SAXSdb — 7yjo

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

atLCB1

Arabidopsis thaliana

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Long chain base biosynthesis protein 2a × 1 （Q9LSZ9） ORMDL family protein × 1 （Q9C5I0） Transmembrane protein, putative (DUF3317) × 1 （A8MSB8） [3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-SERINE × 1 N-[(2S,3R,4E)-1,3-dihydroxyoctadec-4-en-2-yl]tetracosanamide × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LCB1_ARATH
Isoform	—
PDB entities	1, 4
Chains and sequence ranges	Author chain A； PDBConstruct 1–420； UniProt 63–482 Author chain E； PDBConstruct 1–62； UniProt 1–62

Long chain base biosynthesis protein 2a

Arabidopsis thaliana

UniProt Q9LSZ9

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	atLCB1 × 1 （Q94IB8） ORMDL family protein × 1 （Q9C5I0） atLCB1 × 1 （Q94IB8） Transmembrane protein, putative (DUF3317) × 1 （A8MSB8） [3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-SERINE × 1 N-[(2S,3R,4E)-1,3-dihydroxyoctadec-4-en-2-yl]tetracosanamide × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LCB2A_ARATH
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 2–485； UniProt 6–489

ORMDL family protein

Arabidopsis thaliana

UniProt Q9C5I0

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	atLCB1 × 1 （Q94IB8） Long chain base biosynthesis protein 2a × 1 （Q9LSZ9） atLCB1 × 1 （Q94IB8） Transmembrane protein, putative (DUF3317) × 1 （A8MSB8） [3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-SERINE × 1 N-[(2S,3R,4E)-1,3-dihydroxyoctadec-4-en-2-yl]tetracosanamide × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9C5I0_ARATH
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain D； PDBConstruct 1–157； UniProt 1–157

Transmembrane protein, putative (DUF3317)

Arabidopsis thaliana

UniProt A8MSB8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	atLCB1 × 1 （Q94IB8） Long chain base biosynthesis protein 2a × 1 （Q9LSZ9） ORMDL family protein × 1 （Q9C5I0） atLCB1 × 1 （Q94IB8） [3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-SERINE × 1 N-[(2S,3R,4E)-1,3-dihydroxyoctadec-4-en-2-yl]tetracosanamide × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A8MSB8_ARATH
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain C； PDBConstruct 22–77； UniProt 1–56

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	7yjo
Deposition date deposition_date	2022-07-20
Structure title title	Cryo-EM structure of the monomeric atSPT-ORM1 (LCB2a-deltaN5) complex
Keywords keywords	ceramide, TRANSFERASE-INHIBITOR COMPLEX; TRANSFERASE/INHIBITOR
Experimental Method method	ELECTRON MICROSCOPY

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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.

7yjo__assembly_1__model_1

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

Download this curve (.dat)

7yjo__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7yjo__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.47 Å
Rg (electron density)	32.04 Å
Total Rg	32.67 Å
Atom count	8769
Residues	1106
Excluded volume	157770 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7yjo__assembly_1__model_1`	pentameric （5）	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 (7)

Entity 1 Entity 1 polymer

Description description	atLCB1
Molecular weight formula_weight	46276.1 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	8769

PLTEQEIDELCDEWVPEPLIPPITEDMKHEPPVLESAAGPHTTVNGKDVVNFASANYLGLIGHEKLLESCTSALEKYGVGSCGPRGFYGTIDVHLDCETRISKFLGTPDSILYSYGLSTMFSTIPCFCKKGDVIVADEGVHWGIQNGLQLSRSTIVYFKHNDMESLRITLEKIMTKYKRSKNLRRYIVAEAVYQNSGQIAPLDEIVKLKEKYRFRVILDESNSFGVLGRSGRGLAEHHSVPIEKIDVVTAAMGHALATEGGFCTGNARIIDYQRLSSSGYVFSASLPPYLASAAITAIDVIDQNPDMLVKLKQNVALLWKGLSDIKGMSLTSNRESPIVFLKLEKSSGSAKDDLLLLEKMADRALKEDSLLVVSSKRSFLDKCRLPVGIKLYVSAGHSESDLLKASESLKRLASELLLKS

