4q7j

Complex structure of viral RNA polymerase

Method: X-RAY DIFFRACTION

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

Elongation factor Ts

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Elongation factor Tu 1 × 1 （P0CE47） Q beta replicase × 1 （Q8LTE0） 30S ribosomal protein S1 × 1 （P0AG67） SULFATE ION × 2 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Elongation factor Tu 1 × 1 （P0CE47） Q beta replicase × 1 （Q8LTE0） 30S ribosomal protein S1 × 1 （P0AG67） SULFATE ION × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	EFTS_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–282； UniProt 2–283 Author chain E； PDBConstruct 1–282； UniProt 2–283

Elongation factor Tu 1

Escherichia coli

UniProt P0CE47

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Elongation factor Ts × 1 （P0A6P1） Q beta replicase × 1 （Q8LTE0） 30S ribosomal protein S1 × 1 （P0AG67） SULFATE ION × 2 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Elongation factor Ts × 1 （P0A6P1） Q beta replicase × 1 （Q8LTE0） 30S ribosomal protein S1 × 1 （P0AG67） SULFATE ION × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	EFTU1_ECOLI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–393； UniProt 2–394 Author chain F； PDBConstruct 1–393； UniProt 2–394

Q beta replicase

Enterobacteria phage Qbeta

UniProt Q8LTE0

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Elongation factor Ts × 1 （P0A6P1） Elongation factor Tu 1 × 1 （P0CE47） 30S ribosomal protein S1 × 1 （P0AG67） SULFATE ION × 2 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Elongation factor Ts × 1 （P0A6P1） Elongation factor Tu 1 × 1 （P0CE47） 30S ribosomal protein S1 × 1 （P0AG67） SULFATE ION × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8LTE0_BPQBE
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–588； UniProt 2–589 Author chain G； PDBConstruct 1–588； UniProt 2–589

30S ribosomal protein S1

Escherichia coli

UniProt P0AG67

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Elongation factor Ts × 1 （P0A6P1） Elongation factor Tu 1 × 1 （P0CE47） Q beta replicase × 1 （Q8LTE0） SULFATE ION × 2 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Elongation factor Ts × 1 （P0A6P1） Elongation factor Tu 1 × 1 （P0CE47） Q beta replicase × 1 （Q8LTE0） SULFATE ION × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RS1_ECOLI
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–273； UniProt 1–273 Author chain H； PDBConstruct 1–273； UniProt 1–273

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	4q7j
Deposition date deposition_date	2014-04-25
Structure title title	Complex structure of viral RNA polymerase
Keywords keywords	RNA polymerase, RNA binding motif, RNA dependent RNA polymerization, TRANSLATION-TRANSFERASE complex; TRANSLATION/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.

4q7j__assembly_2__model_1

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

Download this curve (.dat)

4q7j__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4q7j__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	39.23 Å
Rg (electron density)	38.80 Å
Total Rg	39.27 Å
Atom count	10564
Residues	1366
Excluded volume	188330 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4q7j__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4q7j__assembly_2__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 (6)

Entity 1 Entity 1 polymer

Description description	Elongation factor Ts
Molecular weight formula_weight	30332.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,E
Atom count atom_count	21369

AEITASLVKELRERTGAGMMDCKKALTEANGDIELAIENMRKSGAIKAAKKAGNVAADGVIKTKIDGNYGIILEVNCQTDFVAKDAGFQAFADKVLDAAVAGKITDVEVLKAQFEEERVALVAKIGENINIRRVAALEGDVLGSYQHGARIGVLVAAKGADEELVKHIAMHVAASKPEFIKPEDVSAEVVEKEYQVQLDIAMQSGKPKEIAEKMVEGRMKKFTGEVSLTGQPFVMEPSKTVGQLLKEHNAEVTGFIRFEVGEGIEKVETDFAAEVAAMSKQS

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Elongation factor Tu 1
Molecular weight formula_weight	43209.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

