SAXSdb — 6fu9

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

NBS-LRR class disease resistance protein

Oryza sativa subsp. japonica

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	AVR-Pik protein × 1 （C4B8B8） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	AVR-Pik protein × 1 （C4B8B8） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	B5UBC1_ORYSJ
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–81； UniProt 186–264 Author chain C； PDBConstruct 3–81； UniProt 186–264

AVR-Pik protein

Magnaporthe oryzae

UniProt C4B8B8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	NBS-LRR class disease resistance protein × 1 （B5UBC1） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	NBS-LRR class disease resistance protein × 1 （B5UBC1） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	C4B8B8_MAGOR
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 2–93； UniProt 22–113 Author chain D； PDBConstruct 2–93； UniProt 22–113

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	6fu9
Deposition date deposition_date	2018-02-26
Structure title title	Complex of rice blast (Magnaporthe oryzae) effector protein AVR-PikD with the HMA domain of Pikm-1 from rice (Oryza sativa)
Keywords keywords	Plant NLR, fungal effector, Plant immunity, Complex, ANTIFUNGAL PROTEIN; ANTIFUNGAL 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.

6fu9__assembly_1__model_1

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

Download this curve (.dat)

6fu9__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6fu9__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	16.63 Å
Rg (electron density)	15.44 Å
Total Rg	16.59 Å
Atom count	1272
Residues	163
Excluded volume	22726 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6fu9__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6fu9__assembly_2__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 (3)

Entity 1 Entity 1 polymer

Description description	NBS-LRR class disease resistance protein
Molecular weight formula_weight	8548.0 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	2919

GPGGEMQKIVFKIPMVDDKSRTKAMSLVASTVGVHSVAIAGDLRDQVVVVGDGIDSINLVSALRKKVGPAMFLEVSQVKED

Source Source

Source organism organism	Oryza sativa subsp. japonica
Common name common_name	Rice
NCBI taxonomy ID ncbi_taxonomy_id	39947
Host organism host_organism	Escherichia coli DH1

Entity 2 Entity 2 polymer

Description description	AVR-Pik protein
Molecular weight formula_weight	10827.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

METGNKYIEKRAIDLSRERDPNFFDHPGIPVPECFWFMFKNNVRQDAGTCYSSWKMDMKVGPNWVHIKSDDNCNLSGDFPPGWIVLGKKRPGF

Source Source

Source organism organism	Magnaporthe oryzae
Common name common_name	Rice blast fungus
NCBI taxonomy ID ncbi_taxonomy_id	318829
Host organism host_organism	Escherichia coli DH1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	288

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	6fu9A00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	6fu9C00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	100 —

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Unit-cell length a length_a	37.090 Å
Unit-cell length b length_b	87.130 Å
Unit-cell length c length_c	103.840 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	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.200 Å
Low-resolution limit resolution_low	29.040 Å
R factor r_factor	0.1502
R_work r_work	0.1485
R_free r_free	0.1844

Complex of rice blast (Magnaporthe oryzae) effector protein AVR-PikD with the HMA domain of Pikm-1 from rice (Oryza sativa)

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

NBS-LRR class disease resistance protein

State in the Current Structure

Other States of the Same Protein in the Database

AVR-Pik protein

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

6fu9__assembly_1__model_1

6fu9__assembly_1__model_1 | I(q)

6fu9__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 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Complex of rice blast (Magnaporthe oryzae) effector protein AVR-PikD with the HMA domain of Pikm-1 from rice (Oryza sativa)

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

NBS-LRR class disease resistance protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

AVR-Pik protein

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

6fu9__assembly_1__model_1

6fu9__assembly_1__model_1 | I(q)

6fu9__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 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)