAN
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	PHAGE DISPLAY DERIVED GAMMA 2 ADAPTIN EAR DOMAIN BINDING PEPTIDE
Molecular weight formula_weight	957.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GEEWGPWVX

Entity 3 Entity 3 non-polymer

Description description	1,3-PROPANDIOL
Molecular weight formula_weight	76.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	125

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	2ymtA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1230 — Gamma-adaptin ear (GAE) domain

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8. Citations (1)

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Unit-cell length a length_a	34.803 Å
Unit-cell length b length_b	37.772 Å
Unit-cell length c length_c	105.471 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 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.802 Å
Low-resolution limit resolution_low	30.708 Å
R factor r_factor	0.1876
R_work r_work	0.1850
R_free r_free	0.2420

fit	/app/data/saxs_computation/ym/2ymt/2ymt.fit
pddf	/app/data/pr_computation/ym/2ymt/2ymt.pr.out
profile	/app/data/saxs_computation/ym/2ymt/2ymt.dat

gamma 2 adaptin EAR domain crystal structure with phage peptide GEEWGPWV

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

AP-1 COMPLEX SUBUNIT GAMMA-LIKE 2

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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)