SAXSdb — 4np9

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

Rabphilin-3A

Rattus norvegicus

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 378–510	Fragment：C2 domain, UNP RESIDUES 378-510	I3P D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；25-28% PEG 4K, 10-20mM Ammonium sulfate, 100mM HEPES pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.92 Å R-free 0.250

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 4NP9	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1ZBD STRUCTURAL BASIS OF RAB EFFECTOR SPECIFICITY: CRYSTAL STRUCTURE OF THE SMALL G PROTEIN RAB3A COMPLEXED WITH THE EFFECTOR DOMAIN OF RABPHILIN-3A Deposited 1998-11-06	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 41–170（130 aa） Fragment：40-170, EFFECTOR DOMAIN	Mutation：C108S Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；pH 8.0	Resolution 2.60 Å R-free 0.263
1ZBD STRUCTURAL BASIS OF RAB EFFECTOR SPECIFICITY: CRYSTAL STRUCTURE OF THE SMALL G PROTEIN RAB3A COMPLEXED WITH THE EFFECTOR DOMAIN OF RABPHILIN-3A Deposited 1998-11-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 41–170（130 aa） Fragment：40-170, EFFECTOR DOMAIN	Mutation：C108S Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；pH 8.0	Resolution 2.60 Å R-free 0.263
2CHD Crystal structure of the C2A domain of Rabphilin-3A Deposited 2006-03-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 371–510（140 aa） Fragment：C2A DOMAIN, RESIDUES 371-510	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions 25% PEG4000, 0.1M AMMONIUM SULPHATE, 0.1M SODIUM ACETATE, PH=4.6	Resolution 1.92 Å R-free 0.269
2CM5 crystal structure of the C2B domain of rabphilin Deposited 2006-05-04	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 519–684（166 aa） Fragment：C2B DOMAIN AND LINKER, RESIDUES 519-684	Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions 0.1M HEPES PH 8.5,20 % PEG MME 2000 OR 20 % PEG 8000	Resolution 1.28 Å R-free 0.194
2CM6 crystal structure of the C2B domain of rabphilin3A Deposited 2006-05-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 519–684（166 aa） Fragment：C2B DOMAIN AND LINKER, RESIDUES 519-684	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions 0.1 M HEPES PH 7.6, 25 % PEG 8000, 200 MM CA	Resolution 1.85 Å R-free 0.268
2CM6 crystal structure of the C2B domain of rabphilin3A Deposited 2006-05-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 519–684（166 aa） Fragment：C2B DOMAIN AND LINKER, RESIDUES 519-684	Not recorded	CA CALCIUM ION × 2 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions 0.1 M HEPES PH 7.6, 25 % PEG 8000, 200 MM CA	Resolution 1.85 Å R-free 0.268
3RPB THE C2B-DOMAIN OF RABPHILIN: STRUCTURAL VARIATIONS IN A JANUS-FACED DOMAIN Deposited 1999-04-19	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 541–680（140 aa） Fragment：C2B DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.1；304.5 K；Ionic strength (raw mmCIF value) 150 mM NMR sample composition 95% WATER/5% D2O	Resolution not provided
4LT7 Crystal structure of the c2a domain of rabphilin-3a in complex with a calcium Deposited 2013-07-23	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 378–510（133 aa） Fragment：C2 1 domain residues 378-510	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；10 mM CaCl2, 150mM NaCl, 25mM HEPES ph 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.50 Å R-free 0.289
4NS0 The C2A domain of Rabphilin 3A in complex with PI(4,5)P2 Deposited 2013-11-27	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 378–510（133 aa） Fragment：C2 domain, UNP RESIDUES 378-510	Not recorded	PIO [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；25mM Hepes, 20mM Ammonuim Sulphate, 25% PEG 4K, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.80 Å R-free 0.226
5LO8 The C2B domain of Rabphilin 3A in complex with PI(4,5)P2 Deposited 2016-08-08	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 536–680（145 aa） Fragment：C2B domain, UNP Residues 536-680	Not recorded	CA CALCIUM ION × 2 GOL GLYCEROL × 4 SO4 SULFATE ION × 1 PIO [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；24% PEG3350 0.1M ammonium sulfate 50mM Tris pH 7.5	Resolution 2.50 Å R-free 0.265
5LO8 The C2B domain of Rabphilin 3A in complex with PI(4,5)P2 Deposited 2016-08-08	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 536–680（145 aa） Fragment：C2B domain, UNP Residues 536-680	Not recorded	CA CALCIUM ION × 2 GOL GLYCEROL × 3 PIO [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；24% PEG3350 0.1M ammonium sulfate 50mM Tris pH 7.5	Resolution 2.50 Å R-free 0.265
5LOB Structure of the Ca2+-bound Rabphilin3A C2B- SNAP25 complex (C2 space group) Deposited 2016-08-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain A 536–680（145 aa） Chain B 536–680（145 aa） Chain C 536–680（145 aa）	Not recorded	CA CALCIUM ION × 6 SO4 SULFATE ION × 10 GOL GLYCEROL × 9	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；30% PEG3350 0.35 M Ammonium sulfate 0.1 M Tris pH 8.5	Resolution 3.30 Å R-free 0.286
5LOW Structure of the Ca2+-bound Rabphilin 3A C2B domain SNAP25 complex (P21 space group) Deposited 2016-08-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain A 536–680（145 aa） Chain B 536–680（145 aa） Chain C 536–680（145 aa）	Not recorded	GOL GLYCEROL × 3 CA CALCIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；20% PEG3350 0.35 M Ammonium sulfate 0.1 M Tris (pH 8.5) al's oil	Resolution 2.80 Å R-free 0.269
5LOW Structure of the Ca2+-bound Rabphilin 3A C2B domain SNAP25 complex (P21 space group) Deposited 2016-08-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain H 536–680（145 aa） Chain I 536–680（145 aa） Chain J 536–680（145 aa）	Not recorded	GOL GLYCEROL × 4 CA CALCIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；20% PEG3350 0.35 M Ammonium sulfate 0.1 M Tris (pH 8.5) al's oil	Resolution 2.80 Å R-free 0.269

