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9e9r

The Structure of ApoB100 from Human Low-Density Lipoprotein

Method: ELECTRON MICROSCOPY Dmax: 255.2 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Apolipoprotein B 100

Homo sapiens

UniProt P04114

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 1–4563 Not recorded No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 9.00 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 9E9R Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
9BD1 beta/alpha1 region of ApoB 100 Deposited 2024-04-10 Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–4563（4563 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.40 Å
9BD8 ApoB 100 beta barrel bound to LDLR beta propeller Deposited 2024-04-11 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–4563（4563 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
9BDE Middle Region of Apolipoprotein B 100 bound to Low Density Lipoprotein Receptor Deposited 2024-04-11 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 1–4563（4563 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 CA CALCIUM ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.18 Å
9BDT Apolipoprotein B 100 bound to LDL receptor and legobody Deposited 2024-04-12 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 7 PDB declaration: heptameric
Chain A 1–4563（4563 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 CA CALCIUM ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.40 Å
9COO Nanobody 4 bound to Apolipoprotein B 100 Deposited 2024-07-17 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 1–4563（4563 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 CA CALCIUM ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.73 Å
9EA7 The Structure of ApoB100 from Human Low-Density Lipoprotein Deposited 2024-11-10 Parsed fields agree Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–4563（4563 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.00 Å
9EAG The Structure of ApoB100 from Human Low-Density Lipoprotein Deposited 2024-11-11 Parsed fields agree Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–4563（4563 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.00 Å

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name APOB_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–4563； UniProt 1–4563

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 9e9r

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9e9r
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9e9r
Deposition date deposition_date2024-11-08
Structure title titleThe Structure of ApoB100 from Human Low-Density Lipoprotein
Keywords keywordsapolipoprotein, LIPID BINDING PROTEIN; LIPID BINDING PROTEIN
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier97.22 Å
Radius of gyration Rg (electron density) rg_electron95.74 Å
Forward intensity I(0) i02343310000.00
Molecular weight molecular_weight417280.0 kDa
Excluded volume excluded_volume525320 ų
Envelope volume envelope_volume2032400 ų
Hydration-shell volume shell_volume188950 ų
Envelope diameter envelope_diameter246.5 Å
Shell Rg shell_rg97.91 Å
Envelope Rg envelope_rg80.51 Å
Shape Rg shape_rg95.73 Å
Total Rg total_rg95.79 Å
Total atoms total_atoms58841
Residues n_residues3715
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 dmax255.2 Å
Rg (real space) rg_real95.95 Å
Rg uncertainty (real space) rg_real_error0.80 Å
I(0) (real space) i0_real2.3320e+09
I(0) uncertainty (real space) i0_real_error4.5160e+07
Rg (reciprocal space) rg_reciprocal99.63 Å
I(0) (reciprocal space) i0_reciprocal2362000000.0000
Solution quality estimate total_estimate0.7791
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary175.4 Å
Skewness Skewness skewness-0.358
Kurtosis Kurtosis kurtosis-0.961
Angular range angular_range— – 0.0800 Å−1
Current regularization parameter α current_alpha0.1425
Highest regularization parameter α highest_alpha153700000.0000
Real-space data points n_real_points17
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.724; Stabil: 0.989; Sysdev: 1.000; Positv: 1.000; Valcen: 0.924; 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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9. Files and Curves (10)