SAXSdb — 3su8

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

Ras-related C3 botulinum toxin substrate 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 2	Plexin-B1 × 1 （O43157） MAGNESIUM ION × 1 PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RAC1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–177； UniProt 1–177

Plexin-B1

Homo sapiens

UniProt O43157

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Ras-related C3 botulinum toxin substrate 1 × 1 （P63000） MAGNESIUM ION × 1 PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PLXB1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain X； PDBConstruct 9–611； UniProt 1533–2135

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	3su8
Deposition date deposition_date	2011-07-11
Structure title title	Crystal structure of a truncated intracellular domain of Plexin-B1 in complex with Rac1
Keywords keywords	Axon guidance, signal transduction, APOPTOSIS-SIGNALING PROTEIN complex; APOPTOSIS/SIGNALING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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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.

3su8__assembly_1__model_1

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

Download this curve (.dat)

3su8__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3su8__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	36.58 Å
Rg (electron density)	36.52 Å
Total Rg	36.90 Å
Atom count	5762
Residues	717
Excluded volume	103220 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3su8__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Ras-related C3 botulinum toxin substrate 1
Molecular weight formula_weight	20668.8 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	5762

MQAIKCVVVGDGAVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPVNLGLWDTAGQEDYDRLRPLSYPQTDVFLICFSLVSPASFENVRAKWYPEVRHHCPNTPIILVGTKLDLRDDKDTIEKLKEKKLTPITYPQGLAMAKEIGAVKYLECSALTQRGLKTVFDEAIRAVLKHHHHHH

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

Entity 2 Entity 2 polymer

Description description	Plexin-B1
Molecular weight formula_weight	69860.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	X

MGHHHHHHESSVRDRCKKEFTDLMTEMTDLTSDLLGSGIPFLDYKVYAERIFFPGHRESPLHRDLGVPESRRPTVEQGLGQLSNLLNSKLFLTKFIHTLETQRTFSARDRAYVASLLTVALHGKLEYFTDILRTLLSDLVAQYVAKNPKLMLRRTETVVEKLLTNWMSICLYTFVRDSVGEPLYMLFRGIKHQVDKGPVDSVTGKAKYTLNDNRLLREDVEYRPLTLNALLAVGPGAGEAQGVPVKVLDCDTISQAKEKMLDQLYKGVPLTQRPDPRTLDVEWRSGVAGHLILSDEDVTSEVQGLWRRLNTLQHYKVPDGATVALVPCLTKHVLRENQDYVPGERTPMLEDVDEGGIRPWHLVKPSDEPEPPRPRRGSLRGGERERAKAIPEIYLTRLLSMKGTLQKFVDDLFQVILSTSRPVPLAVKYFFDLLDEQAQQHGISDQDTIHIWKTNSLPLRFWINIIKNPQFVFDVQTSDNMDAVLLVIAQTFMDACTLADHKLGRDSPINKLLYARDIPRYKRMVERYYADIRQTVPASDQEMNSVLAELSWNYSGDLGARVALHELYKYINKYYDQIITALEEDGTAQKMQLGYRLQQIAAAVENKVTDL

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Spodoptera frugiperda

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	1

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	1

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6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	3su8A00
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	3su8X01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	506 — GTPase Activation - p120GAP; domain 1
Homologous superfamily homologous superfamily	10 — GTPase Activation - p120gap; domain 1

Domain ID domain_id	3su8X02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

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Unit-cell length a length_a	183.450 Å
Unit-cell length b length_b	63.810 Å
Unit-cell length c length_c	84.550 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	107.53 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	3.200 Å
Low-resolution limit resolution_low	45.890 Å
R factor r_factor	0.2082
R_work r_work	0.2066
R_free r_free	0.2377

Crystal structure of a truncated intracellular domain of Plexin-B1 in complex with Rac1

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

Ras-related C3 botulinum toxin substrate 1

State in the Current Structure

Other States of the Same Protein in the Database

Plexin-B1

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

3su8__assembly_1__model_1

3su8__assembly_1__model_1 | I(q)

3su8__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)

Crystal structure of a truncated intracellular domain of Plexin-B1 in complex with Rac1

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

Ras-related C3 botulinum toxin substrate 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

Plexin-B1

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

3su8__assembly_1__model_1

3su8__assembly_1__model_1 | I(q)

3su8__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)