SAXSdb — 9p4j

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

Retron Eco8 OLD nuclease

Escherichia coli

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Heteromer Protein × 8 DNA 4 RNA 4 PDB declaration: 16-meric（16） Consistent with all polymer counts	Chain A； UniProt 1–750 Chain B； UniProt 1–750 Chain C； UniProt 1–750 Chain D； UniProt 1–750	Not recorded	Retron Eco8 reverse transcriptase × 4 （P0DV59） msrRNA × 4 msdDNA × 4	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.68 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9P4J	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9LP9 The cryo-EM structure of retron Eco8 in a standby state Deposited 2025-01-24	Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: hexadecameric	Chain B 1–750（750 aa） Chain E 1–750（750 aa） Chain I 1–750（750 aa） Chain M 1–750（750 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
9LPA The cryo-EM structure of retron Eco8 in an active state Deposited 2025-01-24	Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: hexadecameric	Chain B 1–750（750 aa） Chain E 1–750（750 aa） Chain I 1–750（750 aa） Chain M 1–750（750 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
9P4K The structure of Retron Eco8-SSB complex Deposited 2025-06-17	Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: 16-meric	Chain A 1–750（750 aa） Chain B 1–750（750 aa） Chain C 1–750（750 aa） Chain D 1–750（750 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.07 Å
9X94 Apo Retron-Eco8 complex Deposited 2025-10-20	Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: 16-meric	Chain B 1–750（750 aa） Chain F 1–750（750 aa） Chain J 1–750（750 aa） Chain N 1–750（750 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.57 Å
9X9B Retron-Eco8 complex with ATP-Mg2+ Deposited 2025-10-20	Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: 16-meric	Chain B 1–750（750 aa） Chain F 1–750（750 aa） Chain J 1–750（750 aa） Chain N 1–750（750 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	OLD8_ECOLX
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–750； UniProt 1–750 Author chain B； PDBConstruct 1–750； UniProt 1–750 Author chain C； PDBConstruct 1–750； UniProt 1–750 Author chain D； PDBConstruct 1–750； UniProt 1–750

Retron Eco8 reverse transcriptase

Escherichia coli

UniProt P0DV59

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Heteromer Protein × 8 DNA 4 RNA 4 PDB declaration: 16-meric（16） Consistent with all polymer counts	Chain E； UniProt 2–374 Chain F； UniProt 2–374 Chain G； UniProt 2–374 Chain H； UniProt 2–374	Not recorded	Retron Eco8 OLD nuclease × 4 （P0DV58） msrRNA × 4 msdDNA × 4	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.68 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9P4J	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9LP9 The cryo-EM structure of retron Eco8 in a standby state Deposited 2025-01-24	Different construct Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: hexadecameric	Chain A 1–374（374 aa） Chain F 1–374（374 aa） Chain J 1–374（374 aa） Chain N 1–374（374 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
9LPA The cryo-EM structure of retron Eco8 in an active state Deposited 2025-01-24	Different construct Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: hexadecameric	Chain A 1–374（374 aa） Chain F 1–374（374 aa） Chain J 1–374（374 aa） Chain N 1–374（374 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
9P4K The structure of Retron Eco8-SSB complex Deposited 2025-06-17	Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: 16-meric	Chain E 2–374（373 aa） Chain F 2–374（373 aa） Chain G 2–374（373 aa） Chain H 2–374（373 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.07 Å
9X94 Apo Retron-Eco8 complex Deposited 2025-10-20	Different construct Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: 16-meric	Chain A 1–374（374 aa） Chain E 1–374（374 aa） Chain I 1–374（374 aa） Chain M 1–374（374 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.57 Å
9X9B Retron-Eco8 complex with ATP-Mg2+ Deposited 2025-10-20	Different construct Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 8 PDB declaration: 16-meric	Chain A 1–374（374 aa） Chain E 1–374（374 aa） Chain I 1–374（374 aa） Chain M 1–374（374 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RT8_ECOLX
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain E； PDBConstruct 1–373； UniProt 2–374 Author chain F； PDBConstruct 1–373； UniProt 2–374 Author chain G； PDBConstruct 1–373； UniProt 2–374 Author chain H； PDBConstruct 1–373； UniProt 2–374

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	9p4j
Deposition date deposition_date	2025-06-16
Structure title title	The structure of Retron Eco8 in Apo state
Keywords keywords	anti-phage, bacterial immunity, retron, DNA, RNA, reverse transcription, Transferase-Hydrolase-DNA-RNA complex; Transferase/Hydrolase/DNA/RNA
Experimental Method method	ELECTRON MICROSCOPY

