1pvo

X-ray crystal structure of Rho transcription termination factor in complex with ssRNA substrate and ANPPNP

Method: X-RAY DIFFRACTION D_max: 148.3 Å Quality: REASONABLE

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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 5 PDB declaration: undecameric（11） Consistent with all polymer counts	Chain A； UniProt 1–419 Chain B； UniProt 1–419 Chain C； UniProt 1–419 Chain D； UniProt 1–419 Chain E； UniProt 1–419 Chain F； UniProt 1–419	Not recorded	5'-R(PUPC)-3' × 5 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 6	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；0.05 M Cacodylate (pH 6.5), 0.05 M NaCl, 2.5% PEG 8K, 20% glycerol, 0.3 mM n-Nonyl-beta-D-thiomaltoside, 1mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 18K	Resolution 3.00 Å R-free 0.304

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 1PVO	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1PV4 X-ray crystal structure of the Rho transcription termination factor in complex with single stranded DNA Deposited 2003-06-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 6 PDB declaration: undecameric	Chain A 1–419（419 aa） Fragment：bacterial transcription termination Chain B 1–419（419 aa） Fragment：bacterial transcription termination Chain C 1–419（419 aa） Fragment：bacterial transcription termination Chain D 1–419（419 aa） Fragment：bacterial transcription termination Chain E 1–419（419 aa） Fragment：bacterial transcription termination Chain F 1–419（419 aa） Fragment：bacterial transcription termination	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；0.05M Nacacodylate (pH 6.5), 0.05M NaCl, 2.5% PEG 8K, 20% glycerol, 0.3mM n-Nonyl-beta-D-thiomaltoside, 1mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 18K	Resolution 3.00 Å R-free 0.296
2HT1 The closed ring structure of the Rho transcription termination factor in complex with nucleic acid in the motor domains Deposited 2006-07-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Homooligomer；Protein × 6 PDB declaration: pentadecameric	Chain A 1–411（411 aa） Chain B 1–411（411 aa）	Not recorded	SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions Microbatch under paraffine oil；pH 6.5；291 K；50 mM Na cacodylate, 10 mM MgOAc, 1.8 M LiSO4, 2% benzamidine, 10 mM spermine-HCl, pH 6.5, Microbatch under paraffine oil, temperature 291K	Resolution 3.51 Å R-free 0.328
3ICE Rho transcription termination factor bound to RNA and ADP-BeF3 Deposited 2009-07-17	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Homooligomer；Protein × 6 PDB declaration: heptameric	Chain A 1–419（419 aa） Chain B 1–419（419 aa） Chain C 1–419（419 aa） Chain D 1–419（419 aa） Chain E 1–419（419 aa） Chain F 1–419（419 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	ADP ADENOSINE-5'-DIPHOSPHATE × 6 MG MAGNESIUM ION × 6 BEF BERYLLIUM TRIFLUORIDE ION × 6 SPD SPERMIDINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.9；291 K；2.5% MPD, 50mM HEPES, 5mM Tris-HCL, 160mM sodium chloride, 1.25mM magnesium chloride, 5mM spermidine-HCL, 0.5mM TCEP, 1.25mM ADP-BeF3,, pH 7.9, MICROBATCH, temperature 291K	Resolution 2.80 Å R-free 0.295
6WA8 Crystal structure of the E. coli transcription termination factor Rho Deposited 2020-03-24	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 1–419（419 aa） Chain B 1–419（419 aa） Chain C 1–419（419 aa） Chain D 1–419（419 aa） Chain E 1–419（419 aa） Chain F 1–419（419 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；293 K；100 mM NaCl, 100 mM Tris pH 8.3, 28% PEG2000MME, 20 mM ATP, pH 7.5	Resolution 3.30 Å R-free 0.296
6XAS CryoEM Structure of E. coli Rho-dependent Transcription Pre-termination Complex Deposited 2020-06-04	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric	Chain A 1–419（419 aa） Chain B 1–419（419 aa） Chain C 1–419（419 aa） Chain D 1–419（419 aa） Chain E 1–419（419 aa） Chain F 1–419（419 aa）	Not recorded	MG MAGNESIUM ION × 1 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
6XAV CryoEM Structure of E. coli Rho-dependent Transcription Pre-termination Complex bound with NusG Deposited 2020-06-04	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric	Chain A 1–419（419 aa） Chain B 1–419（419 aa） Chain C 1–419（419 aa） Chain D 1–419（419 aa） Chain E 1–419（419 aa） Chain F 1–419（419 aa）	Not recorded	MG MAGNESIUM ION × 1 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.70 Å
6Z9P Transcription termination intermediate complex 1 Deposited 2020-06-04	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric	Chain a 1–419（419 aa） Chain b 1–419（419 aa） Chain c 1–419（419 aa） Chain d 1–419（419 aa） Chain e 1–419（419 aa） Chain f 1–419（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 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
6Z9R Transcription termination intermediate complex 3 Deposited 2020-06-04	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric	Chain a 1–419（419 aa） Chain b 1–419（419 aa） Chain c 1–419（419 aa） Chain d 1–419（419 aa） Chain e 1–419（419 aa） Chain f 1–419（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 4.10 Å
6Z9T Transcription termination intermediate complex 5 Deposited 2020-06-04	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric	Chain a 1–419（419 aa） Chain b 1–419（419 aa） Chain c 1–419（419 aa） Chain d 1–419（419 aa） Chain e 1–419（419 aa） Chain f 1–419（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 4.10 Å
8PEX Rho P167L-ATPgS-Psu complex II Deposited 2023-06-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 22 PDB declaration: 22-meric	Chain A 1–419（419 aa） Chain B 1–419（419 aa） Chain C 1–419（419 aa） Chain D 1–419（419 aa） Chain E 1–419（419 aa） Chain F 1–419（419 aa） Chain I 1–419（419 aa） Chain J 1–419（419 aa） Chain K 1–419（419 aa） Chain L 1–419（419 aa） Chain M 1–419（419 aa） Chain N 1–419（419 aa）	Not recorded	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 12 MG MAGNESIUM ION × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 3.10 Å
