SAXSdb — 4nsw

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

Arf-GAP with coiled-coil, ANK repeat and PH domain-containing 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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–377 Chain B； UniProt 1–377	Fragment：UNP residues 1-377	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；289 K；0.2M AMMONIUM CITRATE, 10% PEG3350, 6.0MM OCTYL BETA-THIOGLUCOPYRANOSIDE, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.20 Å R-free 0.266

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 4NSW	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3JUE Crystal Structure of ArfGAP and ANK repeat domain of ACAP1 Deposited 2009-09-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 378–740（363 aa） Fragment：ArfGAP and ANK repeat domain, residues 378-740	Not recorded	ZN ZINC ION × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.1；289 K；0.2M ammonium sulfate, 14% PEG 3350, 0.1M Sodium Citrate, pH 5.1, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.30 Å R-free 0.219
3JUE Crystal Structure of ArfGAP and ANK repeat domain of ACAP1 Deposited 2009-09-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 378–740（363 aa） Fragment：ArfGAP and ANK repeat domain, residues 378-740	Not recorded	ZN ZINC ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.1；289 K；0.2M ammonium sulfate, 14% PEG 3350, 0.1M Sodium Citrate, pH 5.1, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.30 Å R-free 0.219
3T9K Crystal Structure of ACAP1 C-portion mutant S554D fused with integrin beta1 peptide Deposited 2011-08-03	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 378–740（363 aa）	Mutation：S554D	ZN ZINC ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；289 K；0.2M ammonium sulfate, 14% PEG 3350, 0.1M Sodium Citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.30 Å R-free 0.225
3T9K Crystal Structure of ACAP1 C-portion mutant S554D fused with integrin beta1 peptide Deposited 2011-08-03	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 378–740（363 aa）	Mutation：S554D	ZN ZINC ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；289 K；0.2M ammonium sulfate, 14% PEG 3350, 0.1M Sodium Citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.30 Å R-free 0.225
4CKG Helical reconstruction of ACAP1(BAR-PH domain) decorated membrane tubules by cryo-electron microscopy Deposited 2014-01-06	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 40 PDB declaration: 40-meric	Chain A 1–377（377 aa） Fragment：BAR-PH DOMAIN, RESIDUES 1-377 Chain B 1–377（377 aa） Fragment：BAR-PH DOMAIN, RESIDUES 1-377 Chain C 1–377（377 aa） Fragment：BAR-PH DOMAIN, RESIDUES 1-377 Chain D 1–377（377 aa） Fragment：BAR-PH DOMAIN, RESIDUES 1-377	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 50MM HEPES, PH7.4, 100MM NACL；pH 7.4；50MM HEPES, PH7.4, 100MM NACL cryo-EM vitrification conditions Cryogen ETHANE；LIQUID ETHANE	Resolution 15.00 Å
4CKH Helical reconstruction of ACAP1(BAR-PH domain) decorated membrane tubules by cryo-electron microscopy Deposited 2014-01-06	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 40 PDB declaration: 40-meric	Chain A 1–377（377 aa） Fragment：BAR-PH DOMAIN, RESIDUES 1-377 Chain B 1–377（377 aa） Fragment：BAR-PH DOMAIN, RESIDUES 1-377 Chain C 1–377（377 aa） Fragment：BAR-PH DOMAIN, RESIDUES 1-377 Chain D 1–377（377 aa） Fragment：BAR-PH DOMAIN, RESIDUES 1-377	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 50MM HEPES, PH7.4, 100MM NACL；pH 7.4；50MM HEPES, PH7.4, 100MM NACL cryo-EM vitrification conditions Cryogen ETHANE；LIQUID ETHANE	Resolution 17.00 Å
4F1P Crystal Structure of mutant S554D for ArfGAP and ANK repeat domain of ACAP1 Deposited 2012-05-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 378–740（363 aa） Fragment：ArfGAP and ANK repeat domains, UNP residues 378-740	Mutation：S554D	ZN ZINC ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.1；289 K；0.2M ammonium sulfate, 12-14% PEG 3350, 0.1M Sodium Citrate, pH 5.1, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.30 Å R-free 0.235
4F1P Crystal Structure of mutant S554D for ArfGAP and ANK repeat domain of ACAP1 Deposited 2012-05-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 378–740（363 aa） Fragment：ArfGAP and ANK repeat domains, UNP residues 378-740	Mutation：S554D	ZN ZINC ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.1；289 K；0.2M ammonium sulfate, 12-14% PEG 3350, 0.1M Sodium Citrate, pH 5.1, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.30 Å R-free 0.235
5H3D Helical structure of membrane tubules decorated by ACAP1 (BARPH doamin) protein by cryo-electron microscopy and MD simulation Deposited 2016-10-22	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 36 PDB declaration: 36-meric	Chain A 1–377（377 aa） Chain B 1–377（377 aa） Chain C 1–377（377 aa） Chain D 1–377（377 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；50mM HEPES, pH7.4, 100mM NaCl, pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 14.00 Å
5H3D Helical structure of membrane tubules decorated by ACAP1 (BARPH doamin) protein by cryo-electron microscopy and MD simulation Deposited 2016-10-22	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–377（377 aa） Chain B 1–377（377 aa） Chain C 1–377（377 aa） Chain D 1–377（377 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；50mM HEPES, pH7.4, 100mM NaCl, pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 14.00 Å
5H3D Helical structure of membrane tubules decorated by ACAP1 (BARPH doamin) protein by cryo-electron microscopy and MD simulation Deposited 2016-10-22	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–377（377 aa） Chain B 1–377（377 aa） Chain C 1–377（377 aa） Chain D 1–377（377 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；50mM HEPES, pH7.4, 100mM NaCl, pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 14.00 Å