SKEKFERTKPHVNVGTIGHVDHGKTTLTAAITTVLAKTYGGAARAFDQIDNAPEEKARGITINTSHVEYDTPTRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHILLGRQVGVPYIIVFLNKCDMVDDEELLELVEMEVRELLSQYDFPGDDTPIVRGSALKALEGDAEWEAKILELAGFLDSYIPEPERAIDKPFLLPIEDVFSISGRGTVVTGRVERGIIKVGEEVEIVGIKETQKSTCTGVEMFRKLLDEGRAGENVGVLLRGIKREEIERGQVLAKPGTIKPHTKFESEVYILSKDEGGRHTPFFKGYRPQFYFRTTDVTGTIELPEGVEMVMPGDNIKMVVTLIHPIAMDDGLRFAIREGGRTVGAGVVAKVLG

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Q beta replicase
Molecular weight formula_weight	66305.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

SKTASSRNSLSAQLRRAANTRIEVEGNLALSIANDLLLAYGQSPFNSEAECISFSPRFDGTPDDFRINYLKAEIMSKYDDFSLGIDTEAVAWEKFLAAEAECALTNARLYRPDYSEDFNFSLGESCIHMARRKIAKLIGDVPSVEGMLRHCRFSGGATTTNNRSYGHPSFKFALPQACTPRALKYVLALRASTHFDIRISDISPFNKAVTVPKNSKTDRCIAIEPGWNMFFQLGIGGILRDRLRCWGIDLNDQTINQRRAHEGSVTNNLATVDLSAASDSISLALCELLLPPGWFEVLMDLRSPKGRLPDGSVVTYEKISSMGNGYTFELESLIFASLARSVCEILDLDSSEVTVYGDDIILPSCAVPALREVFKYVGFTTNTKKTFSEGPFRESCGKHYYSGVDVTPFYIRHRIVSPADLILVLNNLYRWATIDGVWDPRAHSVYLKYRKLLPKQLQRNTIPDGYGDGALVGSVLINPFAKNRGWIRYVPVITDHTRDRERAELGSYLYDLFSRCLSESNDGLPLRGPSGCDSADLFAIDQLICRSNPTKISRSTGKFDIQYIACSSRVLAPYGVFQGTKVASLHEAHHHHHH

Source Source

Source organism organism	Enterobacteria phage Qbeta
NCBI taxonomy ID ncbi_taxonomy_id	39803
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	30S ribosomal protein S1
Molecular weight formula_weight	31340.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MTESFAQLFEESLKEIETRPGSIVRGVVVAIDKDVVLVDAGLKSESAIPAEQFKNAQGELEIQVGDEVDVALDAVEDGFGETLLSREKAKRHEAWITLEKAYEDAETVTGVINGKVKGGFTVELNGIRAFLPGSLVDVRPVRDTLHLEGKELEFKVIKLDQKRNNVVVSRRAVIESENSAERDQLLENLQEGMEVKGIVKNLTDYGAFVDLGGVDGLLHITDMAWKRVKHPSEIVNVGDEITVKVLKFDRERTRVSLGLKQLGEDPWVAIAKRLEHHHHHH

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	253

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6. Fold Classification (SCOP + CATH) 26 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d4q7ja1
Class class	a — All alpha proteins
Fold Fold fold	a.5 — RuvA C-terminal domain-like
Superfamily Superfamily superfamily	a.5.2 — UBA-like
Family Family family	a.5.2.2 — TS-N domain

Domain ID domain_id	d4q7ja2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.43 — EF-Ts domain-like
Superfamily Superfamily superfamily	d.43.1 — Elongation factor Ts (EF-Ts), dimerisation domain
Family Family family	d.43.1.1 — Elongation factor Ts (EF-Ts), dimerisation domain

Domain ID domain_id	d4q7ja3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.43 — EF-Ts domain-like
Superfamily Superfamily superfamily	d.43.1 — Elongation factor Ts (EF-Ts), dimerisation domain
Family Family family	d.43.1.1 — Elongation factor Ts (EF-Ts), dimerisation domain

Domain ID domain_id	d4q7jb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.8 — G proteins

