SAXSdb — 6rva

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

Insulin-like growth factor I

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 X； UniProt 48–118	Not recorded	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 3；313.15 K；Ionic strength (raw mmCIF value) 0；Pressure 1 NMR sample composition：0.18 mM [L-Asp58]-IGF-1 analogue, 0.01 % sodium azide, 50 mM [U-2H] acetic acid, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition：0.05 mM [U-13C; U-15N] [L-Asp58]-IGF-1 analogue, 0.01 % sodium azide, 50 mM [U-2H] acetic acid, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition：0.05 mM [U-13C; U-15N] [L-Asp58]-IGF-1 analogue, 0.01 % sodium azide, 50 mM [U-2H] acetic acid, 100% D2O \| 100% 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 6RVA	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BQT THREE-DIMENSIONAL STRUCTURE OF HUMAN INSULIN-LIKE GROWTH FACTOR-I (IGF-I) DETERMINED BY 1H-NMR AND DISTANCE GEOMETRY, 6 STRUCTURES Deposited 1998-08-18	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 49–118（70 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 3；313 K；Pressure 1 NMR sample composition H2O/D2O=9/1 CONTAINING 10 ACETIC ACID-D4	Resolution not provided
1PMX INSULIN-LIKE GROWTH FACTOR-I BOUND TO A PHAGE-DERIVED PEPTIDE Deposited 2003-06-11	Different construct Different oligomeric state Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 49–118（70 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.1；313 K；Ionic strength (raw mmCIF value) 25 mM；Pressure 1 NMR sample composition 1.4 MM IGF-I (15N), 2.0 MM PEPTIDE, 25 MM SODIUM ACETATE NMR sample composition 1.4 MM IGF-I (13C,15N), 2.0 MM PEPTIDE, 25 MM SODIUM ACETATE NMR sample composition 1.4 MM IGF-I (13C,15N), 2.0 MM PEPTIDE, 25 MM SODIUM ACETATE \| D2O	Resolution not provided
1WQJ Structural Basis for the Regulation of Insulin-Like Growth Factors (IGFs) by IGF Binding Proteins (IGFBPs) Deposited 2004-09-29	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain I 49–118（70 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.8；277 K；23% PEG 1500, 25mM Tris, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.60 Å R-free 0.255
2DSP Structural Basis for the Inhibition of Insulin-like Growth Factors by IGF Binding Proteins Deposited 2006-07-05	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain I 49–118（70 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；290 K；23% PEG 1500, 25mM Tris pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 290K	Resolution 2.50 Å R-free 0.271
2DSQ Structural Basis for the Inhibition of Insulin-like Growth Factors by IGF Binding Proteins Deposited 2006-07-05	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 I 49–118（70 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.3；290 K；20% PEG 3350, 0.2M lithium acetate, pH 7.3, VAPOR DIFFUSION, SITTING DROP, temperature 290K	Resolution 2.80 Å R-free 0.357
2DSQ Structural Basis for the Inhibition of Insulin-like Growth Factors by IGF Binding Proteins Deposited 2006-07-05	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 49–118（70 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.3；290 K；20% PEG 3350, 0.2M lithium acetate, pH 7.3, VAPOR DIFFUSION, SITTING DROP, temperature 290K	Resolution 2.80 Å R-free 0.357
2DSR Structural Basis for the Inhibition of Insulin-like Growth Factors by IGF Binding Proteins Deposited 2006-07-05	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 I 49–118（70 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；290 K；1M lithium sulfate monohydrate, 2% PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 290K	Resolution 2.10 Å R-free 0.256
3LRI Solution structure and backbone dynamics of long-[Arg(3)]insulin-like growth factor-I Deposited 1999-04-13	Different construct Different mutation/modification Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 33–102（70 aa）	Mutation：E3R, 13 RESIDUE N-TERMINAL EXTENSION	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 3；303 K；Pressure 1	Resolution not provided
4XSS Insulin-like growth factor I in complex with site 1 of a hybrid insulin receptor / Type 1 insulin-like growth factor receptor Deposited 2015-01-22	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 49–118（70 aa） Fragment：UNP residues 49-118	Not recorded	SO4 SULFATE ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 10.5；298 K；1.75 M ammonium sulfate, 0.1 M CAPS-NaOH (pH 10.5), 0.2 M LiSO4	Resolution 3.00 Å R-free 0.229
4XSS Insulin-like growth factor I in complex with site 1 of a hybrid insulin receptor / Type 1 insulin-like growth factor receptor Deposited 2015-01-22	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 18 PDB declaration: octadecameric	Chain B 49–118（70 aa） Fragment：UNP residues 49-118	Not recorded	SO4 SULFATE ION × 6 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 10.5；298 K；1.75 M ammonium sulfate, 0.1 M CAPS-NaOH (pH 10.5), 0.2 M LiSO4	Resolution 3.00 Å R-free 0.229
5U8Q Structure of the ectodomain of the human Type 1 insulin-like growth factor receptor in complex with IGF-I Deposited 2016-12-14	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: octameric	Chain B 49–118（70 aa）	Not recorded	SO4 SULFATE ION × 4 MLT D-MALATE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；1.2 M ammonium sulfate, 0.1 M imidazole-malate pH 7.0. IGF-1 was included by soaking directly into the mother crystal. For full details see the primary citation.	Resolution 3.27 Å R-free 0.303
6FF3 Crystal structure of Drosophila neural ectodermal development factor Imp-L1 with Human IGF-I Deposited 2018-01-03	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 49–118（70 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；291 K；cp 10 mg/ml, 4-8% w/v PEG 6K, 5-20 mM MgCl2, 5 mM SB12, 0.1 M TRIS pH 7.5	Resolution 2.57 Å R-free 0.285
6PYH Cryo-EM structure of full-length IGF1R-IGF1 complex. Only the extracellular region of the complex is resolved. Deposited 2019-07-29	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 B 49–118（70 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.30 Å
7S0Q Head region of a complex of IGF-I with the ectodomain of a hybrid insulin receptor / type 1 insulin-like growth factor receptor Deposited 2021-08-30	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 49–118（70 aa）	Not recorded	BMA beta-D-mannopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 8；20mM Tris pH 8.0 160mM NaCl cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
7WRQ Structure of Human IGF1/IGFBP3/ALS Ternary Complex Deposited 2022-01-27	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 33–102（70 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；blot for 2 seconds before plunging	Resolution 3.60 Å
7YRR Cryo-EM structure of IGF1R with two IGF1 complex Deposited 2022-08-10	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 36–95（60 aa） Chain D 36–95（60 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen OTHER	Resolution 4.30 Å
8EYR Cryo-EM structure of two IGF1 bound full-length mouse IGF1R mutant (four glycine residues inserted in the alpha-CT; IGF1R-P674G4): symmetric conformation Deposited 2022-10-28	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–195（195 aa） Chain D 1–195（195 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å
8X06 Cryo-EM structure of the IR/IGF-I complex, conformation 1 Deposited 2023-11-03	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–195（195 aa） Chain D 1–195（195 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.24 Å
8X2M Cryo-EM structure of the IR/IGF-I complex, conformation 2 Deposited 2023-11-09	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 1–195（195 aa） Chain D 1–195（195 aa） Chain E 1–195（195 aa） Chain F 1–195（195 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.31 Å
8XJS Cryo-EM structure of human insulin receptor bound to 3 IGF-I Deposited 2023-12-22	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain C 1–195（195 aa） Chain D 1–195（195 aa） Chain E 1–195（195 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.24 Å
8XK1 Cryo-EM structure of human insulin receptor bound to 4 IGF-I Deposited 2023-12-22	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 1–195（195 aa） Chain D 1–195（195 aa） Chain E 1–195（195 aa） Chain F 1–195（195 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.31 Å
8XKM Cryo-EM structure of human insulin receptor bound to 4 IGF-I, conformation 3 Deposited 2023-12-23	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 1–195（195 aa） Chain D 1–195（195 aa） Chain E 1–195（195 aa） Chain F 1–195（195 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.00 Å
8XKR Cryo-EM structure of human insulin receptor bound to 4 IGF-I, conformation 2 Deposited 2023-12-24	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 1–195（195 aa） Chain D 1–195（195 aa） Chain E 1–195（195 aa） Chain F 1–195（195 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.53 Å