8PEY Rho P167L-ATPgS-Psu complex II locked Deposited 2023-06-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 23 PDB declaration: 23-meric	Chain A 1–419（419 aa） Chain B 1–419（419 aa） Chain C 1–419（419 aa） Chain D 1–419（419 aa） Chain E 1–419（419 aa） Chain F 1–419（419 aa） Chain G 1–419（419 aa） Chain I 1–419（419 aa） Chain J 1–419（419 aa） Chain K 1–419（419 aa） Chain L 1–419（419 aa） Chain M 1–419（419 aa） Chain N 1–419（419 aa）	Not recorded	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 12 MG MAGNESIUM ION × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 3.00 Å
8PTG Structure of the transcription termination factor Rho bound to RNA at the PBS and SBS Deposited 2023-07-14	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Homooligomer；Protein × 6 PDB declaration: heptameric	Chain A 1–419（419 aa） Chain B 1–419（419 aa） Chain C 1–419（419 aa） Chain D 1–419（419 aa） Chain E 1–419（419 aa） Chain F 1–419（419 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 6 MG MAGNESIUM ION × 6 BEF BERYLLIUM TRIFLUORIDE ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 2.90 Å
8PTM Structure of the transcription termination factor Rho in complex with Rof and ADP Deposited 2023-07-14	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: 11-meric	Chain A 1–419（419 aa） Chain B 1–419（419 aa） Chain C 1–419（419 aa） Chain D 1–419（419 aa） Chain E 1–419（419 aa） Chain F 1–419（419 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 3 MG MAGNESIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 2.90 Å
8PTN Structure of the transcription termination factor Rho in complex with Rof Deposited 2023-07-14	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric	Chain A 1–419（419 aa） Chain B 1–419（419 aa） Chain C 1–419（419 aa） Chain D 1–419（419 aa） Chain E 1–419（419 aa） Chain F 1–419（419 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 3.30 Å
8PTO Structure of Rho pentamer in complex with Rof and ADP Deposited 2023-07-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain A 1–419（419 aa） Chain B 1–419（419 aa） Chain C 1–419（419 aa） Chain D 1–419（419 aa） Chain E 1–419（419 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 2.70 Å
8PTP Structure of Rho pentamer in complex with Rof Deposited 2023-07-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain A 1–419（419 aa） Chain B 1–419（419 aa） Chain C 1–419（419 aa） Chain D 1–419（419 aa） Chain E 1–419（419 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 3.00 Å
8Q3P Bacterial transcription termination factor Rho G150D mutant bound to ADP; C-terminal 8xHis-tag Deposited 2023-08-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 18 PDB declaration: 18-meric	Chain a 1–419（419 aa） Chain b 1–419（419 aa） Chain c 1–419（419 aa） Chain d 1–419（419 aa） Chain e 1–419（419 aa） Chain f 1–419（419 aa） Chain g 1–419（419 aa） Chain h 1–419（419 aa） Chain i 1–419（419 aa） Chain j 1–419（419 aa） Chain k 1–419（419 aa） Chain l 1–419（419 aa） Chain m 1–419（419 aa） Chain n 1–419（419 aa） Chain o 1–419（419 aa） Chain p 1–419（419 aa） Chain q 1–419（419 aa） Chain r 1–419（419 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 18 MG MAGNESIUM ION × 18	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
8Q3Q Bacterial transcription termination factor Rho G152D mutant bound to ADP; C-terminal 8xHis-tag Deposited 2023-08-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 18 PDB declaration: 18-meric	Chain a 1–419（419 aa） Chain b 1–419（419 aa） Chain c 1–419（419 aa） Chain d 1–419（419 aa） Chain e 1–419（419 aa） Chain f 1–419（419 aa） Chain g 1–419（419 aa） Chain h 1–419（419 aa） Chain i 1–419（419 aa） Chain j 1–419（419 aa） Chain k 1–419（419 aa） Chain l 1–419（419 aa） Chain m 1–419（419 aa） Chain n 1–419（419 aa） Chain o 1–419（419 aa） Chain p 1–419（419 aa） Chain q 1–419（419 aa） Chain r 1–419（419 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 18 MG MAGNESIUM ION × 18	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
8W8D Structural mechanism of inhibition of the Rho transcription termination factor by Rof Deposited 2023-09-01	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: 12-meric	Chain A 1–419（419 aa） Chain B 1–419（419 aa） Chain C 1–419（419 aa） Chain D 1–419（419 aa） Chain E 1–419（419 aa） Chain F 1–419（419 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
9GCS Rho-ATP-Psu complex II Deposited 2024-08-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 22 PDB declaration: 22-meric	Chain B 1–419（419 aa） Chain C 1–419（419 aa） Chain D 1–419（419 aa） Chain E 1–419（419 aa） Chain F 1–419（419 aa） Chain G 1–419（419 aa） Chain J 1–419（419 aa） Chain K 1–419（419 aa） Chain L 1–419（419 aa） Chain M 1–419（419 aa） Chain N 1–419（419 aa） Chain O 1–419（419 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 12 MG MAGNESIUM ION × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
9GCT Rho-ATP-Psu complex II expanded Deposited 2024-08-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric	Chain A 1–419（419 aa） Chain B 1–419（419 aa） Chain C 1–419（419 aa） Chain D 1–419（419 aa） Chain E 1–419（419 aa） Chain F 1–419（419 aa） Chain G 1–419（419 aa） Chain H 1–419（419 aa） Chain J 1–419（419 aa） Chain K 1–419（419 aa） Chain L 1–419（419 aa） Chain M 1–419（419 aa） Chain N 1–419（419 aa） Chain O 1–419（419 aa） Chain P 1–419（419 aa） Chain Y 1–419（419 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 15 MG MAGNESIUM ION × 15	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
9GCU Rho-P167L-ATP gamma S Deposited 2024-08-02	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–419（419 aa） Chain B 1–419（419 aa） Chain C 1–419（419 aa） Chain D 1–419（419 aa） Chain E 1–419（419 aa） Chain F 1–419（419 aa）	Not recorded	MG MAGNESIUM ION × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å

