SAXSdb — 8e5p

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

Transcription termination factor Rho

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	Protein–RNA Homooligomer Protein × 6 RNA 1 PDB declaration: heptameric（7） Consistent with all polymer counts	Chain a； UniProt 25–443 Chain b； UniProt 25–443 Chain c； UniProt 25–443 Chain d； UniProt 25–443 Chain e； UniProt 25–443 Chain f； UniProt 25–443	Not recorded	RNA with 24 nt long spacer × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 6 MG MAGNESIUM ION × 6 BEF BERYLLIUM TRIFLUORIDE ION × 6	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.9 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 4.40 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 8E5P	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6Z9Q Transcription termination intermediate complex 2 Deposited 2020-06-04	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric	Chain a 25–443（419 aa） Chain b 25–443（419 aa） Chain c 25–443（419 aa） Chain d 25–443（419 aa） Chain e 25–443（419 aa） Chain f 25–443（419 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 5 MG MAGNESIUM ION × 6 BEF BERYLLIUM TRIFLUORIDE ION × 5 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.70 Å
6Z9S Transcription termination intermediate complex 4 Deposited 2020-06-04	Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric	Chain a 25–443（419 aa） Chain b 25–443（419 aa） Chain c 25–443（419 aa） Chain d 25–443（419 aa） Chain e 25–443（419 aa） Chain f 25–443（419 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 5 MG MAGNESIUM ION × 6 BEF BERYLLIUM TRIFLUORIDE ION × 5 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.40 Å
7ADB Transcription termination intermediate complex 1 delta NusG Deposited 2020-09-14	Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric	Chain a 25–443（419 aa） Chain b 25–443（419 aa） Chain c 25–443（419 aa） Chain d 25–443（419 aa） Chain e 25–443（419 aa） Chain f 25–443（419 aa）	Not recorded	BEF BERYLLIUM TRIFLUORIDE ION × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 5 MG MAGNESIUM ION × 6 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.40 Å
7ADC Transcription termination intermediate complex 3 delta NusG Deposited 2020-09-14	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric	Chain a 25–443（419 aa） Chain b 25–443（419 aa） Chain c 25–443（419 aa） Chain d 25–443（419 aa） Chain e 25–443（419 aa） Chain f 25–443（419 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 5 MG MAGNESIUM ION × 6 BEF BERYLLIUM TRIFLUORIDE ION × 5 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å
7ADD Transcription termination intermediate complex IIIa Deposited 2020-09-14	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric	Chain a 25–443（419 aa） Chain b 25–443（419 aa） Chain c 25–443（419 aa） Chain d 25–443（419 aa） Chain e 25–443（419 aa） Chain f 25–443（419 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 5 MG MAGNESIUM ION × 6 BEF BERYLLIUM TRIFLUORIDE ION × 5 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.30 Å
7ADE Transcription termination complex IVa Deposited 2020-09-14	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric	Chain a 25–443（419 aa） Chain b 25–443（419 aa） Chain c 25–443（419 aa） Chain d 25–443（419 aa） Chain e 25–443（419 aa） Chain f 25–443（419 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 5 MG MAGNESIUM ION × 6 BEF BERYLLIUM TRIFLUORIDE ION × 5 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.20 Å
8E3H Escherichia coli Rho-dependent transcription pre-termination complex containing 18 nt long RNA spacer, Mg-ADP-BeF3, and NusG; Rho hexamer part Deposited 2022-08-17	Different structure-quality metrics	Assembly 1 Protein–RNA Homooligomer；Protein × 6 PDB declaration: heptameric	Chain a 25–443（419 aa） Chain b 25–443（419 aa） Chain c 25–443（419 aa） Chain d 25–443（419 aa） Chain e 25–443（419 aa） Chain f 25–443（419 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 6 MG MAGNESIUM ION × 6 BEF BERYLLIUM TRIFLUORIDE ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.50 Å
