SAXSdb — 3fia

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

Intersectin-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 1–111	Fragment：residues 1-111 Mutation：M1V, I14T Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：microbatch under oil；pH 8.5；277 K；1.5M ammonium sulfate, 12% glycerol, 0.1M TrisHCl, pH 8.5, microbatch under oil , temperature 277K	Resolution 1.45 Å R-free 0.176

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 3FIA	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1KI1 Guanine Nucleotide Exchange Region of Intersectin in Complex with Cdc42 Deposited 2001-12-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1229–1581（353 aa） Fragment：Dbl homology and Pleckstrin homology domains (residues 1229-1580)	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；PEG 4000, ammonium sulfate, Tris, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.30 Å R-free 0.247
1KI1 Guanine Nucleotide Exchange Region of Intersectin in Complex with Cdc42 Deposited 2001-12-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1229–1581（353 aa） Fragment：Dbl homology and Pleckstrin homology domains (residues 1229-1580)	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；PEG 4000, ammonium sulfate, Tris, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.30 Å R-free 0.247
2KGR Solution structure of protein ITSN1 from Homo sapiens. Northeast Structural Genomics Consortium target HR5524A Deposited 2009-03-16	Different construct Different mutation/modification 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 210–312（103 aa） Fragment：residues 210-312	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 0.2；Pressure ambient NMR sample composition 1.0 mM [U-100% 13C; U-100% 15N] protein-1, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1.0 mM [U-5% 13C; U-99% 15N] protein-2, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2KHN NMR solution structure of the EH 1 domain from human intersectin-1 protein. Northeast Structural Genomics Consortium target HR3646E. Deposited 2009-04-09	Different construct Different mutation/modification 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 1–111（111 aa） Fragment：UNP residues 1-111	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 430；Pressure ambient NMR sample composition 0.87 mM [U-98% 13C; U-98% 15N] HR3646E-1, 20 mM MES-2, 200 mM sodium chloride-3, 5 mM calcium chloride-4, 10 mM DTT-5, 0.02 % sodium azide-6, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.81 mM [U-5% 13C; U-98% 15N] HR3646E-7, 20 mM MES-8, 200 mM sodium chloride-9, 5 mM calcium chloride-10, 10 mM DTT-11, 0.02 % sodium azide-12, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
3QBV Structure of designed orthogonal interaction between CDC42 and nucleotide exchange domains of intersectin Deposited 2011-01-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1229–1579（351 aa） Fragment：DH AND PH DOMAINS (UNP Residues 1229-1571)	Mutation：S1373E	GDP GUANOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；100mm TRIS pH 7.5, 25% PEG 3350, 150mm ammonium sulfate, and 1mM DTT, temperature 295k, VAPOR DIFFUSION, HANGING DROP	Resolution 2.65 Å R-free 0.284
3QBV Structure of designed orthogonal interaction between CDC42 and nucleotide exchange domains of intersectin Deposited 2011-01-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1229–1579（351 aa） Fragment：DH AND PH DOMAINS (UNP Residues 1229-1571)	Mutation：S1373E	GDP GUANOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；100mm TRIS pH 7.5, 25% PEG 3350, 150mm ammonium sulfate, and 1mM DTT, temperature 295k, VAPOR DIFFUSION, HANGING DROP	Resolution 2.65 Å R-free 0.284
4IIM Crystal structure of the Second SH3 Domain of ITSN1 bound with a synthetic peptide Deposited 2012-12-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 916–970（55 aa） Chain B 916–970（55 aa）	Not recorded	UNX UNKNOWN LIGAND × 11	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；1.2 M NaCitrate and 0.1 M Tris, pH 8.5, vapor diffusion hanging drop, temperature 291K	Resolution 1.80 Å R-free 0.243
4IIM Crystal structure of the Second SH3 Domain of ITSN1 bound with a synthetic peptide Deposited 2012-12-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 916–970（55 aa） Chain B 916–970（55 aa）	Not recorded	UNX UNKNOWN LIGAND × 11	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；1.2 M NaCitrate and 0.1 M Tris, pH 8.5, vapor diffusion hanging drop, temperature 291K	Resolution 1.80 Å R-free 0.243
5HZI Crystal structure of photoinhibitable Intersectin1 containing C450M mutant LOV2 domain Deposited 2016-02-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1230–1308（79 aa） Chain A 1238–1509（272 aa）	Not recorded	FMN FLAVIN MONONUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.1 M HEPES pH 7.5, 9% (w/v) PEG 8000, 9% (v/v) ethylene glycol	Resolution 2.60 Å R-free 0.285
5HZI Crystal structure of photoinhibitable Intersectin1 containing C450M mutant LOV2 domain Deposited 2016-02-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1230–1308（79 aa） Chain B 1238–1509（272 aa）	Not recorded	FMN FLAVIN MONONUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.1 M HEPES pH 7.5, 9% (w/v) PEG 8000, 9% (v/v) ethylene glycol	Resolution 2.60 Å R-free 0.285
5HZJ Crystal structure of photoinhibitable Intersectin1 containing wildtype LOV2 domain Deposited 2016-02-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1230–1308（79 aa） Chain A 1309–1580（272 aa）	Not recorded	FMN FLAVIN MONONUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.1 M HEPES pH 7.5, 9% (w/v) PEG 8000, 9% (v/v) ethylene glycol	Resolution 2.60 Å R-free 0.281
5HZJ Crystal structure of photoinhibitable Intersectin1 containing wildtype LOV2 domain Deposited 2016-02-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1230–1308（79 aa） Chain B 1309–1580（272 aa）	Not recorded	FMN FLAVIN MONONUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.1 M HEPES pH 7.5, 9% (w/v) PEG 8000, 9% (v/v) ethylene glycol	Resolution 2.60 Å R-free 0.281
5HZK Crystal structure of photoinhibitable Intersectin1 containing wildtype LOV2 domain in complex with Cdc42 Deposited 2016-02-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1230–1308（79 aa） Chain B 1309–1580（272 aa）	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 1 FMN FLAVIN MONONUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；0.1 M MES, 20% (w/v) PEG 6000	Resolution 3.30 Å R-free 0.257
5HZK Crystal structure of photoinhibitable Intersectin1 containing wildtype LOV2 domain in complex with Cdc42 Deposited 2016-02-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1230–1308（79 aa） Chain D 1309–1580（272 aa）	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 1 FMN FLAVIN MONONUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；0.1 M MES, 20% (w/v) PEG 6000	Resolution 3.30 Å R-free 0.257
6GBU Crystal structure of the second SH3 domain of FCHSD2 (SH3-2) in complex with the fourth SH3 domain of ITSN1 (SH3d) Deposited 2018-04-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain B 1069–1133（65 aa） Chain D 1069–1133（65 aa） Chain F 1069–1133（65 aa） Chain H 1069–1133（65 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；0.5M ammonium sulfate, 10% Glycerol, Tris pH8.5	Resolution 3.44 Å R-free 0.247
6H5T Intersectin SH3A short isoform Deposited 2018-07-25	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 741–835（95 aa）	Not recorded	7PG 2,5,8,11,14,17,20,23-OCTAOXAPENTACOSAN-25-OL × 1 CL CHLORIDE ION × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；25% (v/v) polyethylene glycol 550 mono-methyl ether, 100 mM MES-NaOH at pH 6.5, and 10 mM ZnSO4	Resolution 1.69 Å R-free 0.191
6H5T Intersectin SH3A short isoform Deposited 2018-07-25	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 741–835（95 aa）	Not recorded	7PG 2,5,8,11,14,17,20,23-OCTAOXAPENTACOSAN-25-OL × 1 ZN ZINC ION × 1 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；25% (v/v) polyethylene glycol 550 mono-methyl ether, 100 mM MES-NaOH at pH 6.5, and 10 mM ZnSO4	Resolution 1.69 Å R-free 0.191

