SAXSdb — 8ubb

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

Reverse transcriptase

Bordetella phage BPP-1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 6 RNA 3	Avd × 5 （Q775D7,Q9FA38） Diversity-generating retroelement (DGR) RNA avd × 1 Diversity-generating retroelement (DGR) RNA TR × 1 Diversity-generating retroelement (DGR) RNA Sp × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q775D8_BPBPP
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–328； UniProt 1–328

Avd

Methylorubrum extorquens

UniProt Q775D7

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 6 RNA 3	Reverse transcriptase × 1 （Q775D8） Diversity-generating retroelement (DGR) RNA avd × 1 Diversity-generating retroelement (DGR) RNA TR × 1 Diversity-generating retroelement (DGR) RNA Sp × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q775D7_BPBPP
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–124； UniProt 1–124 Author chain C； PDBConstruct 1–124； UniProt 1–124 Author chain D； PDBConstruct 1–124； UniProt 1–124 Author chain E； PDBConstruct 1–124； UniProt 1–124 Author chain F； PDBConstruct 1–124； UniProt 1–124

Avd

Methylorubrum extorquens

UniProt Q9FA38

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 6 RNA 3	Reverse transcriptase × 1 （Q775D8） Diversity-generating retroelement (DGR) RNA avd × 1 Diversity-generating retroelement (DGR) RNA TR × 1 Diversity-generating retroelement (DGR) RNA Sp × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	FAE_METEA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 125–290； UniProt 5–170 Author chain C； PDBConstruct 125–290； UniProt 5–170 Author chain D； PDBConstruct 125–290； UniProt 5–170 Author chain E； PDBConstruct 125–290； UniProt 5–170 Author chain F； PDBConstruct 125–290； UniProt 5–170

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	8ubb
Deposition date deposition_date	2023-09-22
Structure title title	Diversity-generating retroelement (DGR) ribonucleoprotein reverse transcriptase - Active State (N-empty) 1b
Keywords keywords	Reverse transcriptase, Ribonucleoprotein, RNA BINDING PROTEIN, RNA BINDING PROTEIN-RNA complex; RNA BINDING PROTEIN/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.

8ubb__assembly_1__model_1

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

Download this curve (.dat)

8ubb__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8ubb__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	39.34 Å
Rg (electron density)	38.09 Å
Total Rg	38.52 Å
Atom count	10349
Residues	1039
Excluded volume	174200 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8ubb__assembly_1__model_1`	nonameric （9）	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 (5)

Entity 1 Entity 1 polymer

Description description	Reverse transcriptase
Molecular weight formula_weight	38099.8 kDa
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	10349

MGKRHRNLIDQITTWENLLDAYRKTSHGKRRTWGYLEFKEYDLANLLALQAELKAGNYERGPYREFLVYEPKPRLISALEFKDRLVQHALCNIVAPIFEAGLLPYTYACRPDKGTHAGVCHVQAELRRTRATHFLKSDFSKFFPSIDRAALYAMIDKKIHCAATRRLLRVVLPDEGVGIPIGSLTSQLFANVYGGAVDRLLHDELKQRHWARYMDDIVVLGDDPEELRAVFYRLRDFASERLGLKISHWQVAPVSRGINFLGYRIWPTHKLLRKSSVKRAKRKVANFIKHGEDESLQRFLASWSGHAQWADTHNLFTWMEEQYGIACH

Source Source

Source organism organism	Bordetella phage BPP-1
NCBI taxonomy ID ncbi_taxonomy_id	2885909
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Avd
Molecular weight formula_weight	31753.6 kDa
Source method src_method	man
Copy count entity_count	5

Polymer Polymer

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

MEPIEEATKCYDQMLIVERYERVISYLYPIAQSIPRKHGVAREMFLKCLLGQVELFIVAGKSNQVSKLYAADAGLAMLRFWLRFLAGIQKPHAMTPHQVETAQVLIAEVGRILGSWIARVNRKGTKVQVGEALVGDGNEVAHIDLIIGPRGSPAETAFCNGLVNNKHGFTSLLAVIAPNLPCKPNTLMFNKVTINDARQAVQMFGPAQHGVAMAVQDAVAEGIIPADEADDLYVLVGVFIHWEAADDAKIQKYNYEATKLSIQRAVNGEPKASVVTEQRKSATHPFAANA

Source Source

Source organism organism	Methylorubrum extorquens
NCBI taxonomy ID ncbi_taxonomy_id	272630
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Diversity-generating retroelement (DGR) RNA avd
Molecular weight formula_weight	6259.8 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	G

GGGGCAGGCUGGGAAAUAA

Entity 4 Entity 4 polymer

Description description	Diversity-generating retroelement (DGR) RNA TR
Molecular weight formula_weight	11383.7 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	H

CGCUGCUGCGCGGCGUCUAUGCCCAUCACCUUCUUG

Entity 5 Entity 5 polymer

Description description	Diversity-generating retroelement (DGR) RNA Sp
Molecular weight formula_weight	45041.7 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	I

CAUGGCUCUGCCAACGCUACGGCUUGGCGGGCUGGCCUUUCCUCAAUAGGUGGUCAGCCGGUUCUGUCCUGCUUCGGCGAACACGUUACACGGUUCGGCAAAACGUCGAUUACUGAAAAUGGAAAGGCGGGGCCGACUUC

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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	3.23 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	127422

Diversity-generating retroelement (DGR) ribonucleoprotein reverse transcriptase - Active State (N-empty) 1b

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

Reverse transcriptase

State in the Current Structure

Other States of the Same Protein in the Database

Avd

State in the Current Structure

Other States of the Same Protein in the Database

Avd

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

8ubb__assembly_1__model_1

8ubb__assembly_1__model_1 | I(q)

8ubb__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 (5)

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

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

7. Citations (1)

Diversity-generating retroelement (DGR) ribonucleoprotein reverse transcriptase - Active State (N-empty) 1b

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

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

Avd

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Avd

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

8ubb__assembly_1__model_1

8ubb__assembly_1__model_1 | I(q)

8ubb__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 (5)

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

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

7. Citations (1)