10nm

CRYO-EM STRUCTURE OF THE A149T DIMER VARIANT OF SERINE HYDROXYMETHYLTRANSFERASE 8 FROM SOYBEAN CULTIVAR ESSEX IN COMPLEX WITH PLP

Method: ELECTRON MICROSCOPY

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

Serine hydroxymethyltransferase

Glycine max

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	No other associated polymer	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	K4FZF8_SOYBN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 26–496； UniProt 1–471 Author chain B； PDBConstruct 26–496； UniProt 1–471

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	10nm
Deposition date deposition_date	2026-01-28
Structure title title	CRYO-EM STRUCTURE OF THE A149T DIMER VARIANT OF SERINE HYDROXYMETHYLTRANSFERASE 8 FROM SOYBEAN CULTIVAR ESSEX IN COMPLEX WITH PLP
Keywords keywords	enzyme, missense variant, TRANSFERASE; TRANSFERASE
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.

10nm__assembly_1__model_1

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

Download this curve (.dat)

10nm__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

10nm__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.31 Å
Rg (electron density)	28.53 Å
Total Rg	29.27 Å
Atom count	6440
Residues	895
Excluded volume	114100 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`10nm__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 (1)

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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	triclinic

Resolution resolution	2.92 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	71315

Description description	Serine hydroxymethyltransferase
Molecular weight formula_weight	54951.1 kDa
EC 编号 ec_number	2.1.2.1
Mutation mutation	A149T
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	6440

CRYO-EM STRUCTURE OF THE A149T DIMER VARIANT OF SERINE HYDROXYMETHYLTRANSFERASE 8 FROM SOYBEAN CULTIVAR ESSEX IN COMPLEX WITH PLP

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

Serine hydroxymethyltransferase

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

10nm__assembly_1__model_1

10nm__assembly_1__model_1 | I(q)

10nm__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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

7. Citations (1)

Source organism organism	Glycine max
Common name common_name	soybean
NCBI taxonomy ID ncbi_taxonomy_id	3847
Host organism host_organism	Escherichia coli

CRYO-EM STRUCTURE OF THE A149T DIMER VARIANT OF SERINE HYDROXYMETHYLTRANSFERASE 8 FROM SOYBEAN CULTIVAR ESSEX IN COMPLEX WITH PLP

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

Serine hydroxymethyltransferase

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

10nm__assembly_1__model_1

10nm__assembly_1__model_1 | I(q)

10nm__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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

7. Citations (1)