SAXSdb — 3kyh

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

mRNA-capping enzyme subunit beta

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	mRNA-capping enzyme subunit alpha × 2 （Q01159）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CET1_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–310； UniProt 241–549 Author chain B； PDBConstruct 2–310； UniProt 241–549

mRNA-capping enzyme subunit alpha

Saccharomyces cerevisiae

UniProt Q01159

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	mRNA-capping enzyme subunit beta × 2 （O13297）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MCE1_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 3–461； UniProt 1–459 Author chain D； PDBConstruct 3–461； UniProt 1–459

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	3kyh
Deposition date deposition_date	2009-12-06
Structure title title	Saccharomyces cerevisiae Cet1-Ceg1 capping apparatus
Keywords keywords	;Capping, RNA, 5' modification, triphosphatase, guanylyltransferase, complex, Hydrolase, mRNA capping, mRNA processing, Nucleus, Phosphoprotein, GTP-binding, Nucleotide-binding, Nucleotidyltransferase, Transferase, PROTEIN BINDING ;; PROTEIN BINDING
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.

3kyh__assembly_1__model_1

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

Download this curve (.dat)

3kyh__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3kyh__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	45.71 Å
Rg (electron density)	45.77 Å
Total Rg	45.96 Å
Atom count	10696
Residues	1326
Excluded volume	191350 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3kyh__assembly_1__model_1`	tetrameric （4）	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 (2)

Entity 1 Entity 1 polymer

Description description	mRNA-capping enzyme subunit beta
Molecular weight formula_weight	35525.3 kDa
EC 编号 ec_number	3.1.3.33
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	10696

MYKNVPIWAQKWKPTIKALQSINVKDLKIDPSFLNIIPDDDLTKSVQDWVYATIYSIAPELRSFIELEMKFGVIIDAKGPDRVNPPVSSQCVFTELDAHLTPNIDASLFKELSKYIRGISEVTENTGKFSIIESQTRDSVYRVGLSTQRPRFLRMSTDIKTGRVGQFIEKRHVAQLLLYSPKDSYDVKISLNLELPVPDNDPPEKYKSQSPISERTKDRVSYIHNDSCTRIDITKVENHNQNSKSRQSETTHEVELEINTPALLNAFDNITNDSKEYASLIRTFLNNGTIIRRKLSSLSYEIFEGSKKVM

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;brewer's yeast,lager beer yeast,yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	mRNA-capping enzyme subunit alpha
Molecular weight formula_weight	53030.3 kDa
EC 编号 ec_number	2.7.7.50
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

SLMVLAMESRVAPEIPGLIQPGNVTQDLKMMVCKLLNSPKPTKTFPGSQPVSFQHSDVEEKLLAHDYYVCEKTDGLRVLMFIVINPVTGEQGCFMIDRENNYYLVNGFRFPRLPQKKKEELLETLQDGTLLDGELVIQTNPMTKLQELRYLMFDCLAINGRCLTQSPTSSRLAHLGKEFFKPYFDLRAAYPNRCTTFPFKISMKHMDFSYQLVKVAKSLDKLPHLSDGLIFTPVKAPYTAGGKDSLLLKWKPEQENTVDFKLILDIPMVEDPSLPKDDRNRWYYNYDVKPVFSLYVWQGGADVNSRLKHFDQPFDRKEFEILERTYRKFAELSVSDEEWQNLKNLEQPLNGRIVECAKNQETGAWEMLRFRDDKLNGNHTSVVQKVLESINDSVSLEDLEEIVGDIKRCWDERRANMAGGSGRPLPSQSQNATLSTSKPVHSQPPSNDKEPKYVDEDDWSD

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;brewer's yeast,lager beer yeast,yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3kyha_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.63 — CYTH-like phosphatases
Superfamily Superfamily superfamily	d.63.1 — CYTH-like phosphatases
Family Family family	d.63.1.1 — mRNA triphosphatase CET1

Domain ID domain_id	d3kyhb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.63 — CYTH-like phosphatases
Superfamily Superfamily superfamily	d.63.1 — CYTH-like phosphatases
Family Family family	d.63.1.1 — mRNA triphosphatase CET1

CATH v4.4 (6 domains)

Domain ID domain_id	3kyhA01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	100 — mRNA Triphosphatase Cet1; Chain A
Homologous superfamily homologous superfamily	10 — mRNA triphosphatase Cet1-like

Domain ID domain_id	3kyhB01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	100 — mRNA Triphosphatase Cet1; Chain A
Homologous superfamily homologous superfamily	10 — mRNA triphosphatase Cet1-like

Domain ID domain_id	3kyhC01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	470 — D-amino Acid Aminotransferase; Chain A, domain 1
Homologous superfamily homologous superfamily	30 — DNA ligase/mRNA capping enzyme

Domain ID domain_id	3kyhC02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

Domain ID domain_id	3kyhD01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	470 — D-amino Acid Aminotransferase; Chain A, domain 1
Homologous superfamily homologous superfamily	30 — DNA ligase/mRNA capping enzyme

Domain ID domain_id	3kyhD02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

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Unit-cell length a length_a	165.993 Å
Unit-cell length b length_b	165.993 Å
Unit-cell length c length_c	172.355 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 63
Space-group number int_tables_number	173
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	19.980 Å
R factor r_factor	0.2516
R_work r_work	0.2492
R_free r_free	0.2980

Saccharomyces cerevisiae Cet1-Ceg1 capping apparatus

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

mRNA-capping enzyme subunit beta

State in the Current Structure

Other States of the Same Protein in the Database

mRNA-capping enzyme subunit alpha

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

3kyh__assembly_1__model_1

3kyh__assembly_1__model_1 | I(q)

3kyh__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (2 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Saccharomyces cerevisiae Cet1-Ceg1 capping apparatus

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

mRNA-capping enzyme subunit beta

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

mRNA-capping enzyme subunit alpha

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

3kyh__assembly_1__model_1

3kyh__assembly_1__model_1 | I(q)

3kyh__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (2 domains)

CATH v4.4 (6 domains)

7. Citations (1)