8E5L Escherichia coli Rho-dependent transcription pre-termination complex containing 21 nt long RNA spacer, Mg-ADP-BeF3, and NusG; Rho hexamer part Deposited 2022-08-22	Different structure-quality metrics	Assembly 1 Protein–RNA Homooligomer；Protein × 6 PDB declaration: heptameric	Chain a 25–443（419 aa） Chain b 25–443（419 aa） Chain c 25–443（419 aa） Chain d 25–443（419 aa） Chain e 25–443（419 aa） Chain f 25–443（419 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 6 MG MAGNESIUM ION × 6 BEF BERYLLIUM TRIFLUORIDE ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.20 Å
8E6W Escherichia coli Rho-dependent transcription pre-termination complex containing 18 nt long RNA spacer, lambda-tR1 rut RNA, Mg-ADP-BeF3, and NusG; Rho part Deposited 2022-08-23	Different structure-quality metrics	Assembly 1 Protein–RNA Homooligomer；Protein × 6 PDB declaration: heptameric	Chain a 25–443（419 aa） Chain b 25–443（419 aa） Chain c 25–443（419 aa） Chain d 25–443（419 aa） Chain e 25–443（419 aa） Chain f 25–443（419 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 6 MG MAGNESIUM ION × 6 BEF BERYLLIUM TRIFLUORIDE ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.27 Å
8E70 Escherichia coli Rho-dependent transcription pre-termination complex containing 18 nt long RNA spacer, dC75 rut mimic RNA, Mg-ADP-BeF3, and NusG; Rho hexamer part Deposited 2022-08-23	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 6 PDB declaration: heptameric	Chain a 25–443（419 aa） Chain b 25–443（419 aa） Chain c 25–443（419 aa） Chain d 25–443（419 aa） Chain e 25–443（419 aa） Chain f 25–443（419 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 6 MG MAGNESIUM ION × 6 BEF BERYLLIUM TRIFLUORIDE ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.10 Å
8PEU Rho-ATPgS-Psu complex III Deposited 2023-06-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 24 PDB declaration: 24-meric	Chain A 25–443（419 aa） Chain B 25–443（419 aa） Chain C 25–443（419 aa） Chain D 25–443（419 aa） Chain E 25–443（419 aa） Chain F 25–443（419 aa） Chain I 25–443（419 aa） Chain J 25–443（419 aa） Chain K 25–443（419 aa） Chain L 25–443（419 aa） Chain M 25–443（419 aa） Chain N 25–443（419 aa）	Not recorded	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 10 MG MAGNESIUM ION × 10	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 3.70 Å
8PEW Rho-ATPgS-Psu complex III expanded Deposited 2023-06-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 34 PDB declaration: 34-meric	Chain A 25–443（419 aa） Chain B 25–443（419 aa） Chain C 25–443（419 aa） Chain D 25–443（419 aa） Chain E 25–443（419 aa） Chain F 25–443（419 aa） Chain G 25–443（419 aa） Chain H 25–443（419 aa） Chain I 25–443（419 aa） Chain J 25–443（419 aa） Chain K 25–443（419 aa） Chain L 25–443（419 aa） Chain M 25–443（419 aa） Chain N 25–443（419 aa） Chain O 25–443（419 aa） Chain P 25–443（419 aa） Chain X 25–443（419 aa） Chain Y 25–443（419 aa）	Not recorded	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 16 MG MAGNESIUM ION × 16	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 4.30 Å
8Q3N Bacterial transcription termination factor Rho + ADP Deposited 2023-08-04	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 25–443（419 aa） Chain B 25–443（419 aa） Chain C 25–443（419 aa） Chain D 25–443（419 aa） Chain E 25–443（419 aa） Chain F 25–443（419 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 6 MG MAGNESIUM ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.63 Å
8Q3O Bacterial transcription termination factor Rho + pppGpp Deposited 2023-08-04	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 25–443（419 aa） Chain B 25–443（419 aa） Chain C 25–443（419 aa） Chain D 25–443（419 aa） Chain E 25–443（419 aa） Chain F 25–443（419 aa）	Not recorded	0O2 guanosine 5'-(tetrahydrogen triphosphate) 3'-(trihydrogen diphosphate) × 4 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å

