SAXSdb — 9r4v

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

Actin nucleation-promoting factor WASL

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 207–275	Not recorded	LEE-encoded effector EspF × 1 （A0A376PNR8）	SOLUTION NMR NMR measurement conditions：pH 6.5；298 K；Ionic strength (raw mmCIF value) 0.1；Pressure ambient NMR sample composition：0.5 mM [U-13C; U-15N] N-WASP GBD, 0.6 mM EspF, 20 mM sodium phosphate, 50 mM sodium chloride, 93% H2O/7% D2O \| 93% H2O/7% D2O NMR sample composition：0.7 mM GBD, 0.5 mM [U-13C; U-15N] EspF, 20 mM sodium phosphate, 50 mM sodium chloride, 93% H2O/7% D2O \| 93% H2O/7% 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 9R4V	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2FF3 Crystal structure of Gelsolin domain 1:N-wasp V2 motif hybrid in complex with actin Deposited 2005-12-19	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 451–465（15 aa） Fragment：N-wasp second WH2 domain	Not recorded	CA CALCIUM ION × 3 ATP ADENOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions MICROBATCH；pH 6.5；293.15 K；5% PEG 8000, 0.1M sodium acetate, 10mM calcium chloride, pH 6.5, microbatch, temperature 293.15K	Resolution 2.00 Å R-free 0.250
2LNH Enterohaemorrhagic E. coli (EHEC) exploits a tryptophan switch to hijack host F-actin assembly Deposited 2011-12-28	Different construct Different oligomeric state Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 207–270（64 aa） Fragment：UNP residues 207-270	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 50；Pressure ambient NMR sample composition 0.3 mM [U-98% 13C; U-98% 15N] protein_1, 0.3 mM protein_2, 0.3 mM protein_3, 93% H2O/7% D2O \| 93% H2O/7% D2O NMR sample composition 0.5 mM protein_1, 0.5 mM [U-98% 13C; U-98% 15N] protein_2, 0.5 mM protein_3, 93% H2O/7% D2O \| 93% H2O/7% D2O NMR sample composition 0.5 mM protein_1, 0.5 mM protein_2, 0.5 mM [U-98% 13C; U-98% 15N] protein_3, 93% H2O/7% D2O \| 93% H2O/7% D2O	Resolution not provided
2VCP Crystal structure of N-Wasp VC domain in complex with skeletal actin Deposited 2007-09-26	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 392–484（93 aa） Fragment：WH2 1,2 AND C DOMAIN, RESIDUES 392-484	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；277 K；VAPOR DIFFUSION METHOD (4 C) PROTEIN SOLUTION: 0.18MM ACTIN, 0.36MM N-WASP PEPTIDE, 5MM TRIS.HCL PH7.0, ATP 0.2MM, CACL2 0.02MM, TCEP 20MM, NAN3 0.01%. RESERVOIR: 10.2% (V/V) TACSIMATE, 13.2%(W/V)PEG 8000, 100MM HEPES PH7.0	Resolution 3.20 Å R-free 0.331
2VCP Crystal structure of N-Wasp VC domain in complex with skeletal actin Deposited 2007-09-26	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 392–484（93 aa） Fragment：WH2 1,2 AND C DOMAIN, RESIDUES 392-484	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；277 K；VAPOR DIFFUSION METHOD (4 C) PROTEIN SOLUTION: 0.18MM ACTIN, 0.36MM N-WASP PEPTIDE, 5MM TRIS.HCL PH7.0, ATP 0.2MM, CACL2 0.02MM, TCEP 20MM, NAN3 0.01%. RESERVOIR: 10.2% (V/V) TACSIMATE, 13.2%(W/V)PEG 8000, 100MM HEPES PH7.0	Resolution 3.20 Å R-free 0.331
4CC2 Complex of human Tuba C-terminal SH3 domain with human N-WASP proline- rich peptide - P212121 Deposited 2013-10-17	Different construct 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 346–357（12 aa） Fragment：N-WASP PROLINE-RICH PEPTIDE, RESIDUES 346-357	Not recorded	GOL GLYCEROL × 3 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；3 M NACL, 0.1 M BIS-TRIS PH 5.5	Resolution 1.55 Å R-free 0.218
4CC2 Complex of human Tuba C-terminal SH3 domain with human N-WASP proline- rich peptide - P212121 Deposited 2013-10-17	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 346–357（12 aa） Fragment：N-WASP PROLINE-RICH PEPTIDE, RESIDUES 346-357	Not recorded	GOL GLYCEROL × 1 CL CHLORIDE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；3 M NACL, 0.1 M BIS-TRIS PH 5.5	Resolution 1.55 Å R-free 0.218