10 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RP3A_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–133； UniProt 378–510

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	4np9
Deposition date deposition_date	2013-11-21
Structure title title	Structure of Rabphilin C2A domain bound to IP3
Keywords keywords	RABPHILIN-3A, C2 DOMAIN, C2A, CALCIUM BINDING, SYNAPTIC EXOCYTOSIS METAL-BINDING, PROTEIN TRANSPORT, C-2 domain fold, EXOPHILIN-1; PROTEIN TRANSPORT
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	16.19 Å
Radius of gyration Rg (electron density) rg_electron	14.94 Å
Forward intensity I(0) i0	5023000.00
Molecular weight molecular_weight	15273.0 kDa
Excluded volume excluded_volume	18795 Å³
Envelope volume envelope_volume	21552 Å³
Hydration-shell volume shell_volume	12516 Å³
Envelope diameter envelope_diameter	54.5 Å
Shell Rg shell_rg	20.58 Å
Envelope Rg envelope_rg	15.39 Å
Shape Rg shape_rg	14.95 Å
Total Rg total_rg	15.97 Å
Total atoms total_atoms	1065
Residues n_residues	129
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	56.3 Å
Rg (real space) rg_real	16.17 Å
Rg uncertainty (real space) rg_real_error	0.34 Å
I(0) (real space) i0_real	5.0230e+06
I(0) uncertainty (real space) i0_real_error	6.2630e+04
Rg (reciprocal space) rg_reciprocal	16.17 Å
I(0) (reciprocal space) i0_reciprocal	5023000.0000
Solution quality estimate total_estimate	0.8625
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	18.8 Å
Skewness Skewness skewness	0.358
Kurtosis Kurtosis kurtosis	-0.184
Angular range angular_range	— – 0.4900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	861900.0000
Real-space data points n_real_points	79
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.746; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.983

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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	Rabphilin-3A
Molecular weight formula_weight	15305.5 kDa
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	1204

DQATTLGALEFSLLYDQDNSNLQCTIIRAKGLKPMDSNGLADPYVKLHLLPGASKSNKLRTKTLRNTRNPVWNETLQYHGITEEDMQRKTLRISVCDEDKFGHNEFIGETRFSLKKLKANQRKNFNICLERVI

来源 Source

来源生物 organism	Rattus norvegicus
通用名 common_name	brown rat,rat,rats
NCBI Class编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE
Molecular weight formula_weight	420.1 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	139

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d4np9a_
Class class	b — All beta proteins
Fold Fold fold	b.7 — C2 domain-like
Superfamily Superfamily superfamily	b.7.1 — C2 domain (Calcium/lipid-binding domain, CaLB)
Family Family family	b.7.1.0 — automated matches

CATH v4.4 (1 domains)

Domain ID domain_id	4np9A00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	150 — C2 domain

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8. Citations (1)

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Unit-cell length a length_a	38.270 Å
Unit-cell length b length_b	39.470 Å
Unit-cell length c length_c	89.260 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.920 Å
Low-resolution limit resolution_low	29.566 Å
R factor r_factor	0.2108
R_work r_work	0.2089
R_free r_free	0.2501

fit	/app/data/saxs_computation/np/4np9/4np9.fit
pddf	/app/data/pr_computation/np/4np9/4np9.pr.out
profile	/app/data/saxs_computation/np/4np9/4np9.dat

Structure of Rabphilin C2A domain bound to IP3

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

Rabphilin-3A

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