SAXSdb — 9nnh

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

Retron I-A effector PtuA

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 8 DNA 2 RNA 2	Retron I-A effector PtuB × 2 （P0DV92） Retron I-A Ec78 reverse transcriptase × 2 （A0AB38GW94） DNA (73-MER) × 2 RNA (41-MER) × 2 ADENOSINE-5'-DIPHOSPHATE × 3	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	1
Chains and sequence ranges	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 Author chain F； PDBConstruct 1–550； UniProt 1–550

Retron I-A effector PtuB

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 8 DNA 2 RNA 2	Retron I-A effector PtuA × 4 （P0DV91） Retron I-A Ec78 reverse transcriptase × 2 （A0AB38GW94） DNA (73-MER) × 2 RNA (41-MER) × 2 ADENOSINE-5'-DIPHOSPHATE × 3	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	2
Chains and sequence ranges	Author chain J； PDBConstruct 1–216； UniProt 1–216 Author chain K； PDBConstruct 1–216； UniProt 1–216

Retron I-A Ec78 reverse transcriptase

Escherichia coli

UniProt A0AB38GW94

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 8 DNA 2 RNA 2	Retron I-A effector PtuA × 4 （P0DV91） Retron I-A effector PtuB × 2 （P0DV92） DNA (73-MER) × 2 RNA (41-MER) × 2 ADENOSINE-5'-DIPHOSPHATE × 3	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0AB38GW94_ECOLX
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 1–311； UniProt 1–311 Author chain B； PDBConstruct 1–311； UniProt 1–311

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	9nnh
Deposition date deposition_date	2025-03-05
Structure title title	Cryo-EM structure of the Retron Ec78 complex, PtuA:PtuB:RT (4:2:2)
Keywords keywords	Retron; ncRNA; msDNA, DNA-RNA HYBRID; DNA-RNA HYBRID
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.

9nnh__assembly_1__model_1

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

Download this curve (.dat)

9nnh__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9nnh__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	54.95 Å
Rg (electron density)	54.77 Å
Total Rg	54.91 Å
Atom count	29478
Residues	3407
Excluded volume	512370 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9nnh__assembly_1__model_1`	dodecameric （12）	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	Retron I-A effector PtuA
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	C,D,E,F
Atom count atom_count	29478

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 I-A effector PtuB
Molecular weight formula_weight	26879.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	J,K

MRELARLERPEILDQYIAGQNDWMEIDQSAVWPKLTEMQGGFCAYCECRLNRCHIEHFRPRGKFPALTFIWNNLFGSCGDSRKSGGWSRCGIYKDNGAGAYNADDLIKPDEENPDDYLLFLTTGEVVPAIGLTGRALKKAQETIRVFNLNGDIKLFGSRRTAVQAIMPNVEYLYTLLEEFDEDDWNEMLRDELEKIESDEYKTALKHAWTFNQEFALEVLFQGPEAHHHHHH

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	Retron I-A Ec78 reverse transcriptase
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	B,A

MSVIRGLAAVLRQSDSDISAFLVTAPRKYKVYKIPKRTTGFRVIAQPAKGLKDIQRAFVQLYSLPVHDASMAYMKGKGIRDNAAAHAGNQYLLKADLEDFFNSITPAIFWRCIEMSSAQTPQFEPQDKLFIEKILFWQPIKRRKTKLILSVGAPSSPVISNFCMYEFDNRIHAACKKVEITYTRYADDLTFSSNIPDVLKAVPSTLEVLLKDLFGSALRLNHSKTVFSSKAHNRHVTGITINNEETLSLGRDRKRFIKHLINQYKYGLLDNEDKAYLIGLLAFASHIEPSFITRMNEKYSLELMERLRGQR

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

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	N,M

TTGAGGAAGCGAAAGTGTCGCAACCCGAGAGAGGAACGATCTCGGGTTGCGACACTTTCGCAACCCTTAATACGTTCA

Entity 5 Entity 5 polymer

Description description	RNA (41-MER)
Molecular weight formula_weight	21425.6 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	L,X

ACUCUUUAGCGUUGGACGGUUACGUCUAGUCGGGUGAUUAGCCAGACUCUAACUUAUUGAACGUAUU

Entity 6 Entity 6 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	3

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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	triclinic

Resolution resolution	2.69 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	301183

Cryo-EM structure of the Retron Ec78 complex, PtuA:PtuB:RT (4:2:2)

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

Retron I-A effector PtuA

State in the Current Structure

Other States of the Same Protein in the Database

Retron I-A effector PtuB

State in the Current Structure

Other States of the Same Protein in the Database

Retron I-A Ec78 reverse transcriptase

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

9nnh__assembly_1__model_1

9nnh__assembly_1__model_1 | I(q)

9nnh__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

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

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 non-polymer

7. Citations (1)

Cryo-EM structure of the Retron Ec78 complex, PtuA:PtuB:RT (4:2:2)

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

Retron I-A effector PtuA

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 I-A effector PtuB

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 I-A 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9nnh__assembly_1__model_1

9nnh__assembly_1__model_1 | I(q)

9nnh__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

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

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 non-polymer

7. Citations (1)