SAXSdb — 2mj7

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

AP-4 complex subunit beta-1

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 610–739	Fragment：UNP residues 610-739	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 6.5；295 K；Pressure ambient NMR sample composition：0.4 mM HR8998C NC5, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition：0.2 mM HR8998C NC5, 4% PEG/hexanol, 80% H2O/20% D2O \| 80% H2O/20% D2O NMR sample composition：0.2 mM HR8998C NC5, Pf1 phage, 80% H2O/20% D2O \| 80% H2O/20% D2O NMR sample composition：0.2 mM HR8998C NC, 90% H2O/10% D2O \| 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 2MJ7	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9U9I M4-CTD-undocked AP-4 core in apo form Deposited 2025-03-28	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–568（568 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8	Resolution 4.00 Å
9U9J M4-CTD-docked AP-4 core in apo form Deposited 2025-03-28	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–568（568 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8	Resolution 4.20 Å
9U9R ARF1(Q71L) bound M4-CTD-undocked AP-4 core Deposited 2025-03-29	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain B 1–576（576 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8	Resolution 6.60 Å
9U9S ARF1(Q71L) bound M4-CTD-docked AP-4 core Deposited 2025-03-29	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain B 1–576（576 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8	Resolution 6.80 Å

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	AP4B1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 12–141； UniProt 610–739

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	2mj7
Deposition date deposition_date	2013-12-26
Structure title title	Solution NMR structure of beta-adaptin appendage domain of human adaptor protein complex 4 subunit beta, Northeast Structural Genomics Consortium (NESG) Target HR8998C
Keywords keywords	Structural Genomics, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM, NESG, PSI-Biology, Protein Structure Initiative, TRANSPORT PROTEIN; TRANSPORT PROTEIN
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	21.00 Å
Radius of gyration Rg (electron density) rg_electron	20.25 Å
Forward intensity I(0) i0	1473630000.00
Molecular weight molecular_weight	319580.0 kDa
Excluded volume excluded_volume	397710 Å³
Envelope volume envelope_volume	114050 Å³
Hydration-shell volume shell_volume	29747 Å³
Envelope diameter envelope_diameter	114.4 Å
Shell Rg shell_rg	36.78 Å
Envelope Rg envelope_rg	37.96 Å
Shape Rg shape_rg	20.27 Å
Total Rg total_rg	20.55 Å
Total atoms total_atoms	44680
Residues n_residues	2820
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	58.2 Å
Rg (real space) rg_real	18.49 Å
Rg uncertainty (real space) rg_real_error	0.18 Å
I(0) (real space) i0_real	1.3890e+09
I(0) uncertainty (real space) i0_real_error	1.5950e+07
Rg (reciprocal space) rg_reciprocal	21.77 Å
I(0) (reciprocal space) i0_reciprocal	1473000000.0000
Solution quality estimate total_estimate	0.6216
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	19.4 Å
Skewness Skewness skewness	0.704
Kurtosis Kurtosis kurtosis	0.126
Angular range angular_range	— – 0.3800 Å⁻¹
Current regularization parameter α current_alpha	1.2660
Highest regularization parameter α highest_alpha	798800.0000
Real-space data points n_real_points	70
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.009; Oscil: 0.765; Stabil: 0.991; Sysdev: 0.000; Positv: 1.000; Valcen: 0.942; 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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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	2mj7A00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	310 — TATA-Binding Protein
Homologous superfamily homologous superfamily	10 — TATA-Binding Protein

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8. Citations (1)

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Description description	AP-4 complex subunit beta-1
Molecular weight formula_weight	16004.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	44680

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

fit	/app/data/saxs_computation/mj/2mj7/2mj7.fit
pddf	/app/data/pr_computation/mj/2mj7/2mj7.pr.out
profile	/app/data/saxs_computation/mj/2mj7/2mj7.dat

Solution NMR structure of beta-adaptin appendage domain of human adaptor protein complex 4 subunit beta, Northeast Structural Genomics Consortium (NESG) Target HR8998C

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

AP-4 complex subunit beta-1

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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)