4CC7 Crystal structure of the sixth or C-terminal SH3 domain of human Tuba in complex with proline-rich peptides of N-WASP. Space group P41 Deposited 2013-10-18	Different construct 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 346–357（12 aa） Fragment：PROLINE-RICH REGION, RESIDUES 346-357	Not recorded	GOL GLYCEROL × 1 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；3 M NACL, 0.1 M BIS-TRIS PH 5.5	Resolution 1.97 Å R-free 0.215
4CC7 Crystal structure of the sixth or C-terminal SH3 domain of human Tuba in complex with proline-rich peptides of N-WASP. Space group P41 Deposited 2013-10-18	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 346–357（12 aa） Fragment：PROLINE-RICH REGION, RESIDUES 346-357	Not recorded	GOL GLYCEROL × 1 CL CHLORIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；3 M NACL, 0.1 M BIS-TRIS PH 5.5	Resolution 1.97 Å R-free 0.215
4CC7 Crystal structure of the sixth or C-terminal SH3 domain of human Tuba in complex with proline-rich peptides of N-WASP. Space group P41 Deposited 2013-10-18	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 346–357（12 aa） Fragment：PROLINE-RICH REGION, RESIDUES 346-357	Not recorded	CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；3 M NACL, 0.1 M BIS-TRIS PH 5.5	Resolution 1.97 Å R-free 0.215
4CC7 Crystal structure of the sixth or C-terminal SH3 domain of human Tuba in complex with proline-rich peptides of N-WASP. Space group P41 Deposited 2013-10-18	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 346–357（12 aa） Fragment：PROLINE-RICH REGION, RESIDUES 346-357	Not recorded	CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；3 M NACL, 0.1 M BIS-TRIS PH 5.5	Resolution 1.97 Å R-free 0.215
4CC7 Crystal structure of the sixth or C-terminal SH3 domain of human Tuba in complex with proline-rich peptides of N-WASP. Space group P41 Deposited 2013-10-18	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain J 346–357（12 aa） Fragment：PROLINE-RICH REGION, RESIDUES 346-357	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；3 M NACL, 0.1 M BIS-TRIS PH 5.5	Resolution 1.97 Å R-free 0.215
4CC7 Crystal structure of the sixth or C-terminal SH3 domain of human Tuba in complex with proline-rich peptides of N-WASP. Space group P41 Deposited 2013-10-18	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 346–357（12 aa） Fragment：PROLINE-RICH REGION, RESIDUES 346-357	Not recorded	GOL GLYCEROL × 1 CL CHLORIDE ION × 3 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；3 M NACL, 0.1 M BIS-TRIS PH 5.5	Resolution 1.97 Å R-free 0.215
4CC7 Crystal structure of the sixth or C-terminal SH3 domain of human Tuba in complex with proline-rich peptides of N-WASP. Space group P41 Deposited 2013-10-18	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 7 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain N 346–357（12 aa） Fragment：PROLINE-RICH REGION, RESIDUES 346-357	Not recorded	GOL GLYCEROL × 1 CL CHLORIDE ION × 4 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；3 M NACL, 0.1 M BIS-TRIS PH 5.5	Resolution 1.97 Å R-free 0.215
9DLX Bovine Arp2/3 complex with N-WASP CA bound to Arp3 and Arp2-ArpC1 Deposited 2024-09-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain H 465–505（41 aa） Chain I 465–505（41 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.91 Å
9R3Y Solution NMR structure of N-WASP GBD in complex with EspFu R5 Deposited 2025-05-06	Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 207–275（69 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 0.11；Pressure ambient NMR sample composition 0.5 mM [U-13C; U-15N] N-WASP GBD, 0.6 mM EspFu R5, 20 mM sodium phosphate, 50 mM sodium chloride, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 0.4 mM N-WASP GBD, 0.3 mM [U-13C; U-15N] EspFu R5, 20 mM sodium phosphate, 50 mM sodium chloride, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided

7 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	WASL_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–73； UniProt 207–275

