6fg8

Crystal structure of the BIR3 - SERK1 complex from Arabidopsis thaliana.

Method: X-RAY DIFFRACTION

▼

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

Somatic embryogenesis receptor kinase 1

Arabidopsis thaliana

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 2 其他Polymer 6	Probable inactive receptor kinase At1g27190 × 1 （O04567） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 4 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose × 1 DI(HYDROXYETHYL)ETHER × 4 PENTAETHYLENE GLYCOL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SERK1_ARATH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 24–208； UniProt 24–208

Probable inactive receptor kinase At1g27190

Arabidopsis thaliana

UniProt O04567

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 2 其他Polymer 6	Somatic embryogenesis receptor kinase 1 × 1 （Q94AG2） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 4 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose × 1 DI(HYDROXYETHYL)ETHER × 4 PENTAETHYLENE GLYCOL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Y1719_ARATH
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–214； UniProt 1–214

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	6fg8
Deposition date deposition_date	2018-01-10
Structure title title	Crystal structure of the BIR3 - SERK1 complex from Arabidopsis thaliana.
Keywords keywords	leucine rich repeat receptor, membrane receptor, pseudokinase, ectodomain, receptor complex, negative regulator, 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.

6fg8__assembly_1__model_1

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

Download this curve (.dat)

6fg8__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6fg8__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.65 Å
Rg (electron density)	23.58 Å
Total Rg	24.37 Å
Atom count	3071
Residues	377
Excluded volume	54807 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6fg8__assembly_1__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 (8)

Entity 1 Entity 1 polymer

Description description	Somatic embryogenesis receptor kinase 1
Molecular weight formula_weight	28410.8 kDa
EC 编号 ec_number	2.7.10.1,2.7.11.1
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	3628

MTRLTVLALLAGLLASSRAGSSMASANLEGDALHTLRVTLVDPNNVLQSWDPTLVNPCTWFHVTCNNENSVIRVDLGNAELSGHLVPELGVLKNLQYLELYSNNITGPIPSNLGNLTNLVSLDLYLNSFSGPIPESLGKLSKLRFLRLNNNSLTGSIPMSLTNITTLQVLDLSNNRLSGSVPDNGSFSLFTPISFANNLDLCGPVTSHPCPGSLEGSENLYFQGSAWSHPQFEKGGGSGGGSGGSAWSHPQFEKGAHHHHHHHHH

Source Source

Source organism organism	Arabidopsis thaliana
Common name common_name	Mouse-ear cress
NCBI taxonomy ID ncbi_taxonomy_id	3702
Host organism host_organism	Trichoplusia ni

Entity 2 Entity 2 polymer

Description description	Probable inactive receptor kinase At1g27190
Molecular weight formula_weight	26406.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MKKIFITLLWLLFISSFLCSSSSAEDDVLCLQGLKNSLIDPSSRLSSWSFPNSSASSICKLTGVSCWNEKENRIISLQLQSMQLAGEIPESLKLCRSLQSLDLSGNDLSGSIPSQICSWLPYLVTLDLSGNKLGGSIPTQIVECKFLNALILSDNKLSGSIPSQLSRLDRLRRLSLAGNDLSGTIPSELARFGGDDFSGNNGLCGKPLSRCGALENLYFQGAWSHPQFEKGSHHHHHHHHH

Source Source

Source organism organism	Arabidopsis thaliana
Common name common_name	Mouse-ear cress
NCBI taxonomy ID ncbi_taxonomy_id	3702
Host organism host_organism	Trichoplusia ni

Entity 3 Entity 3 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	4

Entity 4 Entity 4 branched

Description description	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	586.5 kDa
Source method src_method	man
Copy count entity_count	1

Entity 5 Entity 5 branched

Description description	alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	570.5 kDa
Source method src_method	man
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 7 Entity 7 non-polymer

Description description	PENTAETHYLENE GLYCOL
Molecular weight formula_weight	238.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	433

▼

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	6fg8A00
Class class	3 — Alpha Beta
Architecture architecture	80 — Alpha-Beta Horseshoe
Topology topology	10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
Homologous superfamily homologous superfamily	10 — Ribonuclease Inhibitor

▶

Unit-cell length a length_a	52.173 Å
Unit-cell length b length_b	50.757 Å
Unit-cell length c length_c	77.425 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	96.72 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.250 Å
Low-resolution limit resolution_low	40.810 Å
R factor r_factor	0.1531
R_work r_work	0.1515
R_free r_free	0.1839

Crystal structure of the BIR3 - SERK1 complex from Arabidopsis thaliana.

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

Somatic embryogenesis receptor kinase 1

State in the Current Structure

Other States of the Same Protein in the Database

Probable inactive receptor kinase At1g27190

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

6fg8__assembly_1__model_1

6fg8__assembly_1__model_1 | I(q)

6fg8__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 branched

Entity 4 Entity 4 branched

Entity 5 Entity 5 branched

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)

Crystal structure of the BIR3 - SERK1 complex from Arabidopsis thaliana.

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

Somatic embryogenesis receptor kinase 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

Probable inactive receptor kinase At1g27190

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

6fg8__assembly_1__model_1

6fg8__assembly_1__model_1 | I(q)

6fg8__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 branched

Entity 4 Entity 4 branched

Entity 5 Entity 5 branched

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)