SAXSdb — 4pz6

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

mRNA-capping enzyme subunit alpha

Schizosaccharomyces pombe

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	DNA-directed RNA polymerase II subunit rpb1 × 1 （P36594） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	DNA-directed RNA polymerase II subunit rpb1 × 1 （P36594） GUANOSINE × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MCE1_SCHPO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–403； UniProt 1–402 Author chain B； PDBConstruct 2–403； UniProt 1–402

DNA-directed RNA polymerase II subunit rpb1

OrganismNot specified

UniProt P36594

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	mRNA-capping enzyme subunit alpha × 1 （P40997） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	mRNA-capping enzyme subunit alpha × 1 （P40997） GUANOSINE × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RPB1_SCHPO
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain P； PDBConstruct 1–21； UniProt 1578–1598 Author chain Q； PDBConstruct 1–21； UniProt 1578–1598

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	4pz6
Deposition date deposition_date	2014-03-28
Structure title title	PCE1 guanylyltransferase bound to SER2/SER5 phosphorylated RNA pol II CTD
Keywords keywords	Nucleotidyl transferase, RNA capping enzyme, RNA polymerase II, Spt5, guanylation, nuclear, TRANSFERASE-TRANSCRIPTION complex; TRANSFERASE/TRANSCRIPTION
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.

4pz6__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4pz6__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4pz6__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	25.49 Å
Rg (electron density)	24.53 Å
Total Rg	25.25 Å
Atom count	3144
Residues	377
Excluded volume	56200 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4pz6__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4pz6__assembly_2__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 (4)

Entity 1 Entity 1 polymer

Description description	mRNA-capping enzyme subunit alpha
Molecular weight formula_weight	47034.1 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	A,B
Atom count atom_count	6496

SMAPSEKDIEEVSVPGVLAPRDDVRVLKTRIAKLLGTSPDTFPGSQPVSFSKKHLQALKEKNYFVCEKSDGIRCLLYMTEHPRYENRPSVYLFDRKMNFYHVEKIFYPVENDKSGKKYHVDTLLDGELVLDIYPGGKKQLRYLVFDCLACDGIVYMSRLLDKRLGIFAKSIQKPLDEYTKTHMRETAIFPFLTSLKKMELGHGILKLFNEVIPRLRHGNDGLIFTCTETPYVSGTDQSLLKWKPKEMNTIDFMLKLEFAQPEEGDIDYSAMPEFQLGVWEGRNMYSFFAFMYVDEKEWEKLKSFNVPLSERIVECYLDDENRWRFLRFRDDKRDANHISTVKSVLQSIEDGVSKEDLLKEMPIIREAYYNRKKPSVTKRKLDETSNDDAPAIKKVAKESEKEI

Source Source

Source organism organism	Schizosaccharomyces pombe
Common name common_name	Fission yeast
NCBI taxonomy ID ncbi_taxonomy_id	284812
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	DNA-directed RNA polymerase II subunit rpb1
Molecular weight formula_weight	2657.1 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P,Q

YSPTSPSYSPTSPSYSPTSPS

Entity 3 Entity 3 non-polymer

Description description	GUANOSINE
Molecular weight formula_weight	283.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	212

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	4pz6A01
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	4pz6A02
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	4pz6B01
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	4pz6B02
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

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Unit-cell length a length_a	56.406 Å
Unit-cell length b length_b	78.614 Å
Unit-cell length c length_c	115.716 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.42 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.406 Å
Low-resolution limit resolution_low	36.274 Å
R factor r_factor	0.1826
R_work r_work	0.1798
R_free r_free	0.2327

PCE1 guanylyltransferase bound to SER2/SER5 phosphorylated RNA pol II CTD

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

mRNA-capping enzyme subunit alpha

State in the Current Structure

Other States of the Same Protein in the Database

DNA-directed RNA polymerase II subunit rpb1

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

4pz6__assembly_2__model_1

4pz6__assembly_2__model_1 | I(q)

4pz6__assembly_2__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

PCE1 guanylyltransferase bound to SER2/SER5 phosphorylated RNA pol II CTD

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

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

DNA-directed RNA polymerase II subunit rpb1

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

4pz6__assembly_2__model_1

4pz6__assembly_2__model_1 | I(q)

4pz6__assembly_2__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)