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2fic

The crystal structure of the BAR domain from human Bin1/Amphiphysin II and its implications for molecular recognition

Method: X-RAY DIFFRACTION Dmax: 127.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Myc box-dependent-interacting protein 1

Homo sapiens

UniProt O00499

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 1–241 Chain B； UniProt 1–241 Fragment：BAR domain 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
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–241 Fragment：BAR domain 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
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 1–241 Fragment：BAR domain 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

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 2FIC 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics 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
2RMY Structure of the N-terminal BARpeptide in SDS micelles Deposited 2007-12-03 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–33（33 aa） Fragment：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
2RND Structure of the N-terminal BARpeptide in DPC micelles Deposited 2007-12-16 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics 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 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name BIN1_HUMAN
Isoform O00499-2
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 11–251； UniProt 1–241 Author chain B； PDBConstruct 11–251； UniProt 1–241

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 2fic

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2fic
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2fic
Deposition date deposition_date2005-12-29
Structure title titleThe crystal structure of the BAR domain from human Bin1/Amphiphysin II and its implications for molecular recognition
Keywords keywordsBAR domain, homodimer, coiled-coils, ENDOCYTOSIS/EXOCYTOSIS, MEMBRANE PROTEIN COMPLEX, ENDOCYTOSIS-EXOCYTOSIS; ENDOCYTOSIS/EXOCYTOSIS, MEMBRANE PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier35.41 Å
Radius of gyration Rg (electron density) rg_electron35.53 Å
Forward intensity I(0) i035306400.00
Molecular weight molecular_weight45803.0 kDa
Excluded volume excluded_volume56746 ų
Envelope volume envelope_volume84601 ų
Hydration-shell volume shell_volume22203 ų
Envelope diameter envelope_diameter134.1 Å
Shell Rg shell_rg37.38 Å
Envelope Rg envelope_rg35.01 Å
Shape Rg shape_rg35.58 Å
Total Rg total_rg35.51 Å
Total atoms total_atoms3208
Residues n_residues392
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 dmax127.4 Å
Rg (real space) rg_real35.68 Å
Rg uncertainty (real space) rg_real_error1.59 Å
I(0) (real space) i0_real3.5310e+07
I(0) uncertainty (real space) i0_real_error6.4520e+05
Rg (reciprocal space) rg_reciprocal35.51 Å
I(0) (reciprocal space) i0_reciprocal35300000.0000
Solution quality estimate total_estimate0.8198
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary45.3 Å
Skewness Skewness skewness0.434
Kurtosis Kurtosis kurtosis-0.085
Angular range angular_range— – 0.2250 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1270000.0000
Real-space data points n_real_points46
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.647; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.806; Smooth: 0.906
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd2fica_
Class classa — All alpha proteins
Fold Fold folda.238 — BAR/IMD domain-like
Superfamily Superfamily superfamilya.238.1 — BAR/IMD domain-like
Family Family familya.238.1.0 — automated matches
Domain ID domain_idd2ficb_
Class classa — All alpha proteins
Fold Fold folda.238 — BAR/IMD domain-like
Superfamily Superfamily superfamilya.238.1 — BAR/IMD domain-like
Family Family familya.238.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id2ficA00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
Homologous superfamily homologous superfamily60 — Arfaptin homology (AH) domain/BAR domain
Domain ID domain_id2ficB00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
Homologous superfamily homologous superfamily60 — Arfaptin homology (AH) domain/BAR domain
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8. Citations (1)

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9. Files and Curves (10)