8pjc

Crystal structure of human insulin desB30 precursor with an Alanine-Alanine-Lysine C-peptide in dimer (T2) conformation

Method: X-RAY DIFFRACTION D_max: 37.7 Å Quality: GOOD

▼

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

Insulin

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–51	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；298 K；TBD	Resolution 2.14 Å R-free 0.207

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 8PJC	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8PJH Crystal structure of human insulin desB30 precursor with an Aspartate-Glycine-Lysine C-peptide in dimer (T2) conformation Deposited 2023-06-23	Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–51（51 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；TBD	Resolution 1.50 Å R-free 0.182
8YYL Cryo-EM structure of the complex IR with one insulin Deposited 2024-04-04	Different construct 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 3–51（49 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.01 Å
8YYT Cryo-EM structure of the complex IR with four insulin Deposited 2024-04-04	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain C 3–51（49 aa） Chain D 3–51（49 aa） Chain E 3–51（49 aa） Chain F 3–51（49 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å

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

View Construct and Data Evidence

UniProt name	INS_BALPH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–53； UniProt 1–51

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	8pjc
Deposition date deposition_date	2023-06-23
Structure title title	Crystal structure of human insulin desB30 precursor with an Alanine-Alanine-Lysine C-peptide in dimer (T2) conformation
Keywords keywords	insulin, precursor, dimer, HORMONE; HORMONE
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	11.35 Å
Radius of gyration Rg (electron density) rg_electron	10.02 Å
Forward intensity I(0) i0	856256.00
Molecular weight molecular_weight	5964.0 kDa
Excluded volume excluded_volume	7420 Å³
Envelope volume envelope_volume	7931 Å³
Hydration-shell volume shell_volume	7046 Å³
Envelope diameter envelope_diameter	36.1 Å
Shell Rg shell_rg	15.26 Å
Envelope Rg envelope_rg	10.41 Å
Shape Rg shape_rg	10.03 Å
Total Rg total_rg	11.50 Å
Total atoms total_atoms	416
Residues n_residues	53
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

▼

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

Maximum dimension Dmax dmax	37.7 Å
Rg (real space) rg_real	11.29 Å
Rg uncertainty (real space) rg_real_error	0.24 Å
I(0) (real space) i0_real	8.5630e+05
I(0) uncertainty (real space) i0_real_error	8.4310e+03
Rg (reciprocal space) rg_reciprocal	11.30 Å
I(0) (reciprocal space) i0_reciprocal	856300.0000
Solution quality estimate total_estimate	0.8783
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	14.8 Å
Skewness Skewness skewness	0.168
Kurtosis Kurtosis kurtosis	-0.251
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	89910.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.826; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.937

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

▶

8. Citations (1)

▶

Unit-cell length a length_a	77.874 Å
Unit-cell length b length_b	77.874 Å
Unit-cell length c length_c	77.874 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	24

Space group space_group	I 21 3
Space-group number int_tables_number	199
Crystal system crystal_system	cubic

Resolution resolution	2.140 Å
Low-resolution limit resolution_low	18.360 Å
R factor r_factor	0.1752
R_work r_work	0.1736
R_free r_free	0.2070

Description description	Insulin
Molecular weight formula_weight	5969.9 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	450

Crystal structure of human insulin desB30 precursor with an Alanine-Alanine-Lysine C-peptide in dimer (T2) conformation

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

Insulin

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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	Saccharomyces cerevisiae

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	34

fit	/app/data/saxs_computation/pj/8pjc/8pjc.fit
pddf	/app/data/pr_computation/pj/8pjc/8pjc.pr.out
profile	/app/data/saxs_computation/pj/8pjc/8pjc.dat