6 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ACAP1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–382； UniProt 1–377 Author chain B； PDBConstruct 6–382； UniProt 1–377

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	4nsw
Deposition date deposition_date	2013-11-29
Structure title title	Crystal structure of the BAR-PH domain of ACAP1
Keywords keywords	COILED-COIL, BAR DOMAIN, PH DOMAIN, GTPASE ACTIVATION, PROTEIN TRANSPORT, membrane remodeling; 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	49.34 Å
Radius of gyration Rg (electron density) rg_electron	50.84 Å
Forward intensity I(0) i0	107466000.00
Molecular weight molecular_weight	83061.0 kDa
Excluded volume excluded_volume	103550 Å³
Envelope volume envelope_volume	156990 Å³
Hydration-shell volume shell_volume	30336 Å³
Envelope diameter envelope_diameter	166.9 Å
Shell Rg shell_rg	42.32 Å
Envelope Rg envelope_rg	51.38 Å
Shape Rg shape_rg	50.83 Å
Total Rg total_rg	50.49 Å
Total atoms total_atoms	5839
Residues n_residues	730
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	160.2 Å
Rg (real space) rg_real	50.71 Å
Rg uncertainty (real space) rg_real_error	2.31 Å
I(0) (real space) i0_real	1.0750e+08
I(0) uncertainty (real space) i0_real_error	2.2560e+06
Rg (reciprocal space) rg_reciprocal	49.35 Å
I(0) (reciprocal space) i0_reciprocal	107300000.0000
Solution quality estimate total_estimate	0.6096
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	25.0 Å
Skewness Skewness skewness	0.550
Kurtosis Kurtosis kurtosis	-0.688
Angular range angular_range	— – 0.1600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3077000.0000
Real-space data points n_real_points	33
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.279; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.090; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	4nswA01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
Homologous superfamily homologous superfamily	60 — Arfaptin homology (AH) domain/BAR domain

Domain ID domain_id	4nswA02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	29 — PH-domain like
Homologous superfamily homologous superfamily	30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)

Domain ID domain_id	4nswB01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
Homologous superfamily homologous superfamily	60 — Arfaptin homology (AH) domain/BAR domain

Domain ID domain_id	4nswB02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	29 — PH-domain like
Homologous superfamily homologous superfamily	30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)

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8. Citations (1)

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Unit-cell length a length_a	42.460 Å
Unit-cell length b length_b	59.720 Å
Unit-cell length c length_c	168.950 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.40 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	29.850 Å
R factor r_factor	0.2140
R_work r_work	0.2110
R_free r_free	0.2660

Description description	Arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 1
Molecular weight formula_weight	43334.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	5985

Crystal structure of the BAR-PH domain of ACAP1

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

Arf-GAP with coiled-coil, ANK repeat and PH domain-containing 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

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	146

fit	/app/data/saxs_computation/ns/4nsw/4nsw.fit
pddf	/app/data/pr_computation/ns/4nsw/4nsw.pr.out
profile	/app/data/saxs_computation/ns/4nsw/4nsw.dat