10 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ITSN1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 11–121； UniProt 1–111

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	3fia
Deposition date deposition_date	2008-12-11
Structure title title	Crystal structure of the EH 1 domain from human intersectin-1 protein. Northeast Structural Genomics Consortium target HR3646e.
Keywords keywords	;Intersectin-1; EH 1 domain; NESG, Structural Genomics, PSI-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, Alternative splicing, Calcium, Cell junction, Cell projection, Coiled coil, Endocytosis, Membrane, Phosphoprotein, SH3 domain, Synapse, Synaptosome, PROTEIN BINDING ;; PROTEIN BINDING
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	13.94 Å
Radius of gyration Rg (electron density) rg_electron	12.90 Å
Forward intensity I(0) i0	2669150.00
Molecular weight molecular_weight	11254.0 kDa
Excluded volume excluded_volume	13981 Å³
Envelope volume envelope_volume	15489 Å³
Hydration-shell volume shell_volume	10411 Å³
Envelope diameter envelope_diameter	48.9 Å
Shell Rg shell_rg	18.40 Å
Envelope Rg envelope_rg	13.36 Å
Shape Rg shape_rg	12.98 Å
Total Rg total_rg	13.94 Å
Total atoms total_atoms	777
Residues n_residues	94
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	49.5 Å
Rg (real space) rg_real	13.88 Å
Rg uncertainty (real space) rg_real_error	0.39 Å
I(0) (real space) i0_real	2.6690e+06
I(0) uncertainty (real space) i0_real_error	3.2970e+04
Rg (reciprocal space) rg_reciprocal	13.88 Å
I(0) (reciprocal space) i0_reciprocal	2669000.0000
Solution quality estimate total_estimate	0.8322
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	16.3 Å
Skewness Skewness skewness	0.253
Kurtosis Kurtosis kurtosis	-0.124
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	783500.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.618; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.978; Smooth: 0.981

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Intersectin-1
Molecular weight formula_weight	13817.0 kDa
Mutation mutation	M1V, I14T
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	917

MGHHHHHHSHVAQFPTPFGGSLDTWAITVEERAKHDQQFHSLKPISGFITGDQARNFFFQSGLPQPVLAQIWALADMNNDGRMDQVEFSIAMKLIKLKLQGYQLPSALPPVMKQQPVAISS

来源 Source

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

Entity 2 Entity 2 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	133

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3fiaa_
Class class	a — All alpha proteins
Fold Fold fold	a.39 — EF Hand-like
Superfamily Superfamily superfamily	a.39.1 — EF-hand
Family Family family	a.39.1.0 — automated matches

CATH v4.4 (1 domains)

Domain ID domain_id	3fiaA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	10 — EF-hand

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8. Citations (1)

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Unit-cell length a length_a	94.848 Å
Unit-cell length b length_b	32.021 Å
Unit-cell length c length_c	33.287 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	106.45 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.450 Å
Low-resolution limit resolution_low	45.500 Å
R factor r_factor	0.1605
R_work r_work	0.1596
R_free r_free	0.1764

fit	/app/data/saxs_computation/fi/3fia/3fia.fit
pddf	/app/data/pr_computation/fi/3fia/3fia.pr.out
profile	/app/data/saxs_computation/fi/3fia/3fia.dat

Crystal structure of the EH 1 domain from human intersectin-1 protein. Northeast Structural Genomics Consortium target HR3646e.

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

Intersectin-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

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction