9l7p

Cryo-EM structure of retron Ec78 system complex

Method: ELECTRON MICROSCOPY

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

AAA family ATPase

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 7 DNA 2 RNA 2	Retron St85 family RNA-directed DNA polymerase × 2 （A0AAW7FAU3） TIGR02646 family protein × 1 （A0AAW7FAE2） RNA (40-MER) × 2 DNA (73-MER) × 2 ADENOSINE-5'-TRIPHOSPHATE × 3 ZINC ION × 1 MAGNESIUM ION × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0AAW7FAT4_9ENTR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–550； UniProt 1–550 Author chain B； PDBConstruct 1–550； UniProt 1–550 Author chain C； PDBConstruct 1–550； UniProt 1–550 Author chain D； PDBConstruct 1–550； UniProt 1–550

Retron St85 family RNA-directed DNA polymerase

Escherichia coli

UniProt A0AAW7FAU3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 7 DNA 2 RNA 2	AAA family ATPase × 4 （A0AAW7FAT4） TIGR02646 family protein × 1 （A0AAW7FAE2） RNA (40-MER) × 2 DNA (73-MER) × 2 ADENOSINE-5'-TRIPHOSPHATE × 3 ZINC ION × 1 MAGNESIUM ION × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0AAW7FAU3_9ENTR
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain E； PDBConstruct 1–311； UniProt 1–311 Author chain F； PDBConstruct 1–311； UniProt 1–311

TIGR02646 family protein

Escherichia coli

UniProt A0AAW7FAE2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 7 DNA 2 RNA 2	AAA family ATPase × 4 （A0AAW7FAT4） Retron St85 family RNA-directed DNA polymerase × 2 （A0AAW7FAU3） RNA (40-MER) × 2 DNA (73-MER) × 2 ADENOSINE-5'-TRIPHOSPHATE × 3 ZINC ION × 1 MAGNESIUM ION × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0AAW7FAE2_9ENTR
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain H； PDBConstruct 1–216； UniProt 1–216

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	9l7p
Deposition date deposition_date	2024-12-26
Structure title title	Cryo-EM structure of retron Ec78 system complex
Keywords keywords	a protein complex, ANTIVIRAL PROTEIN/DNA/RNA, ANTIVIRAL PROTEIN-DNA-RNA complex; ANTIVIRAL PROTEIN/DNA/RNA
Experimental Method method	ELECTRON MICROSCOPY

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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.

9l7p__assembly_1__model_1

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

Download this curve (.dat)

9l7p__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9l7p__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	56.23 Å
Rg (electron density)	55.76 Å
Total Rg	55.94 Å
Atom count	24962
Residues	2836
Excluded volume	432060 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9l7p__assembly_1__model_1`	undecameric （11）	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 (8)

Entity 1 Entity 1 polymer

Description description	AAA family ATPase
Molecular weight formula_weight	62467.8 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	24962

MTKQYERKAKGGNLLSAFELYQRNSDKAPGLGEMLVGEWFEMCRDYIQDGHVDESGIFRPDNAFYLRRLTLKDFRRFSLLEIKLEEDLTVIIGNNGKGKTSILYAIAKTLSWFVANILKEGGSGQRLSEMTDIKNDAEDRYSDVSSTFFFGKGLKSVPIRLSRSALGTAERRDSEVKPAKDLADIWRVINEVNTINLPTFALYNVERSQPFNRNIKDNTGRREERFDAYSQTLGGAGRFDHFVEWYIYLHKRTVSDISSSIKELEQQVNDLQRTVDGGMVSVKSLLEQMKFKLSEAIERNDAAVSSRVLTESVQKSIVEKAICSVVPSISNIWVEMITGSDLVKVTNDGHDVTIDQLSDGQRVFLSLVADLARRMVMLNPLLENPLEGRGIVLIDEIELHLHPKWQQEVILNLRSAFPNIQFIITTHSPIVLSTIEKRCIREFEPNDDGDQSFLDSPDMQTKGSENAQILEQVMNVHSTPPGIAESHWLGNFELLLLDNSGELDNHSQVLYDQIKAHFGIDSIELKKADSLIRINKMKNKLNKIRAEKGK

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Retron St85 family RNA-directed DNA polymerase
Molecular weight formula_weight	35538.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MSVIRGLAAVLRQSDSDISAFLVTAPRKYKVYKIPKRTTGFRVIAQPAKGLKDIQRAFVQLYSLPVHDASMAYMKGKGIRDNAAAHAGNQYLLKADLEDFFNSITPAIFWRCIEMSSAQTPQFEPQDKLFIEKILFWQPIKRRKTKLILSVGAPSSPVISNFCMYEFDNRIHAACKKVEITYTRYADDLTFSSNIPDVLKAVPSTLEVLLKDLFGSALRLNHSKTVFSSKAHNRHVTGITINNEETLSLGRDRKRFIKHLINQYKYGLLDNEDKAYLIGLLAFASHIEPSFITRMNEKYSLELMERLRGQR

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	TIGR02646 family protein
Molecular weight formula_weight	24966.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

MRELARLERPEILDQYIAGQNDWMEIDQSAVWPKLTEMQGGFCAYCECRLNRCHIEHFRPRGKFPALTFIWNNLFGSCGDSRKSGGWSRCGIYKDNGAGAYNADDLIKPDEENPDDYLLFLTTGEVVPAIGLTGRALKKAQETIRVFNLNGDIKLFGSRRTAVQAIMPNVEYLYTLLEEFDEDDWNEMLRDELEKIESDEYKTALKHAWTFNQEFA

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	RNA (40-MER)
Molecular weight formula_weight	46153.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	I,K

ACUCUUUAGCGUUGGACGGUUACGUCUAGUCGGGUGAUUAGCCAGACUCUAACUUAUUGAACGUAUUAAGGGUUGCGAAAGUGUCGCAACCCGAGAUCGUUCCUCUCUCGGGUUGCGACACUUUCGCUUCCUCAAGUAAAGAGU

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 polymer

Description description	DNA (73-MER)
Molecular weight formula_weight	24120.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	J,L

TTGAGGAAGCGAAAGTGTCGCAACCCGAGAGAGGAACGATCTCGGGTTGCGACACTTTCGCAACCCTTAATACGTTCA

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 6 Entity 6 non-polymer

Description description	ADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 7 Entity 7 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

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Resolution resolution	3.03 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	41832

Cryo-EM structure of retron Ec78 system complex

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

AAA family ATPase

State in the Current Structure

Other States of the Same Protein in the Database

Retron St85 family RNA-directed DNA polymerase

State in the Current Structure

Other States of the Same Protein in the Database

TIGR02646 family protein

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

9l7p__assembly_1__model_1

9l7p__assembly_1__model_1 | I(q)

9l7p__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (8)

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 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

7. Citations (1)

Cryo-EM structure of retron Ec78 system complex

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

AAA family ATPase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Retron St85 family RNA-directed DNA polymerase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

TIGR02646 family protein

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

9l7p__assembly_1__model_1

9l7p__assembly_1__model_1 | I(q)

9l7p__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (8)

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 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

7. Citations (1)