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2e9g

Solution structure of the alpha adaptinC2 domain from human Adapter-related protein complex 1 gamma 2 subunit

Method: SOLUTION NMR Dmax: 67.2 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

AP-1 complex subunit gamma-2

Homo sapiens

UniProt O75843

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 662–785 Fragment：Alpha adaptinC2 domain, GAE No other associated polymer 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

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 2E9G Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2YMT gamma 2 adaptin EAR domain crystal structure with phage peptide GEEWGPWV Deposited 2012-10-10 Different construct Different oligomeric state Different ligand/ion Different experimental method 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 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
3ZHF gamma 2 adaptin EAR domain crystal structure with preS1 site1 peptide NPDWDFN Deposited 2012-12-21 Different construct Different oligomeric state Different ligand/ion Different experimental method 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 construct 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 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 8–131； UniProt 662–785

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.

SAXS scattering curve SAXS Profile

SAXS profile for 2e9g

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2e9g
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2e9g
Deposition date deposition_date2007-01-25
Structure title titleSolution structure of the alpha adaptinC2 domain from human Adapter-related protein complex 1 gamma 2 subunit
Keywords keywords;beta-sandwich, immunoglobulin-like fold, adaptin, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, PROTEIN BINDING ;; PROTEIN BINDING
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier17.29 Å
Radius of gyration Rg (electron density) rg_electron16.56 Å
Forward intensity I(0) i01062140000.00
Molecular weight molecular_weight286850.0 kDa
Excluded volume excluded_volume363340 ų
Envelope volume envelope_volume37596 ų
Hydration-shell volume shell_volume16564 ų
Envelope diameter envelope_diameter72.1 Å
Shell Rg shell_rg25.86 Å
Envelope Rg envelope_rg21.86 Å
Shape Rg shape_rg16.57 Å
Total Rg total_rg16.69 Å
Total atoms total_atoms40840
Residues n_residues2620
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax67.2 Å
Rg (real space) rg_real17.43 Å
Rg uncertainty (real space) rg_real_error0.67 Å
I(0) (real space) i0_real1.0620e+09
I(0) uncertainty (real space) i0_real_error1.4930e+07
Rg (reciprocal space) rg_reciprocal17.41 Å
I(0) (reciprocal space) i0_reciprocal1062000000.0000
Solution quality estimate total_estimate0.7360
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary17.7 Å
Skewness Skewness skewness0.555
Kurtosis Kurtosis kurtosis0.032
Angular range angular_range— – 0.4600 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha576500.0000
Real-space data points n_real_points77
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.339; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.547; Smooth: 0.999
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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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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd2e9ga1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.10 — Clathrin adaptor appendage domain
Family Family familyb.1.10.0 — automated matches
Domain ID domain_idd2e9ga2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id2e9gA00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily1230 — Gamma-adaptin ear (GAE) domain
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8. Citations (1)

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9. Files and Curves (10)