1go3

Structure of an archeal homolog of the eukaryotic RNA polymerase II RPB4/RPB7 complex

Method: X-RAY DIFFRACTION

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

DNA-DIRECTED RNA POLYMERASE SUBUNIT E

METHANOCOCCUS JANNASCHII

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 SUBUNIT F × 1 （Q60351） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	DNA-DIRECTED RNA POLYMERASE SUBUNIT F × 1 （Q60351） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RPE1_METJA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain E； PDBConstruct 1–187； UniProt 1–187 Author chain M； PDBConstruct 1–187； UniProt 1–187

DNA-DIRECTED RNA POLYMERASE SUBUNIT F

METHANOCOCCUS JANNASCHII

UniProt Q60351

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 SUBUNIT E × 1 （Q57840） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	DNA-DIRECTED RNA POLYMERASE SUBUNIT E × 1 （Q57840） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Y039_METJA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain F； PDBConstruct 1–107； UniProt 9–115 Author chain N； PDBConstruct 1–107； UniProt 9–115

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	1go3
Deposition date deposition_date	2001-10-17
Structure title title	Structure of an archeal homolog of the eukaryotic RNA polymerase II RPB4/RPB7 complex
Keywords keywords	TRANSFERASE, TRANSFERASE; TRANSCRIPTION; DNA-DIRECTED RNA POLYMERASE; TRANSFERASE
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.

1go3__assembly_1__model_1

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

Download this curve (.dat)

1go3__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1go3__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.13 Å
Rg (electron density)	21.26 Å
Total Rg	21.95 Å
Atom count	2192
Residues	284
Excluded volume	39823 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1go3__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1go3__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 (3)

Entity 1 Entity 1 polymer

Description description	DNA-DIRECTED RNA POLYMERASE SUBUNIT E
Molecular weight formula_weight	21246.6 kDa
EC 编号 ec_number	2.7.7.6
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,M
Atom count atom_count	4695

MYKILEIADVVKVPPEEFGKDLKETVKKILMEKYEGRLDKDVGFVLSIVDVKDIGEGKVVHGDGSAYHPVVFETLVYIPEMYELIEGEVVDVVEFGSFVRLGPLDGLIHVSQIMDDYVSYDPKREAIIGKETGKVLEIGDYVRARIVAISLKAERKRGSKIALTMRQPYLGKLEWIEEEKAKKQNQE

Source Source

Source organism organism	METHANOCOCCUS JANNASCHII
NCBI taxonomy ID ncbi_taxonomy_id	2190
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	DNA-DIRECTED RNA POLYMERASE SUBUNIT F
Molecular weight formula_weight	12342.2 kDa
EC 编号 ec_number	2.7.7.6
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F,N

MIGKKILGERYVTVSEAAEIMYNRAQIGELSYEQGCALDYLQKFAKLDKEEAKKLVEELISLGIDEKTAVKIADILPEDLDDLRAIYYKRELPENAEEILEIVRKYI

Source Source

Source organism organism	METHANOCOCCUS JANNASCHII
NCBI taxonomy ID ncbi_taxonomy_id	2190
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	328

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6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1go3e1
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
Family Family family	b.40.4.5 — Cold shock DNA-binding domain-like

Domain ID domain_id	d1go3e2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.230 — Dodecin subunit-like
Superfamily Superfamily superfamily	d.230.1 — N-terminal, heterodimerisation domain of RBP7 (RpoE)
Family Family family	d.230.1.1 — N-terminal, heterodimerisation domain of RBP7 (RpoE)

Domain ID domain_id	d1go3f_
Class class	a — All alpha proteins
Fold Fold fold	a.60 — SAM domain-like
Superfamily Superfamily superfamily	a.60.8 — HRDC-like
Family Family family	a.60.8.2 — RNA polymerase II subunit RBP4 (RpoF)

Domain ID domain_id	d1go3m1
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
Family Family family	b.40.4.5 — Cold shock DNA-binding domain-like

Domain ID domain_id	d1go3m2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.230 — Dodecin subunit-like
Superfamily Superfamily superfamily	d.230.1 — N-terminal, heterodimerisation domain of RBP7 (RpoE)
Family Family family	d.230.1.1 — N-terminal, heterodimerisation domain of RBP7 (RpoE)

Domain ID domain_id	d1go3n_
Class class	a — All alpha proteins
Fold Fold fold	a.60 — SAM domain-like
Superfamily Superfamily superfamily	a.60.8 — HRDC-like
Family Family family	a.60.8.2 — RNA polymerase II subunit RBP4 (RpoF)

CATH v4.4 (8 domains)

Domain ID domain_id	1go3E01
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	1go3E02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily	120 — RNA polymerase Rpb7-like, N-terminal domain

Domain ID domain_id	1go3F01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	80 — HRDC domain

Domain ID domain_id	1go3F02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1go3M01
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	1go3M02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily	120 — RNA polymerase Rpb7-like, N-terminal domain

Domain ID domain_id	1go3N01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	80 — HRDC domain

Domain ID domain_id	1go3N02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	10 —

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Unit-cell length a length_a	92.391 Å
Unit-cell length b length_b	92.391 Å
Unit-cell length c length_c	91.109 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	8

Space group space_group	P 43
Space-group number int_tables_number	78
Crystal system crystal_system	—

Resolution resolution	1.750 Å
Low-resolution limit resolution_low	27.800 Å
R factor r_factor	0.2170
R_work r_work	0.2170
R_free r_free	0.2380

Structure of an archeal homolog of the eukaryotic RNA polymerase II RPB4/RPB7 complex

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

DNA-DIRECTED RNA POLYMERASE SUBUNIT E

State in the Current Structure

Other States of the Same Protein in the Database

DNA-DIRECTED RNA POLYMERASE SUBUNIT F

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

1go3__assembly_1__model_1

1go3__assembly_1__model_1 | I(q)

1go3__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Structure of an archeal homolog of the eukaryotic RNA polymerase II RPB4/RPB7 complex

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

DNA-DIRECTED RNA POLYMERASE SUBUNIT E

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 SUBUNIT F

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

1go3__assembly_1__model_1

1go3__assembly_1__model_1 | I(q)

1go3__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

CATH v4.4 (8 domains)

7. Citations (1)