SAXSdb — 2gco

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

Rho-related GTP-binding protein RhoC

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 A； UniProt 1–181	Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.4；291.15 K；30% PEG 8000, 0.2M Sodium Acetate,1.2% Inositol, 0.1M Sodium Cacodylate, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K	Resolution 1.40 Å R-free 0.219
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–181	Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.4；291.15 K；30% PEG 8000, 0.2M Sodium Acetate,1.2% Inositol, 0.1M Sodium Cacodylate, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K	Resolution 1.40 Å R-free 0.219

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 2GCO	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1Z2C Crystal structure of mDIA1 GBD-FH3 in complex with RhoC-GMPPNP Deposited 2005-03-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–193（193 aa）	Mutation：F25N	MG MAGNESIUM ION × 4 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；293 K；PEG 2000-MME, magnesium sulphate, Tris buffer, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.00 Å R-free 0.285
1Z2C Crystal structure of mDIA1 GBD-FH3 in complex with RhoC-GMPPNP Deposited 2005-03-08	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 C 1–193（193 aa）	Mutation：F25N	MG MAGNESIUM ION × 2 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；293 K；PEG 2000-MME, magnesium sulphate, Tris buffer, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.00 Å R-free 0.285
2GCN Crystal structure of the human RhoC-GDP complex Deposited 2006-03-14	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–181（181 aa）	Not recorded	MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 EDO 1,2-ETHANEDIOL × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291.15 K；20% PEG 3350, 0.1M Bis Tris, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K	Resolution 1.85 Å R-free 0.225
2GCP Crystal structure of the human RhoC-GSP complex Deposited 2006-03-14	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–181（181 aa）	Not recorded	MG MAGNESIUM ION × 3 GSP 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE × 1 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.8；291.15 K；3M Sodium Chloride, 0.1M Sodium Acetate, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K	Resolution 2.15 Å R-free 0.226

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

View Construct and Data Evidence

UniProt name	RHOC_HUMAN
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 21–201； UniProt 1–181 Author chain B； PDBConstruct 21–201； UniProt 1–181

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	2gco
Deposition date deposition_date	2006-03-14
Structure title title	Crystal structure of the human RhoC-GppNHp complex
Keywords keywords	GTP-binding protein, GTPase, 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	25.03 Å
Radius of gyration Rg (electron density) rg_electron	24.04 Å
Forward intensity I(0) i0	33292100.00
Molecular weight molecular_weight	42891.0 kDa
Excluded volume excluded_volume	53066 Å³
Envelope volume envelope_volume	65100 Å³
Hydration-shell volume shell_volume	23146 Å³
Envelope diameter envelope_diameter	86.5 Å
Shell Rg shell_rg	30.41 Å
Envelope Rg envelope_rg	24.36 Å
Shape Rg shape_rg	24.03 Å
Total Rg total_rg	24.79 Å
Total atoms total_atoms	3001
Residues n_residues	369
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	83.9 Å
Rg (real space) rg_real	25.10 Å
Rg uncertainty (real space) rg_real_error	0.72 Å
I(0) (real space) i0_real	3.3290e+07
I(0) uncertainty (real space) i0_real_error	4.8230e+05
Rg (reciprocal space) rg_reciprocal	25.08 Å
I(0) (reciprocal space) i0_reciprocal	33290000.0000
Solution quality estimate total_estimate	0.8669
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.0 Å
Skewness Skewness skewness	0.371
Kurtosis Kurtosis kurtosis	-0.536
Angular range angular_range	— – 0.3150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8699000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.811; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.837; Smooth: 0.998

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Rho-related GTP-binding protein RhoC
Molecular weight formula_weight	22740.9 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	3573

MGSSHHHHHHSSGLVPRGSHMAAIRKKLVIVGDGACGKTCLLIVFSKDQFPEVYVPTVFENYIADIEVDGKQVELALWDTAGQEDYDRLRPLSYPDTDVILMCFSIDSPDSLENIPEKWTPEVKHFCPNVPIILVGNKKDLRQDEHTRRELAKMKQEPVRSEEGRDMANRISAFGYLECSAKTKEGVREVFEMATRAGLQV

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	Rho-related GTP-binding protein RhoC
Molecular weight formula_weight	22724.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MGSSHHHHHHSSGLVPRGSHMAAIRKKLVIVGDGACGKTCLLIVFSKDQFPEVYVPTVFENYIADIEVDGKQVELALWDTAGQEDYDRLRPLSYPDTDVILMCFSIDSPDSLENIPEKWTPEVKHFCPNVPIILVGNKKDLRQDEHTRRELAKMKQEPVRSEEGRDMANRISAFGYLECSAKTKEGVREVFEMATRAGLQV

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 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
Molecular weight formula_weight	522.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	502

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2gcoa1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.8 — G proteins

Domain ID domain_id	d2gcoa2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2gcob1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.8 — G proteins

Domain ID domain_id	d2gcob2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id	2gcoA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	2gcoB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

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8. Citations (1)

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Unit-cell length a length_a	64.092 Å
Unit-cell length b length_b	75.645 Å
Unit-cell length c length_c	82.903 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 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	1.400 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.1980
R_work r_work	0.1970
R_free r_free	0.2190

fit	/app/data/saxs_computation/gc/2gco/2gco.fit
pddf	/app/data/pr_computation/gc/2gco/2gco.pr.out
profile	/app/data/saxs_computation/gc/2gco/2gco.dat

Crystal structure of the human RhoC-GppNHp complex

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

Rho-related GTP-binding protein RhoC

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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)