21 other PDB entries and 23 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	IGF1_HUMAN
Isoform	P05019-2
PDB entities	1
Chains and sequence ranges	Author chain X； PDBConstruct 1–71； UniProt 48–118

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	6rva
Deposition date deposition_date	2019-05-31
Structure title title	STRUCTURE OF [ASP58]-IGF-I ANALOGUE
Keywords keywords	IGF-I ANALOGUE, HORMONE; HORMONE
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	14.18 Å
Radius of gyration Rg (electron density) rg_electron	14.04 Å
Forward intensity I(0) i0	370818000.00
Molecular weight molecular_weight	153320.0 kDa
Excluded volume excluded_volume	188440 Å³
Envelope volume envelope_volume	37999 Å³
Hydration-shell volume shell_volume	17450 Å³
Envelope diameter envelope_diameter	65.2 Å
Shell Rg shell_rg	24.52 Å
Envelope Rg envelope_rg	19.15 Å
Shape Rg shape_rg	14.04 Å
Total Rg total_rg	14.35 Å
Total atoms total_atoms	20960
Residues n_residues	1420
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	57.9 Å
Rg (real space) rg_real	14.26 Å
Rg uncertainty (real space) rg_real_error	0.62 Å
I(0) (real space) i0_real	3.7080e+08
I(0) uncertainty (real space) i0_real_error	4.3790e+06
Rg (reciprocal space) rg_reciprocal	14.25 Å
I(0) (reciprocal space) i0_reciprocal	370800000.0000
Solution quality estimate total_estimate	0.7554
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	47.7 Å
Skewness Skewness skewness	0.471
Kurtosis Kurtosis kurtosis	0.051
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	112300.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.442; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.509; Smooth: 0.982

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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_id	d6rvax1
Class class	g — Small proteins
Fold Fold fold	g.1 — Insulin-like
Superfamily Superfamily superfamily	g.1.1 — Insulin-like
Family Family family	g.1.1.1 — Insulin-like

Domain ID domain_id	d6rvax2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id	6rvaX00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	100 — Insulin-like, subunit E
Homologous superfamily homologous superfamily	10 — Insulin-like

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8. Citations (1)

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Description description	Insulin-like growth factor I
Molecular weight formula_weight	7706.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	X
Atom count atom_count	20960

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/rv/6rva/6rva.fit
pddf	/app/data/pr_computation/rv/6rva/6rva.pr.out
profile	/app/data/saxs_computation/rv/6rva/6rva.dat

STRUCTURE OF [ASP58]-IGF-I ANALOGUE

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

Insulin-like growth factor I

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) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)