SAXSdb — 7nzc

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

E3 ubiquitin-protein ligase SH3RF1

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 AAA； UniProt 135–194	Not recorded	EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 8；293 K；0.2 M NaF, 22% PEG 3350	Resolution 1.11 Å R-free 0.177

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 7NZC	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7NZD Fourth SH3 domain of POSH (Plenty of SH3 Domains protein) Deposited 2021-03-23	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain AAA 829–888（60 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 1 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；0.1M MES pH 6.5, 23% PEG 4000	Resolution 1.45 Å R-free 0.228
9RFB Crystal Structure of Human Rac1 in Complex with the Scaffold Protein POSH (residues 321-348) Deposited 2025-06-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 321–348（28 aa）	Not recorded	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；0.05 M phosphate, 20% (w/v) PEG 8000. RAC1 6 mg/mL , GMPPNP 1mM, POSH 3 mM	Resolution 1.85 Å R-free 0.226
9RFB Crystal Structure of Human Rac1 in Complex with the Scaffold Protein POSH (residues 321-348) Deposited 2025-06-04	Different construct 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 321–348（28 aa）	Not recorded	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 PO4 PHOSPHATE ION × 2 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；0.05 M phosphate, 20% (w/v) PEG 8000. RAC1 6 mg/mL , GMPPNP 1mM, POSH 3 mM	Resolution 1.85 Å R-free 0.226
9RFF Crystal Structure of Human Rac1 Fused with the Scaffold Protein POSH (residues 319-371) Deposited 2025-06-04	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 319–371（53 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.12 M ethylene glycol, 0.1 M imidazole-MES pH 6.5, 37% (v/v) 2-methyl-2,4-pentanediol (MPD)-PEG 1000-PEG 3500 2 mg/mL Rac1-POSH	Resolution 1.25 Å R-free 0.164

3 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SH3R1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain AAA； PDBConstruct 4–63； UniProt 135–194

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	7nzc
Deposition date deposition_date	2021-03-23
Structure title title	First SH3 domain of POSH (Plenty of SH3 Domains protein)
Keywords keywords	MAP-kinase scaffold activity ubiquitin protein ligase activity, SIGNALING PROTEIN; SIGNALING PROTEIN
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	12.55 Å
Radius of gyration Rg (electron density) rg_electron	11.11 Å
Forward intensity I(0) i0	1161550.00
Molecular weight molecular_weight	7314.0 kDa
Excluded volume excluded_volume	9252 Å³
Envelope volume envelope_volume	10176 Å³
Hydration-shell volume shell_volume	8093 Å³
Envelope diameter envelope_diameter	42.9 Å
Shell Rg shell_rg	16.41 Å
Envelope Rg envelope_rg	11.66 Å
Shape Rg shape_rg	11.02 Å
Total Rg total_rg	12.80 Å
Total atoms total_atoms	517
Residues n_residues	61
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	44.7 Å
Rg (real space) rg_real	12.50 Å
Rg uncertainty (real space) rg_real_error	0.26 Å
I(0) (real space) i0_real	1.1620e+06
I(0) uncertainty (real space) i0_real_error	1.1710e+04
Rg (reciprocal space) rg_reciprocal	12.50 Å
I(0) (reciprocal space) i0_reciprocal	1162000.0000
Solution quality estimate total_estimate	0.8374
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	16.4 Å
Skewness Skewness skewness	0.220
Kurtosis Kurtosis kurtosis	-0.096
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	224900.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.635; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.988

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	E3 ubiquitin-protein ligase SH3RF1
Molecular weight formula_weight	7299.4 kDa
EC 编号 ec_number	2.3.2.27
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	AAA
Atom count atom_count	684

GRRQLPCAKALYNYEGKEPGDLKFSKGDIIILRRQVDENWYHGEVNGIHGFFPTNFVQIIKPL

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 BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
Molecular weight formula_weight	238.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	138

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8. Citations (1)

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Unit-cell length a length_a	35.962 Å
Unit-cell length b length_b	35.962 Å
Unit-cell length c length_c	181.333 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 65 2 2
Space-group number int_tables_number	179
Crystal system crystal_system	—

Resolution resolution	1.111 Å
Low-resolution limit resolution_low	30.694 Å
R factor r_factor	—
R_work r_work	0.1468
R_free r_free	0.1775

fit	/app/data/saxs_computation/nz/7nzc/7nzc.fit
pddf	/app/data/pr_computation/nz/7nzc/7nzc.pr.out
profile	/app/data/saxs_computation/nz/7nzc/7nzc.dat

First SH3 domain of POSH (Plenty of SH3 Domains protein)

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

E3 ubiquitin-protein ligase SH3RF1

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