SAXSdb — 2vsz

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

ENGULFMENT AND CELL MOTILITY 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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 532–675 Chain B； UniProt 532–675	Fragment：PLECKSTRIN HOMOLOGY DOMAIN, RESIDUES 532-675	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.75；2.1 M SODIUM MALONATE [PH 6.75]	Resolution 2.30 Å R-free 0.239

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 2VSZ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2RQR The solution structure of human DOCK2 SH3 domain - ELMO1 peptide chimera complex Deposited 2009-10-21	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 697–722（26 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；296 K；Ionic strength (raw mmCIF value) 120；Pressure ambient NMR sample composition 1mM [U-100% 13C; U-100% 15N] protein, 20mM [U-2H] TRIS-2, 100mM sodium chloride-3, 0.02% sodium azide-4, 1mM [U-2H] DTT-5, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
3A98 Crystal structure of the complex of the interacting regions of DOCK2 and ELMO1 Deposited 2009-10-21	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 532–727（196 aa） Fragment：C-terminal domains, PH domain, residues 532-727	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；12% PEG 3350, 0.1M di-ammonium hydrogen citrate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.10 Å R-free 0.268
3A98 Crystal structure of the complex of the interacting regions of DOCK2 and ELMO1 Deposited 2009-10-21	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 532–727（196 aa） Fragment：C-terminal domains, PH domain, residues 532-727	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；12% PEG 3350, 0.1M di-ammonium hydrogen citrate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.10 Å R-free 0.268
6JPP Solution structure of ELMO1 RBD Deposited 2019-03-27	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–113（113 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 100；Pressure ambient NMR sample composition 1 mM [U-100% 13C; U-100% 15N] Elmo1 RBD, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
6TGB CryoEM structure of the binary DOCK2-ELMO1 complex Deposited 2019-11-15	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–727（727 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.50 Å
6TGC CryoEM structure of the ternary DOCK2-ELMO1-RAC1 complex. Deposited 2019-11-15	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 1–727（727 aa） Chain E 1–727（727 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.10 Å
7DPA Cryo-EM structure of the human ELMO1-DOCK5-Rac1 complex Deposited 2020-12-18	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain C 1–727（727 aa） Chain F 1–727（727 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
7Y4A Crystal structure of human ELMO1 RBD-RhoG complex Deposited 2022-06-14	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 1–82（82 aa）	Not recorded	MG MAGNESIUM ION × 1 PO4 PHOSPHATE ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.91 M potassium phosphate dibasic and 0.49 M sodium phosphate monobasic monohydrate	Resolution 1.60 Å R-free 0.235
7Y4A Crystal structure of human ELMO1 RBD-RhoG complex Deposited 2022-06-14	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 1–82（82 aa）	Not recorded	MG MAGNESIUM ION × 1 PO4 PHOSPHATE ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.91 M potassium phosphate dibasic and 0.49 M sodium phosphate monobasic monohydrate	Resolution 1.60 Å R-free 0.235
7Y4A Crystal structure of human ELMO1 RBD-RhoG complex Deposited 2022-06-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 1–82（82 aa）	Not recorded	MG MAGNESIUM ION × 1 PO4 PHOSPHATE ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.91 M potassium phosphate dibasic and 0.49 M sodium phosphate monobasic monohydrate	Resolution 1.60 Å R-free 0.235
7Y4A Crystal structure of human ELMO1 RBD-RhoG complex Deposited 2022-06-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 1–82（82 aa）	Not recorded	MG MAGNESIUM ION × 1 PO4 PHOSPHATE ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.91 M potassium phosphate dibasic and 0.49 M sodium phosphate monobasic monohydrate	Resolution 1.60 Å R-free 0.235
8JHK Cryo-EM structure of the DOCK5/ELMO1 complex, focused on one protomer Deposited 2023-05-23	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–727（727 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.76 Å
8XM7 Cryo-EM structure of the RhoG/DOCK5/ELMO1/Rac1 complex: RhoG/DOCK5/ELMO1 focused map Deposited 2023-12-27	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 × 3 PDB declaration: trimeric	Chain A 1–727（727 aa）	Not recorded	MG MAGNESIUM ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.91 Å
8ZJ2 Cryo-EM structure of the RhoG/DOCK5/ELMO1/Rac1 complex Deposited 2024-05-14	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain A 1–727（727 aa） Chain E 1–727（727 aa）	Not recorded	MG MAGNESIUM ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.66 Å
8ZJI Structure of DOCK5/ELMO1/Rac1 core (RhoG/DOCK5/ELMO1/Rac1 dataset, class 1) Deposited 2024-05-15	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–727（727 aa） Chain D 1–727（727 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.23 Å
8ZJJ Structure of DOCK5/ELMO1/Rac1 core (RhoG/DOCK5/ELMO1/Rac1 dataset, class 2) Deposited 2024-05-15	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–727（727 aa） Chain D 1–727（727 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.23 Å
8ZJK Structure of DOCK5/ELMO1/Rac1 core (RhoG/DOCK5/ELMO1/Rac1 dataset, class 3) Deposited 2024-05-15	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–727（727 aa） Chain D 1–727（727 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.23 Å
8ZJL Structure of DOCK5/ELMO1/Rac1 core (RhoG/DOCK5/ELMO1/Rac1 dataset, class 4) Deposited 2024-05-15	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–727（727 aa） Chain D 1–727（727 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.31 Å
8ZJM Structure of DOCK5/ELMO1/Rac1 core (RhoG/DOCK5/ELMO1/Rac1 dataset, class 5) Deposited 2024-05-15	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–727（727 aa） Chain D 1–727（727 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.52 Å
9LX0 DOCK5/ELMO1 complex with RhoG and Rac1 on lipid membrane Deposited 2025-02-17	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–727（727 aa） Chain E 1–727（727 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.98 Å
9LXH DOCK5/ELMO1 complex with RhoG and Rac1 on lipid membrane Deposited 2025-02-18	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–727（727 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.52 Å

