SAXSdb — 2rmy

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

Myc box-dependent-interacting protein 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 1–33	Fragment：UNP residues 1-33	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 7.4；298 K；Ionic strength (raw mmCIF value) 0；Pressure ambient NMR sample composition：1mM [U-100% 15N] protein, 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 2RMY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1MUZ NMR STRUCTURE OF THE TUMOR SUPPRESSOR BIN1: ALTERNATIVE SPLICING IN MELANOMA AND INTERACTION WITH C-MYC Deposited 2002-09-24	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 513–593（81 aa） Fragment：residues 513-593	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 300e-3；Pressure ambient NMR sample composition 1.5 mM Bin1(402-482) U-15N, 13C 25 mM sodium phosphate buffer, 150 mM NaCl, 1 mM DTT, 95% H2O, 5% D2O pH=6.5 \| 95% H2O/5% D2O	Resolution not provided
1MV0 NMR STRUCTURE OF THE TUMOR SUPPRESSOR BIN1: ALTERNATIVE SPLICING IN MELANOMA AND INTERACTION WITH C-MYC Deposited 2002-09-24	Different construct Different oligomeric state Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 513–593（81 aa） Fragment：residues 513-593	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 300e-3；Pressure ambient NMR sample composition 1.4 mM Bin1(402-482)/c-Myc(55-68) U-15N, 13C, 25 mM sodium phosphate, 150 mM NaCl, 1 mM DTT, 95% H2O, 5% D2O pH=6.5 \| 95% H2O/5% D2O	Resolution not provided
1MV3 NMR STRUCTURE OF THE TUMOR SUPPRESSOR BIN1: ALTERNATIVE SPLICING IN MELANOMA AND INTERACTION WITH C-MYC Deposited 2002-09-24	Different construct Different mutation/modification Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 301–377（77 aa） Fragment：isoform BIN1+12A (residues 301-377, 458-594) Chain A 458–593（136 aa） Fragment：isoform BIN1+12A (residues 301-377, 458-594)	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 300e-3；Pressure ambient NMR sample composition 1.3 mM Bin1(270-482,+12A) U-15N, 13C, 25 mM sodium phosphate, 150 mM NaCl, 1 mM DTT, 95 % H2O, 5% D2O \| 95% H2O/5% D2O	Resolution not provided
2FIC The crystal structure of the BAR domain from human Bin1/Amphiphysin II and its implications for molecular recognition Deposited 2005-12-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–241（241 aa） Fragment：BAR domain Chain B 1–241（241 aa） Fragment：BAR domain	Not recorded	XE XENON × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；20% monomethylether-PEG550, 100mM Tris (pH 8), 100mM NaCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.99 Å R-free 0.280
2FIC The crystal structure of the BAR domain from human Bin1/Amphiphysin II and its implications for molecular recognition Deposited 2005-12-29	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–241（241 aa） Fragment：BAR domain	Not recorded	XE XENON × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；20% monomethylether-PEG550, 100mM Tris (pH 8), 100mM NaCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.99 Å R-free 0.280
2FIC The crystal structure of the BAR domain from human Bin1/Amphiphysin II and its implications for molecular recognition Deposited 2005-12-29	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–241（241 aa） Fragment：BAR domain	Not recorded	XE XENON × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；20% monomethylether-PEG550, 100mM Tris (pH 8), 100mM NaCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.99 Å R-free 0.280
2RND Structure of the N-terminal BARpeptide in DPC micelles Deposited 2007-12-16	Different construct	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–33（33 aa） Fragment：BARpeptide, UNP residues 1-33	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.4；298 K；Ionic strength (raw mmCIF value) 0；Pressure ambient NMR sample composition 1mM [U-100% 15N] protein, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
5I22 Amphiphysin SH3 in complex with Chikungunya virus nsP3 peptide Deposited 2016-02-04	Different construct Different oligomeric state Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 513–593（81 aa） Fragment：SH3 fragment, UNP residue 513-593	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298.15 K；Pressure 1 NMR sample composition 0.5 mM [U-13C; U-15N] amphiphysin 2 SH3, 0.5 mM [U-13C; U-15N] CHIKV nsP3 peptide, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided

6 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	BIN1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–33； UniProt 1–33

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	2rmy
Deposition date deposition_date	2007-12-03
Structure title title	Structure of the N-terminal BARpeptide in SDS micelles
Keywords keywords	;BARpeptide, micelle, NMR-structure, Alternative splicing, Anti-oncogene, Cell cycle, Coiled coil, Cytoplasm, Developmental protein, Differentiation, Endocytosis, Host-virus interaction, Nucleus, Phosphoprotein, SH3 domain ;; ENDOCYTOSIS
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	14.78 Å
Radius of gyration Rg (electron density) rg_electron	15.03 Å
Forward intensity I(0) i0	19871400.00
Molecular weight molecular_weight	37125.0 kDa
Excluded volume excluded_volume	47143 Å³
Envelope volume envelope_volume	14380 Å³
Hydration-shell volume shell_volume	8215 Å³
Envelope diameter envelope_diameter	59.2 Å
Shell Rg shell_rg	20.78 Å
Envelope Rg envelope_rg	17.86 Å
Shape Rg shape_rg	14.95 Å
Total Rg total_rg	15.66 Å
Total atoms total_atoms	5440
Residues n_residues	340
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	57.5 Å
Rg (real space) rg_real	15.20 Å
Rg uncertainty (real space) rg_real_error	0.68 Å
I(0) (real space) i0_real	1.9870e+07
I(0) uncertainty (real space) i0_real_error	2.7570e+05
Rg (reciprocal space) rg_reciprocal	15.17 Å
I(0) (reciprocal space) i0_reciprocal	19870000.0000
Solution quality estimate total_estimate	0.6501
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	8.0 Å
Skewness Skewness skewness	0.566
Kurtosis Kurtosis kurtosis	-0.482
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	10350.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.150; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.014; Smooth: 0.983

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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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Description description	Myc box-dependent-interacting protein 1
Molecular weight formula_weight	3714.4 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	5440

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/rm/2rmy/2rmy.fit
pddf	/app/data/pr_computation/rm/2rmy/2rmy.pr.out
profile	/app/data/saxs_computation/rm/2rmy/2rmy.dat

Structure of the N-terminal BARpeptide in SDS micelles

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

Myc box-dependent-interacting protein 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

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)