SAXSdb — 8bv0

▼

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

NRC1

Solanum lycopersicum

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Truncated secreted SPRY domain-containing protein 15 (Fragment) × 1 （A0A024E1S8） ADENOSINE-5'-DIPHOSPHATE × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Truncated secreted SPRY domain-containing protein 15 (Fragment) × 1 （A0A024E1S8） ADENOSINE-5'-DIPHOSPHATE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A1X877_SOLLC
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–347； UniProt 150–494 Author chain C； PDBConstruct 3–347； UniProt 150–494

Truncated secreted SPRY domain-containing protein 15 (Fragment)

Globodera rostochiensis

UniProt A0A024E1S8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	NRC1 × 1 （A1X877） ADENOSINE-5'-DIPHOSPHATE × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	NRC1 × 1 （A1X877） ADENOSINE-5'-DIPHOSPHATE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A024E1S8_GLORO
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 3–224； UniProt 1–222 Author chain D； PDBConstruct 3–224； UniProt 1–222

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	8bv0
Deposition date deposition_date	2022-12-01
Structure title title	Binary complex between the NB-ARC domain from the Tomato immune receptor NRC1 and the SPRY domain-containing effector SS15 from the potato cyst nematode
Keywords keywords	NLR, inhibitor, effector, SPRYSEC, nematode, PROTEIN BINDING; PROTEIN BINDING
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.

8bv0__assembly_1__model_1

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

Download this curve (.dat)

8bv0__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8bv0__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.92 Å
Rg (electron density)	26.33 Å
Total Rg	27.07 Å
Atom count	4425
Residues	548
Excluded volume	78626 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8bv0__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`8bv0__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	NRC1
Molecular weight formula_weight	40151.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	8850

GPPVVEEDDVVGFDDEAQTVIDRLLEGSGDLEVIPVVGMPGLGKTTLATKIFKHPKIEYEFFTRLWLYVSQSYKTRELYLNIISKFTGNTKHCRDMSEKDLALKVQEILEEGGKYLIVLDDVWSTDAWDRIKIAFPKNDKGNRVLLTTRDHRVARYCNRSPHDLKFLTDEESWILLEKRAFHKAKCLPELETNGKSIARKCKGLPLAIVVIAGALIGKSKTIKEWEQVDQSVGEHFINRDQPNSCDKLVRMSYDVLPYDWKACFLYFGTFPRGYLIPARKLIRLWIAEGFIQYRGDLSPECKAEEYLNELVNRNLVMVMQRTVDGQIKTCRVHDMLYEFCWQEATTE

Source Source

Source organism organism	Solanum lycopersicum
Common name common_name	tomato
NCBI taxonomy ID ncbi_taxonomy_id	4081
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Truncated secreted SPRY domain-containing protein 15 (Fragment)
Molecular weight formula_weight	24511.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

GPSPKANAKLEKVPSGNAESTPVLTLQNRWAYSARDEKLAWDSAARDEKLELTEPAGLIVQFIGENSKHRSVRAKLPIPKGNSGIFYYEVTISGDGDAIYIGLATEQMPLRDTHVGYNEGTYGYGSSGKFWGHEVGGCSHWGNERPYIDGQPKFDRNNIIGCGVNLKTRQIIYTHNGRPLETTGLLVAESAAELYPCVSLFTSGNEIEANFGTKPFKFNIAEGI

Source Source

Source organism organism	Globodera rostochiensis
NCBI taxonomy ID ncbi_taxonomy_id	31243
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	2

▶

Unit-cell length a length_a	128.560 Å
Unit-cell length b length_b	128.560 Å
Unit-cell length c length_c	170.680 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 61
Space-group number int_tables_number	169
Crystal system crystal_system	—

Resolution resolution	4.500 Å
Low-resolution limit resolution_low	51.340 Å
R factor r_factor	0.2409
R_work r_work	0.2374
R_free r_free	0.2751

Binary complex between the NB-ARC domain from the Tomato immune receptor NRC1 and the SPRY domain-containing effector SS15 from the potato cyst nematode

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

NRC1

State in the Current Structure

Other States of the Same Protein in the Database

Truncated secreted SPRY domain-containing protein 15 (Fragment)

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

8bv0__assembly_1__model_1

8bv0__assembly_1__model_1 | I(q)

8bv0__assembly_1__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

7. Citations (1)

Binary complex between the NB-ARC domain from the Tomato immune receptor NRC1 and the SPRY domain-containing effector SS15 from the potato cyst nematode

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

NRC1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Truncated secreted SPRY domain-containing protein 15 (Fragment)

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

8bv0__assembly_1__model_1

8bv0__assembly_1__model_1 | I(q)

8bv0__assembly_1__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

7. Citations (1)