SAXSdb — 1nvv

▼

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

Transforming protein p21/H-RAS-1

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Son of sevenless protein homolog 1 × 1 （Q07889） MAGNESIUM ION × 1 PHOSPHATE ION × 5 PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 24	Son of sevenless protein homolog 1 × 8 （Q07889） MAGNESIUM ION × 8 PHOSPHATE ION × 40 PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 8 water × 24	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 12	Son of sevenless protein homolog 1 × 4 （Q07889） MAGNESIUM ION × 4 PHOSPHATE ION × 20 PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 4 water × 12	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 6	Son of sevenless protein homolog 1 × 2 （Q07889） MAGNESIUM ION × 2 PHOSPHATE ION × 10 PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RASH_HUMAN
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain Q； PDBConstruct 1–166； UniProt 1–166 Author chain R； PDBConstruct 1–166； UniProt 1–166

Son of sevenless protein homolog 1

Homo sapiens

UniProt Q07889

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Transforming protein p21/H-RAS-1 × 1 （P01112） Transforming protein p21/H-RAS-1 × 1 （P01112） MAGNESIUM ION × 1 PHOSPHATE ION × 5 PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 24	Transforming protein p21/H-RAS-1 × 8 （P01112） Transforming protein p21/H-RAS-1 × 8 （P01112） MAGNESIUM ION × 8 PHOSPHATE ION × 40 PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 8 water × 24	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 12	Transforming protein p21/H-RAS-1 × 4 （P01112） Transforming protein p21/H-RAS-1 × 4 （P01112） MAGNESIUM ION × 4 PHOSPHATE ION × 20 PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 4 water × 12	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 6	Transforming protein p21/H-RAS-1 × 2 （P01112） Transforming protein p21/H-RAS-1 × 2 （P01112） MAGNESIUM ION × 2 PHOSPHATE ION × 10 PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SOS1_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain S； PDBConstruct 1–481； UniProt 566–1046

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1nvv
Deposition date deposition_date	2003-02-04
Structure title title	Structural evidence for feedback activation by RasGTP of the Ras-specific nucleotide exchange factor SOS
Keywords keywords	Proto-oncogene, GTP-binding, Guanine-nucleotide releasing factor, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

▼

3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

1nvv__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1nvv__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1nvv__assembly_2__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	64.22 Å
Rg (electron density)	63.59 Å
Total Rg	63.64 Å
Atom count	52744
Residues	6408
Excluded volume	935630 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1nvv__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1nvv__assembly_2__model_1`	24-meric （24）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1nvv__assembly_3__model_1`	dodecameric （12）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1nvv__assembly_4__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Transforming protein p21/H-RAS-1
Molecular weight formula_weight	18783.1 kDa
Mutation mutation	Y64A
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Q
Atom count atom_count	6908

MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEASAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCDLAARTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREIRQH

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Transforming protein p21/H-RAS-1
Molecular weight formula_weight	18875.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	R

MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCDLAARTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREIRQH

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 polymer

Description description	Son of sevenless protein homolog 1
Molecular weight formula_weight	56532.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	S

QMRLPSADVYRFAEPDSEENIIFEENMQPKAGIPIIKAGTVIKLIERLTYHMYADPNFVRTFLTTYRSFCKPQELLSLIIERFEIPEPEPTEADRIAIENGDQPLSAELKRFRKEYIQPVQLRVLNVCRHWVEHHFYDFERDAYLLQRMEEFIGTVRGKAMKKWVESITKIIQRKKIARDNGPGHNITFQSSPPTVEWHISRPGHIETFDLLTLHPIEIARQLTLLESDLYRAVQPSELVGSVWTKEDKEINSPNLLKMIRHTTNLTLWFEKCIVETENLEERVAVVSRIIEILQVFQELNNFNGVLEVVSAMNSSPVYRLDHTFEQIPSRQKKILEEAHELSEDHYKKYLAKLRSINPPCVPFFGIYLTNILKTEEGNPEVLKRHGKELINFSKRRKVAEITGEIQQYQNQPYCLRVESDIKRFFENLNPMGNSMEKEFTDYLFNKSLEIEPRNPKPLPRFPKKYSYPLKSPGVRPSNPR

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 6 Entity 6 non-polymer

Description description	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
Molecular weight formula_weight	522.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	315

▼

6. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1nvvq_
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	d1nvvr_
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	d1nvvs_
Class class	a — All alpha proteins
Fold Fold fold	a.117 — Ras GEF
Superfamily Superfamily superfamily	a.117.1 — Ras GEF
Family Family family	a.117.1.1 — Ras GEF

CATH v4.4 (4 domains)

Domain ID domain_id	1nvvQ00
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	1nvvR00
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	1nvvS01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	870 — Son of sevenless (SoS) protein; Chain S, domain 1
Homologous superfamily homologous superfamily	10 — Son of sevenless (SoS) protein Chain: S domain 1

Domain ID domain_id	1nvvS02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	840 — Son of Sevenless (SoS) protein; Chain S, domain 2
Homologous superfamily homologous superfamily	10 — Ras guanine-nucleotide exchange factors catalytic domain

▶

Unit-cell length a length_a	184.163 Å
Unit-cell length b length_b	184.163 Å
Unit-cell length c length_c	179.076 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	16

Space group space_group	I 4 2 2
Space-group number int_tables_number	97
Crystal system crystal_system	—

Resolution resolution	2.180 Å
Low-resolution limit resolution_low	64.190 Å
R factor r_factor	0.2080
R_work r_work	0.2080
R_free r_free	0.2410

Structural evidence for feedback activation by RasGTP of the Ras-specific nucleotide exchange factor SOS

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

Transforming protein p21/H-RAS-1

State in the Current Structure

Other States of the Same Protein in the Database

Son of sevenless protein homolog 1

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1nvv__assembly_2__model_1

1nvv__assembly_2__model_1 | I(q)

1nvv__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Structural evidence for feedback activation by RasGTP of the Ras-specific nucleotide exchange factor SOS

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

Transforming protein p21/H-RAS-1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Son of sevenless protein homolog 1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1nvv__assembly_2__model_1

1nvv__assembly_2__model_1 | I(q)

1nvv__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

CATH v4.4 (4 domains)

7. Citations (1)