LEE-encoded effector EspF

Escherichia coli

UniProt A0A376PNR8

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 115–161	Not recorded	Actin nucleation-promoting factor WASL × 1 （O00401）	SOLUTION NMR NMR measurement conditions：pH 6.5；298 K；Ionic strength (raw mmCIF value) 0.1；Pressure ambient NMR sample composition：0.5 mM [U-13C; U-15N] N-WASP GBD, 0.6 mM EspF, 20 mM sodium phosphate, 50 mM sodium chloride, 93% H2O/7% D2O \| 93% H2O/7% D2O NMR sample composition：0.7 mM GBD, 0.5 mM [U-13C; U-15N] EspF, 20 mM sodium phosphate, 50 mM sodium chloride, 93% H2O/7% D2O \| 93% H2O/7% 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 9R4V	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9R4W Solution NMR structure of SNX9 SH3 in complex with EspF Deposited 2025-05-08	Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 115–161（47 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 150；Pressure ambient NMR sample composition 1.3 mM [U-13C; U-15N] SNX9 SH3, 1.5 mM EspF, 20 mM sodium phosphate, 50 mM sodium chloride, 93% H2O/7% D2O \| 93% H2O/7% D2O NMR sample composition 1.9 mM SNX9 SH3, 1.5 mM [U-13C; U-15N] EspF, 20 mM sodium phosphate, 50 mM sodium chloride, 93% H2O/7% D2O \| 93% H2O/7% D2O	Resolution not provided

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A376PNR8_ECOLX
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 2–48； UniProt 115–161

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	9r4v
Deposition date deposition_date	2025-05-08
最后修订 last_revision	2025-10-22
Structure title title	Solution structure of N-WASP GBD in complex with EspF
Keywords keywords	complex, CELL INVASION; CELL INVASION
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	19.40 Å
Radius of gyration Rg (electron density) rg_electron	19.68 Å
Forward intensity I(0) i0	1051810000.00
Molecular weight molecular_weight	264000.0 kDa
Excluded volume excluded_volume	326870 Å³
Envelope volume envelope_volume	122150 Å³
Hydration-shell volume shell_volume	33021 Å³
Envelope diameter envelope_diameter	120.6 Å
Shell Rg shell_rg	36.30 Å
Envelope Rg envelope_rg	35.31 Å
Shape Rg shape_rg	19.66 Å
Total Rg total_rg	20.25 Å
Total atoms total_atoms	36740
Residues n_residues	2420
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	52.0 Å
Rg (real space) rg_real	17.07 Å
Rg uncertainty (real space) rg_real_error	0.14 Å
I(0) (real space) i0_real	9.8900e+08
I(0) uncertainty (real space) i0_real_error	9.9670e+06
Rg (reciprocal space) rg_reciprocal	20.15 Å
I(0) (reciprocal space) i0_reciprocal	1052000000.0000
Solution quality estimate total_estimate	0.6603
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	18.3 Å
Skewness Skewness skewness	0.514
Kurtosis Kurtosis kurtosis	-0.066
Angular range angular_range	— – 0.4100 Å⁻¹
Current regularization parameter α current_alpha	1.4660
Highest regularization parameter α highest_alpha	599600.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.034; Oscil: 0.876; Stabil: 0.994; Sysdev: 0.000; Positv: 1.000; Valcen: 0.994; 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)

Entity 1 Entity 1 polymer

Description description	Actin nucleation-promoting factor WASL
Molecular weight formula_weight	8303.2 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	36740

GSHMSNFQHIGHVGWDPNTGFDLNNLDPELKNLFDMCGISEAQLKDRETSKVIYDFIEKTGGVEAVKNELRRQ

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 polymer

Description description	LEE-encoded effector EspF
Molecular weight formula_weight	4915.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GTVNFKPSRPAPPPPTSGQASGASRPLPPIAQALKDHLAAYELSKASE

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

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8. Citations (1)

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fit	/app/data/saxs_computation/r4/9r4v/9r4v.fit
pddf	/app/data/pr_computation/r4/9r4v/9r4v.pr.out
profile	/app/data/saxs_computation/r4/9r4v/9r4v.dat

Solution structure of N-WASP GBD in complex with EspF

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

Actin nucleation-promoting factor WASL

State in the Current Structure

Other States of the Same Protein in the Database

LEE-encoded effector EspF

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)