Domain ID domain_id	d4q7jb2
Class class	b — All beta proteins
Fold Fold fold	b.43 — Reductase/isomerase/elongation factor common domain
Superfamily Superfamily superfamily	b.43.3 — Translation proteins
Family Family family	b.43.3.1 — Elongation factors

Domain ID domain_id	d4q7jb3
Class class	b — All beta proteins
Fold Fold fold	b.44 — Elongation factor/aminomethyltransferase common domain
Superfamily Superfamily superfamily	b.44.1 — EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain
Family Family family	b.44.1.1 — EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain

Domain ID domain_id	d4q7je1
Class class	a — All alpha proteins
Fold Fold fold	a.5 — RuvA C-terminal domain-like
Superfamily Superfamily superfamily	a.5.2 — UBA-like
Family Family family	a.5.2.2 — TS-N domain

Domain ID domain_id	d4q7je2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.43 — EF-Ts domain-like
Superfamily Superfamily superfamily	d.43.1 — Elongation factor Ts (EF-Ts), dimerisation domain
Family Family family	d.43.1.1 — Elongation factor Ts (EF-Ts), dimerisation domain

Domain ID domain_id	d4q7je3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.43 — EF-Ts domain-like
Superfamily Superfamily superfamily	d.43.1 — Elongation factor Ts (EF-Ts), dimerisation domain
Family Family family	d.43.1.1 — Elongation factor Ts (EF-Ts), dimerisation domain

Domain ID domain_id	d4q7jf1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.8 — G proteins

Domain ID domain_id	d4q7jf2
Class class	b — All beta proteins
Fold Fold fold	b.43 — Reductase/isomerase/elongation factor common domain
Superfamily Superfamily superfamily	b.43.3 — Translation proteins
Family Family family	b.43.3.1 — Elongation factors

Domain ID domain_id	d4q7jf3
Class class	b — All beta proteins
Fold Fold fold	b.44 — Elongation factor/aminomethyltransferase common domain
Superfamily Superfamily superfamily	b.44.1 — EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain
Family Family family	b.44.1.1 — EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain

CATH v4.4 (14 domains)

Domain ID domain_id	4q7jA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	10 — Ubiquitin-associated (UBA) domain

Domain ID domain_id	4q7jA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	479 — Tetrahydropterin Synthase; Chain A
Homologous superfamily homologous superfamily	20 — Elongation factor Ts, dimerisation domain

Domain ID domain_id	4q7jA03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	479 — Tetrahydropterin Synthase; Chain A
Homologous superfamily homologous superfamily	20 — Elongation factor Ts, dimerisation domain

Domain ID domain_id	4q7jA04
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	286 — GTP Cyclohydrolase I; Chain A, domain 1
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	4q7jB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	4q7jB02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	10 — Translation factors

Domain ID domain_id	4q7jB03
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	10 — Translation factors

Domain ID domain_id	4q7jE01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	10 — Ubiquitin-associated (UBA) domain

Domain ID domain_id	4q7jE02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	479 — Tetrahydropterin Synthase; Chain A
Homologous superfamily homologous superfamily	20 — Elongation factor Ts, dimerisation domain

Domain ID domain_id	4q7jE03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	479 — Tetrahydropterin Synthase; Chain A
Homologous superfamily homologous superfamily	20 — Elongation factor Ts, dimerisation domain

Domain ID domain_id	4q7jE04
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	286 — GTP Cyclohydrolase I; Chain A, domain 1
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	4q7jF01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	4q7jF02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	10 — Translation factors

Domain ID domain_id	4q7jF03
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	10 — Translation factors

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Unit-cell length a length_a	132.190 Å
Unit-cell length b length_b	150.830 Å
Unit-cell length c length_c	189.780 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 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	19.982 Å
R factor r_factor	0.2580
R_work r_work	0.2553
R_free r_free	0.3088

Complex structure of viral RNA polymerase

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

Elongation factor Ts

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Elongation factor Tu 1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Q beta replicase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

30S ribosomal protein S1

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

4q7j__assembly_2__model_1

4q7j__assembly_2__model_1 | I(q)

4q7j__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 26 domains

SCOP 2.08 (12 domains)

CATH v4.4 (14 domains)

7. Citations (1)