22 other PDB entries and 22 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RHO_ECOLI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–419； UniProt 1–419 Author chain B； PDBConstruct 1–419； UniProt 1–419 Author chain C； PDBConstruct 1–419； UniProt 1–419 Author chain D； PDBConstruct 1–419； UniProt 1–419 Author chain E； PDBConstruct 1–419； UniProt 1–419 Author chain F； PDBConstruct 1–419； UniProt 1–419

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1pvo
Deposition date deposition_date	2003-06-27
Structure title title	X-ray crystal structure of Rho transcription termination factor in complex with ssRNA substrate and ANPPNP
Keywords keywords	Rho-ANPPNP-ssRNA complex, TRANSCRIPTION-RNA COMPLEX; TRANSCRIPTION/RNA
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	46.67 Å
Radius of gyration Rg (electron density) rg_electron	46.09 Å
Forward intensity I(0) i0	1116730000.00
Molecular weight molecular_weight	274650.0 kDa
Excluded volume excluded_volume	343090 Å³
Envelope volume envelope_volume	491030 Å³
Hydration-shell volume shell_volume	84385 Å³
Envelope diameter envelope_diameter	151.9 Å
Shell Rg shell_rg	55.03 Å
Envelope Rg envelope_rg	45.20 Å
Shape Rg shape_rg	46.09 Å
Total Rg total_rg	46.43 Å
Total atoms total_atoms	19232
Residues n_residues	2407
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	148.3 Å
Rg (real space) rg_real	46.39 Å
Rg uncertainty (real space) rg_real_error	0.87 Å
I(0) (real space) i0_real	1.1170e+09
I(0) uncertainty (real space) i0_real_error	1.8720e+07
Rg (reciprocal space) rg_reciprocal	46.67 Å
I(0) (reciprocal space) i0_reciprocal	1117000000.0000
Solution quality estimate total_estimate	0.6912
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	65.4 Å
Skewness Skewness skewness	0.056
Kurtosis Kurtosis kurtosis	-0.616
Angular range angular_range	— – 0.1700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	146500000.0000
Real-space data points n_real_points	35
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.910; Stabil: 1.000; Sysdev: 0.115; Positv: 1.000; Valcen: 0.980; Smooth: 0.927