17 other PDB entries and 21 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ELMO1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–149； UniProt 532–675 Author chain B； PDBConstruct 6–149； UniProt 532–675

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	2vsz
Deposition date deposition_date	2008-05-01
Structure title title	Crystal Structure of the ELMO1 PH domain
Keywords keywords	APOPTOSIS, RAC SIGNALLING, SH3-BINDING, PHAGOCYTOSIS, ELMO, DOCK180, PHOSPHOINOSITIDE BINDING, GUANINE NUCLEOTIDE EXCHANGE FACTOR; APOPTOSIS
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	29.70 Å
Radius of gyration Rg (electron density) rg_electron	29.05 Å
Forward intensity I(0) i0	17094700.00
Molecular weight molecular_weight	32450.0 kDa
Excluded volume excluded_volume	40942 Å³
Envelope volume envelope_volume	55522 Å³
Hydration-shell volume shell_volume	17125 Å³
Envelope diameter envelope_diameter	107.5 Å
Shell Rg shell_rg	33.69 Å
Envelope Rg envelope_rg	29.00 Å
Shape Rg shape_rg	29.06 Å
Total Rg total_rg	29.58 Å
Total atoms total_atoms	2284
Residues n_residues	289
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	103.2 Å
Rg (real space) rg_real	30.09 Å
Rg uncertainty (real space) rg_real_error	1.22 Å
I(0) (real space) i0_real	1.7090e+07
I(0) uncertainty (real space) i0_real_error	2.6060e+05
Rg (reciprocal space) rg_reciprocal	29.93 Å
I(0) (reciprocal space) i0_reciprocal	17090000.0000
Solution quality estimate total_estimate	0.6757
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.4 Å
Skewness Skewness skewness	0.445
Kurtosis Kurtosis kurtosis	-0.801
Angular range angular_range	— – 0.2650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3057000.0000
Real-space data points n_real_points	54
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.212; Stabil: 0.995; Sysdev: 1.000; Positv: 1.000; Valcen: 0.186; Smooth: 0.974

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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	2vszA01
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	810 —

Domain ID domain_id	2vszA02
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	2vszB01
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	810 —

Domain ID domain_id	2vszB02
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	166.016 Å
Unit-cell length b length_b	166.016 Å
Unit-cell length c length_c	81.704 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	24

Space group space_group	P 61 2 2
Space-group number int_tables_number	178
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	144.340 Å
R factor r_factor	0.2090
R_work r_work	0.2080
R_free r_free	0.2390

Description description	ENGULFMENT AND CELL MOTILITY PROTEIN 1
Molecular weight formula_weight	17102.8 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	2523

Crystal Structure of the ELMO1 PH domain

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

ENGULFMENT AND CELL MOTILITY 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

Diffraction experiment Diffraction

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	159

fit	/app/data/saxs_computation/vs/2vsz/2vsz.fit
pddf	/app/data/pr_computation/vs/2vsz/2vsz.pr.out
profile	/app/data/saxs_computation/vs/2vsz/2vsz.dat