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	65.66 Å
Radius of gyration Rg (electron density) rg_electron	62.85 Å
Forward intensity I(0) i0	8613140000.00
Molecular weight molecular_weight	681850.0 kDa
Excluded volume excluded_volume	810050 Å³
Envelope volume envelope_volume	1327800 Å³
Hydration-shell volume shell_volume	169280 Å³
Envelope diameter envelope_diameter	236.8 Å
Shell Rg shell_rg	68.66 Å
Envelope Rg envelope_rg	61.79 Å
Shape Rg shape_rg	62.73 Å
Total Rg total_rg	63.31 Å
Total atoms total_atoms	47375
Residues n_residues	4960
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	221.9 Å
Rg (real space) rg_real	65.39 Å
Rg uncertainty (real space) rg_real_error	2.27 Å
I(0) (real space) i0_real	8.6130e+09
I(0) uncertainty (real space) i0_real_error	1.7760e+08
Rg (reciprocal space) rg_reciprocal	65.85 Å
I(0) (reciprocal space) i0_reciprocal	8620000000.0000
Solution quality estimate total_estimate	0.8691
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	74.0 Å
Skewness Skewness skewness	0.246
Kurtosis Kurtosis kurtosis	-0.395
Angular range angular_range	— – 0.1200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	818900000.0000
Real-space data points n_real_points	25
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.830; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.970; Smooth: 0.834

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Retron Eco8 OLD nuclease
Molecular weight formula_weight	87373.8 kDa
EC 编号 ec_number	3.1.-.-
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	47375

MTIESIRVKNLLSFDDVILRDFRDINCIIGRNNVGKSNLLKVIRYFYAKLENKKVIPLDFHTNYNAVGEITFTFDTTRIKKIVTSRKNNGRFHKHIYNTLFKSSSVKLNFEELIARKNSTNKSFFSLTLTICKDDSVMWSVDDPKVRSLLATLYPFLYIETRHIDLYDWNPIWKLISNLNSFNFDDVDHDELVNFLDEKISSRKGDYKKYIDRVVSVIDTKPYTYKEKVINYIKVAIKGDSFVNAGEELFTQSDGTNSNKFLETLLHLLITLTRTEFISPIVYIDEPEVGLHPKLAESFVSNLNKIYSKFKKTSELSGPGRYKTPYPNIFYSTHSPSILKQTIKLFGKDQQVLHFSKKKDGSTRVNKINSTYSDERFLNIFSDNEARLFFSEYIVFVEGATELELFRNLSLLNLYPAFSLADIYDANEVILANINPGYSKASIPFVIIKDIDTLIDYSIKTEKFSLRPLFEKMIKELTKEFDYYDTGFGRVRKEIDLFSDIQSSTKKHMDSGLFFKRFSLHNLSSRINKVSRKLNRYFMTTTIEGALINEQSLPYFFNWIGDVILTQMTINNPNPDKFIEAMRRRYNIKSQVVPLFKSVFCIGLNHPVYSSAVDKQALRIKLSFLNYLKRKVYSDFNNEKEIVLALRLAFGGKTETQYTLDKLRKDGEAELFREKIKNYKNNELFFLEPQMTKTSGWVTTFLNYTIEKITSEESDDDRIRQKLSFIFPEIISIIEQASSSIEAEESSLTG

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Retron Eco8 reverse transcriptase
Molecular weight formula_weight	44213.1 kDa
EC 编号 ec_number	2.7.7.49
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

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

KTKKMILVDKVFYEKILSVESFKENIITQSAIPKISNKEVRLISSGSKIFYAINNTSPHSHVQLRLNRFFLSHIPLNSAAKAFVRGGSYLKYLEPHIYGSSYCRLDISSFFNNISFDDVKQSLSPYIKDEYLIGTEQKLIDAILNSVGYESPIRKDKGMIIPMGFRTSPAISNIVFRKMDLLIQDFCAKKGVIYSRYADDMLFSNPRESKLLMSDYFIDEISSLLSIMGFNINQSKYISREKEISINGYVIENKGGNGSIGTIRLSKSKLNTVLKVTHALAQNIPYKNICNKYIKVRLKEKNIKYESKKDEFEKKYYRDQLINYLGGYRSYLISLVKFHSEYKCVNSDFIIQINGILNDIQNHIQKIKKNRRLLEHHHHHH

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	msrRNA
Molecular weight formula_weight	25986.4 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	I,J,K,L

AAGCUUCUUCUUCGAUAGAAGCUGAGGAGUCCAGUUUGACUGGAUAAGGUGUUCGCCAUCUCUAGCCUCAGUAAAAACUAG

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	msdDNA
Molecular weight formula_weight	23126.8 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	M,N,O,P

CAAGACCAATCTTTACACTCTGTGAGTATTAAAGTTACCTATAGCGCCAAGTGCGCAAAGGATGAGCTAGTTTTT

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

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8. Citations (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	2.68 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	421879

fit	/app/data/saxs_computation/p4/9p4j/9p4j.fit
pddf	/app/data/pr_computation/p4/9p4j/9p4j.pr.out
profile	/app/data/saxs_computation/p4/9p4j/9p4j.dat

The structure of Retron Eco8 in Apo state

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

Retron Eco8 OLD nuclease

State in the Current Structure

Other States of the Same Protein in the Database

Retron Eco8 reverse transcriptase

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)