14 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A0A0GPI6_ECOLX
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain a； PDBConstruct 1–419； UniProt 25–443 Author chain b； PDBConstruct 1–419； UniProt 25–443 Author chain c； PDBConstruct 1–419； UniProt 25–443 Author chain d； PDBConstruct 1–419； UniProt 25–443 Author chain e； PDBConstruct 1–419； UniProt 25–443 Author chain f； PDBConstruct 1–419； UniProt 25–443

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	8e5p
Deposition date deposition_date	2022-08-22
Structure title title	Escherichia coli Rho-dependent transcription pre-termination complex containing 24 nt long RNA spacer, Mg-ADP-BeF3, and NusG; Rho hexamer part
Keywords keywords	;factor-dependent termination, Rho, transcription termination, transcription elongation complex, helicase, ATPase, TRANSCRIPTION-RNA complex ;; TRANSCRIPTION/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	44.93 Å
Radius of gyration Rg (electron density) rg_electron	44.44 Å
Forward intensity I(0) i0	1220050000.00
Molecular weight molecular_weight	286090.0 kDa
Excluded volume excluded_volume	357160 Å³
Envelope volume envelope_volume	508210 Å³
Hydration-shell volume shell_volume	89678 Å³
Envelope diameter envelope_diameter	141.1 Å
Shell Rg shell_rg	53.77 Å
Envelope Rg envelope_rg	44.23 Å
Shape Rg shape_rg	44.44 Å
Total Rg total_rg	44.81 Å
Total atoms total_atoms	20038
Residues n_residues	2510
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	141.6 Å
Rg (real space) rg_real	44.70 Å
Rg uncertainty (real space) rg_real_error	0.91 Å
I(0) (real space) i0_real	1.2200e+09
I(0) uncertainty (real space) i0_real_error	1.9920e+07
Rg (reciprocal space) rg_reciprocal	44.93 Å
I(0) (reciprocal space) i0_reciprocal	1220000000.0000
Solution quality estimate total_estimate	0.9011
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	52.6 Å
Skewness Skewness skewness	0.141
Kurtosis Kurtosis kurtosis	-0.588
Angular range angular_range	— – 0.1750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	135000000.0000
Real-space data points n_real_points	36
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.927; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.940

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	RNA with 24 nt long spacer
Molecular weight formula_weight	12912.3 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	7
Atom count atom_count	20038

AUGUUUUUUUUUUUUUUUUUUUUUUUUGAUUUGGUGAGAGG

Entity 2 Entity 2 polymer

Description description	Transcription termination factor Rho
Molecular weight formula_weight	47070.2 kDa
EC 编号 ec_number	3.6.4.-
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	e,f,c,b,a,d

MNLTELKNTPVSELITLGENMGLENLARMRKQDIIFAILKQHAKSGEDIFGDGVLEILQDGFGFLRSADSSYLAGPDDIYVSPSQIRRFNLRTGDTISGKIRPPKEGERYFALLKVNEVNFDKPENARNKILFENLTPLHANSRLRMERGNGSTEDLTARVLDLASPIGRGQRGLIVAPPKAGKTMLLQNIAQSIAYNHPDCVLMVLLIDERPEEVTEMQRLVKGEVVASTFDEPASRHVQVAEMVIEKAKRLVEHKKDVIILLDSITRLARAYNTVVPASGKVLTGGVDANALHRPKRFFGAARNVEEGGSLTIIATALIDTGSKMDEVIYEEFKGTGNMELHLSRKIAEKRVFPAIDYNRSGTRKEELLTTQEELQKMWILRKIIHPMGEIDAMEFLINKLAMTKTNDDFFEMMKRS

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 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 5 Entity 5 non-polymer

Description description	BERYLLIUM TRIFLUORIDE ION
Molecular weight formula_weight	66.0 kDa
Source method src_method	syn
Copy count entity_count	6

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8. Citations (2)

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Resolution resolution	4.40 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	270373

fit	/app/data/saxs_computation/e5/8e5p/8e5p.fit
pddf	/app/data/pr_computation/e5/8e5p/8e5p.pr.out
profile	/app/data/saxs_computation/e5/8e5p/8e5p.dat

Escherichia coli Rho-dependent transcription pre-termination complex containing 24 nt long RNA spacer, Mg-ADP-BeF3, and NusG; Rho hexamer part

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

Transcription termination factor Rho

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)