9vhl

cryoEM structure of retron-Eco7 complex (form II)

Method: ELECTRON MICROSCOPY

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

Retron Ec78 reverse transcriptase

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 6 DNA 1 RNA 1	Retron Ec78 probable ATPase × 4 （P0DV91） Retron Ec78 putative HNH endonuclease × 1 （P0DV92） msdDNA × 1 msrRNA × 1 ADENOSINE-5'-TRIPHOSPHATE × 3 MAGNESIUM ION × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RT78_ECOLX
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–311； UniProt 1–311

Retron Ec78 probable ATPase

Escherichia coli

UniProt P0DV91

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 6 DNA 1 RNA 1	Retron Ec78 reverse transcriptase × 1 （Q46666） Retron Ec78 putative HNH endonuclease × 1 （P0DV92） msdDNA × 1 msrRNA × 1 ADENOSINE-5'-TRIPHOSPHATE × 3 MAGNESIUM ION × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ATP78_ECOLX
Isoform	—
PDB entities	2
Chains and sequence ranges	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 Author chain E； PDBConstruct 1–550； UniProt 1–550

Retron Ec78 putative HNH endonuclease

Escherichia coli

UniProt P0DV92

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 6 DNA 1 RNA 1	Retron Ec78 reverse transcriptase × 1 （Q46666） Retron Ec78 probable ATPase × 4 （P0DV91） msdDNA × 1 msrRNA × 1 ADENOSINE-5'-TRIPHOSPHATE × 3 MAGNESIUM ION × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HNH78_ECOLX
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain F； 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	9vhl
Deposition date deposition_date	2025-06-17
Structure title title	cryoEM structure of retron-Eco7 complex (form II)
Keywords keywords	retron-Eco7, toxin-antitoxin, DNA BINDING PROTEIN/RNA/DNA, DNA BINDING PROTEIN-RNA-DNA complex; DNA BINDING PROTEIN/RNA/DNA
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.

9vhl__assembly_1__model_1

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

Download this curve (.dat)

9vhl__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9vhl__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	46.24 Å
Rg (electron density)	45.84 Å
Total Rg	46.10 Å
Atom count	19055
Residues	2176
Excluded volume	330860 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9vhl__assembly_1__model_1`	octameric （8）	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 (7)

Entity 1 Entity 1 polymer

Description description	Retron Ec78 reverse transcriptase
Molecular weight formula_weight	35629.2 kDa
EC 编号 ec_number	2.7.7.49
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	19055

MSVIRRLAAVLRQSDSGISAFLVTAPRKYKVYKIPKRTTGFRVIAQPAKGLKDIQRAFVQLYNFPVHDASMAYMKGKGIRDNAAAHAGNQYLLKADLEDFFNSITPAIFWRCIEMSSALTPQFEPQDKFFIEKILFWQPIKHRKTKLILSVGAPSSPVISNFCMYEFDNRIHAACNKLEITYTRYADDLTFSCNIPNVLKAVPSTIEALLKDLFGSELRLNHSKTVFSSKAHNRHVTGVTINNEETLSLGRDRKRFIKHLINQYKYGLLDNEDKAYLTGLLAFASHIEPGFITRMNEKYSLELMERLRGQR

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Retron Ec78 probable ATPase
Molecular weight formula_weight	62466.6 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

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

MTKQYERKAKGGNLLSAFELYQRNTDNMPGLGEMLVDEWFETCRDYIQDGHVDESGTFRPDNAFYLRRLTLKDFRRFSLLEIKFEEDLTVIIGNNGKGKTSILYAIAKTLSWFVANILKEGGSGQRLSELTDIKNDAENRYADVSSTFFFGKGLKSVPIRLSRSALGTAERRDSEVKPARDLADIWRVINEAKTINLPTFALYNVERSQPFNRNTKDNAGRREERFDAYSQALGGAGRFDHFVEWYIYLHKRTISDISSSIKELEQQVNDLQRSVDGGMVSVKSLLEQMKLKLSEASERNDAAVSSKMVTESVQKSIVEKSICSVVPSISKIWVEMTTGSDLVKVTNDGHDVTIDQLSDGQRVFLSLVADLARRMVMLNPLLENPLEGRGIVLIDEIELHLHPKWQQEVILNLRSVFPNIQFIITTHSPIVLSTIEKRCIREFDPNDDGNQSFLDSPDMQTKGSENAQILEQVMNVHPTPPGIAESHWLGDFELLLLDNSGELDNQSQELYDKIKTHFGIDSAELKKADSLIRINKMKNKINKIRAEKGK

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 polymer

Description description	Retron Ec78 putative HNH endonuclease
Molecular weight formula_weight	24816.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

MKELARLESPEILDQYTAGQNDWMEIDQSAVWPKLTEMQGEFCAYCECRLNRRHIEHFRPRGKFPALTFIWSNLFGSCGDSKKSGGWSRCGIYKDNGAGAYNADDLIKPDEENPDDYLLFLTTGEVVPAIGLTGRALKKAQETIRVFNLNGDIKLLGSRRTAVQAIMPNVEYLYSLLEEFEEDDWNEMLRDELEKIESDEFKTALKHAWTSNQEFA

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 4 Entity 4 polymer

Description description	msdDNA
Molecular weight formula_weight	22869.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	G

GGAAGCGAAAGTGTCGCAACCCGAGAGAGGAACGATCTCGGGTTGCGACACTTTCGCAACCCTTAATACGTTCA

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 5 Entity 5 polymer

Description description	msrRNA
Molecular weight formula_weight	20813.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	H

ACUCUUUAGCGUUGGACGGUUACGUCUAGUCGGGUGAUUAGCCAGACUCUAACUUAUUGAACGUA

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli BL21(DE3)

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	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

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

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	2.60 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	291980

cryoEM structure of retron-Eco7 complex (form II)

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

Retron Ec78 reverse transcriptase

State in the Current Structure

Other States of the Same Protein in the Database

Retron Ec78 probable ATPase

State in the Current Structure

Other States of the Same Protein in the Database

Retron Ec78 putative HNH endonuclease

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

9vhl__assembly_1__model_1

9vhl__assembly_1__model_1 | I(q)

9vhl__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (7)

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

7. Citations (1)

cryoEM structure of retron-Eco7 complex (form II)

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

Retron Ec78 reverse transcriptase

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 Ec78 probable 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 Ec78 putative HNH endonuclease

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

9vhl__assembly_1__model_1

9vhl__assembly_1__model_1 | I(q)

9vhl__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (7)

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

7. Citations (1)