SAXSdb — 4h5i

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

Guanine nucleotide-exchange factor SEC12

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	POTASSIUM ION × 2 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	POTASSIUM ION × 2 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SEC12_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–357； UniProt 1–354 Author chain B； PDBConstruct 4–357； UniProt 1–354

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	4h5i
Deposition date deposition_date	2012-09-18
Structure title title	Crystal Structure of the Guanine Nucleotide Exchange Factor Sec12 (P1 form)
Keywords keywords	COPII vesicle budding, potassium binding site, beta propeller, PROTEIN TRANSPORT; PROTEIN TRANSPORT
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.

4h5i__assembly_1__model_1

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

Download this curve (.dat)

4h5i__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4h5i__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.73 Å
Rg (electron density)	19.48 Å
Total Rg	20.46 Å
Atom count	2624
Residues	339
Excluded volume	47225 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4h5i__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4h5i__assembly_2__model_1`	monomeric （1）	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	Guanine nucleotide-exchange factor SEC12
Molecular weight formula_weight	40229.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	5681

MASMKFVTASYNVGYPAYGAKFLNNDTLLVAGGGGEGNNGIPNKLTVLRVDPTKDTEKEQFHILSEFALEDNDDSPTAIDASKGIILVGCNENSTKITQGKGNKHLRKFKYDKVNDQLEFLTSVDFDASTNADDYTKLVYISREGTVAAIASSKVPAIMRIIDPSDLTEKFEIETRGEVKDLHFSTDGKVVAYITGSSLEVISTVTGSCIARKTDFDKNWSLSKINFIADDTVLIAASLKKGKGIVLTKISIKSGNTSVLRSKQVTNRFKGITSMDVDMKGELAVLASNDNSIALVKLKDLSMSKIFKQAHSFAITEVTISPDSTYVASVSAANTIHIIKLPLNYANYTSMKQKISKLEHHHHHH

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	yeast
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	428

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	4h5iA00
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

Domain ID domain_id	4h5iB00
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

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Unit-cell length a length_a	53.400 Å
Unit-cell length b length_b	53.474 Å
Unit-cell length c length_c	61.976 Å
Unit-cell angle α angle_alpha	81.68 °
Unit-cell angle β angle_beta	73.37 °
Unit-cell angle γ angle_gamma	87.58 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	1.360 Å
Low-resolution limit resolution_low	42.359 Å
R factor r_factor	0.1795
R_work r_work	0.1786
R_free r_free	0.1971

Crystal Structure of the Guanine Nucleotide Exchange Factor Sec12 (P1 form)

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

Guanine nucleotide-exchange factor SEC12

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

4h5i__assembly_1__model_1

4h5i__assembly_1__model_1 | I(q)

4h5i__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 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Crystal Structure of the Guanine Nucleotide Exchange Factor Sec12 (P1 form)

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

Guanine nucleotide-exchange factor SEC12

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

4h5i__assembly_1__model_1

4h5i__assembly_1__model_1 | I(q)

4h5i__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 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)