Source Source

Source organism organism	Arabidopsis thaliana
Common name common_name	thale cress
NCBI taxonomy ID ncbi_taxonomy_id	3702
Host organism host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	Long chain base biosynthesis protein 2a
Molecular weight formula_weight	53934.9 kDa
EC 编号 ec_number	2.3.1.50
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MYLTAVSTYFSYGLLFAFGQLRDFFRRFIDWWFTSNLQGYAPICLGHEDFYIRRLYHRIQDCFERPISSAPDAWFDVVERYSNDNNKTLKRTTKTSRCLNLGSYNYLGFGSFDEYCTPRVIESLKKFSASTCSSRVDAGTTSVHAELEECVTRFVGKPAAVVFGMGYATNSAIIPVLIGKGGLIISDSLNHSSIVNGARGSGATIRVFQHNTPSHLERVLREQIAEGQPRTHRPWKKIIVVVEGIYSMEGEICHLPEVVAICKKYKAYVYLDEAHSIGAIGKTGKGICELLGVDTADVDVMMGTFTKSFGSCGGYIAGSKELIQYLKHQCPAHLYATSIPTPSAQQIISAIKVILGEDGSNRGAQKLARIRENSNFFRAELQKMGFEVLGDNDSPVMPIMLYNPAKIPAFSRECLRQKVAVVVVGFPATPLLLARARICISASHSREDLIRALKVISKVGDLSGIKYFPAEPKKIEQSKNDIKLD

Source Source

Source organism organism	Arabidopsis thaliana
Common name common_name	thale cress
NCBI taxonomy ID ncbi_taxonomy_id	3702
Host organism host_organism	Homo sapiens

Entity 3 Entity 3 polymer

Description description	ORMDL family protein
Molecular weight formula_weight	18220.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MANLYVKAVPPPDMNRNTEWFMYPGVWTTYMLILFFGWLVVLSVSGCSPGMAWTVVNLAHFVVTYHSFHWMKGTPFADDQGIYNGLTWWEQMDNGQQLTRNRKFLTLVPVVLYLIASHTTDYRHPWLFLNTLAVMVLVVAKFPNMHKVRIFGINGDK

Source Source

Source organism organism	Arabidopsis thaliana
Common name common_name	thale cress
NCBI taxonomy ID ncbi_taxonomy_id	3702
Host organism host_organism	Homo sapiens

Entity 4 Entity 4 polymer

Description description	atLCB1
Molecular weight formula_weight	6949.4 kDa
EC 编号 ec_number	2.3.1.50
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

MASNLVEMFNAALNWVTMILESPSARVVLFGVPIRGHFFVEGLLGVVIIILLTRKSYKPPKR

Source Source

Source organism organism	Arabidopsis thaliana
Common name common_name	thale cress
NCBI taxonomy ID ncbi_taxonomy_id	3702
Host organism host_organism	Homo sapiens

Entity 5 Entity 5 polymer

Description description	Transmembrane protein, putative (DUF3317)
Molecular weight formula_weight	9442.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MADYKDDDDKSGPDEVDASGRMNWVQRKIYLYNVTFGLYMLDWWERYLFNSLVVVLMWFVLYNGTRYFSELFQRHLT

Source Source

Source organism organism	Arabidopsis thaliana
Common name common_name	thale cress
NCBI taxonomy ID ncbi_taxonomy_id	3702
Host organism host_organism	Homo sapiens

Entity 6 Entity 6 non-polymer

Description description	[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-SERINE
Molecular weight formula_weight	336.2 kDa
Source method src_method	man
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	N-[(2S,3R,4E)-1,3-dihydroxyoctadec-4-en-2-yl]tetracosanamide
Molecular weight formula_weight	650.1 kDa
Source method src_method	syn
Copy count entity_count	1

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	7yjoA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	640 — Aspartate Aminotransferase; domain 2
Homologous superfamily homologous superfamily	10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

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

Resolution resolution	2.80 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	279059

Cryo-EM structure of the monomeric atSPT-ORM1 (LCB2a-deltaN5) complex

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

atLCB1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Long chain base biosynthesis protein 2a

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

ORMDL family 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

Transmembrane protein, putative (DUF3317)

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

7yjo__assembly_1__model_1

7yjo__assembly_1__model_1 | I(q)

7yjo__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

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 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)