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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	5'-R(PUPC)-3'
Molecular weight formula_weight	566.4 kDa
Source method src_method	syn
Copy count entity_count	5

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	G,H,J,K,L
Atom count atom_count	19246

Entity 2 Entity 2 polymer

Description description	Transcription termination factor rho
Molecular weight formula_weight	47070.2 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

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

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	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Molecular weight formula_weight	506.2 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	14

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7. Fold Classification (SCOP + CATH) 29 domains

SCOP 2.08 (17 domains)

Domain ID domain_id	d1pvoa1
Class class	a — All alpha proteins
Fold Fold fold	a.140 — LEM/SAP HeH motif
Superfamily Superfamily superfamily	a.140.3 — Rho N-terminal domain-like
Family Family family	a.140.3.1 — Rho termination factor, N-terminal domain

Domain ID domain_id	d1pvoa2
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
Family Family family	b.40.4.5 — Cold shock DNA-binding domain-like

Domain ID domain_id	d1pvoa3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.11 — RecA protein-like (ATPase-domain)

Domain ID domain_id	d1pvob1
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
Family Family family	b.40.4.5 — Cold shock DNA-binding domain-like

Domain ID domain_id	d1pvob2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.11 — RecA protein-like (ATPase-domain)

Domain ID domain_id	d1pvoc1
Class class	a — All alpha proteins
Fold Fold fold	a.140 — LEM/SAP HeH motif
Superfamily Superfamily superfamily	a.140.3 — Rho N-terminal domain-like
Family Family family	a.140.3.1 — Rho termination factor, N-terminal domain

Domain ID domain_id	d1pvoc2
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
Family Family family	b.40.4.5 — Cold shock DNA-binding domain-like

Domain ID domain_id	d1pvoc3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.11 — RecA protein-like (ATPase-domain)

Domain ID domain_id	d1pvod1
Class class	a — All alpha proteins
Fold Fold fold	a.140 — LEM/SAP HeH motif
Superfamily Superfamily superfamily	a.140.3 — Rho N-terminal domain-like
Family Family family	a.140.3.1 — Rho termination factor, N-terminal domain

Domain ID domain_id	d1pvod2
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
Family Family family	b.40.4.5 — Cold shock DNA-binding domain-like

Domain ID domain_id	d1pvod3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.11 — RecA protein-like (ATPase-domain)

Domain ID domain_id	d1pvoe1
Class class	a — All alpha proteins
Fold Fold fold	a.140 — LEM/SAP HeH motif
Superfamily Superfamily superfamily	a.140.3 — Rho N-terminal domain-like
Family Family family	a.140.3.1 — Rho termination factor, N-terminal domain

Domain ID domain_id	d1pvoe2
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
Family Family family	b.40.4.5 — Cold shock DNA-binding domain-like

Domain ID domain_id	d1pvoe3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.11 — RecA protein-like (ATPase-domain)

Domain ID domain_id	d1pvof1
Class class	a — All alpha proteins
Fold Fold fold	a.140 — LEM/SAP HeH motif
Superfamily Superfamily superfamily	a.140.3 — Rho N-terminal domain-like
Family Family family	a.140.3.1 — Rho termination factor, N-terminal domain

Domain ID domain_id	d1pvof2
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
Family Family family	b.40.4.5 — Cold shock DNA-binding domain-like

Domain ID domain_id	d1pvof3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.11 — RecA protein-like (ATPase-domain)

CATH v4.4 (12 domains)

Domain ID domain_id	1pvoA01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

Domain ID domain_id	1pvoA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	1pvoB01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

Domain ID domain_id	1pvoB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	1pvoC01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

Domain ID domain_id	1pvoC02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	1pvoD01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

Domain ID domain_id	1pvoD02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	1pvoE01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

Domain ID domain_id	1pvoE02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	1pvoF01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

Domain ID domain_id	1pvoF02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

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8. Citations (1)

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Unit-cell length a length_a	119.249 Å
Unit-cell length b length_b	204.649 Å
Unit-cell length c length_c	147.788 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	96.54 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2738
R_work r_work	0.2708
R_free r_free	0.3037

fit	/app/data/saxs_computation/pv/1pvo/1pvo.fit
pddf	/app/data/pr_computation/pv/1pvo/1pvo.pr.out
profile	/app/data/saxs_computation/pv/1pvo/1pvo.dat

X-ray crystal structure of Rho transcription termination factor in complex with ssRNA substrate and ANPPNP

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

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (4)

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 water

7. Fold Classification (SCOP + CATH) 29 domains

SCOP 2.08 (17 domains)

CATH v4.4 (12 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)