PDB-1pvo: X-ray crystal structure of Rho transcription termination factor i...

ID or keywords:

Entry

Database: PDB / ID: 1pvo

Title

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

Components

5'-R(P*UP*C)-3'
Transcription termination factor rho

Keywords

TRANSCRIPTION/RNA / Rho-ANPPNP-ssRNA complex / TRANSCRIPTION-RNA COMPLEX

Function / homology

Function and homology information

ATP-dependent activity, acting on RNA /

helicase activity / DNA-templated transcription termination /

Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement /

ATP hydrolysis activity /

RNA binding /

ATP binding /

membrane / identical protein binding /

cytosol
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3 Å

Authors

Skordalakes, E. / Berger, J.M.

Citation

Journal: Cell(Cambridge,Mass.) / Year: 2003
Title: Structure of the Rho transcription terminator: mechanism of mRNA recognition and helicase loading
Authors: Skordalakes, E. / Berger, J.M.

History

Deposition	Jun 27, 2003	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 22, 2003	Provider: repository / Type: Initial release
Revision 1.1	Apr 29, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.3	Jan 31, 2018	Group: Experimental preparation / Category: exptl_crystal_grow Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4	Aug 16, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	1pvo.cif.gz	469.6 KB	Display	PDBx/mmCIF format
PDB format	pdb1pvo.ent.gz	387.1 KB	Display	PDB format
PDBx/mmJSON format	1pvo.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pv/1pvo ftp://data.pdbj.org/pub/pdb/validation_reports/pv/1pvo	HTTPS FTP

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Related structure data

Related structure data	1pv4SC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1pv4-d 1xpu-d 6059 1xpo-d 9386 1xpr-d 6056 6062 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#219 - Mar 2018 Vacuolar ATPase similarity (2) #131 - Nov 2010 Inteins similarity (2) #72 - Dec 2005 ATP Synthase similarity (2) #108 - Dec 2008 Hsp90 similarity (1) #168 - Dec 2013 DNA Helicase similarity (1) #182 - Feb 2015 Insulin receptor similarity (1) #214 - Oct 2017 Chimeric Antigen Receptors similarity (1) #238 - Oct 2019 Ribonucleotide Reductase similarity (1) #43 - Jul 2003 Src Tyrosine Kinase similarity (1) #50 - Feb 2004 Glycolytic Enzymes similarity (1) #60 - Dec 2004 Ubiquitin similarity (1) #73 - Jan 2006 Topoisomerase similarity (1) #80 - Aug 2006 AAA+ Proteases similarity (1) #95 - Nov 2007 Multidrug Resistance Transporters similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#219 - Mar 2018
Vacuolar ATPase
similarity (2)
#131 - Nov 2010
Inteins
similarity (2)
#72 - Dec 2005
ATP Synthase
similarity (2)
#108 - Dec 2008
Hsp90
similarity (1)
#168 - Dec 2013
DNA Helicase
similarity (1)
#182 - Feb 2015
Insulin receptor
similarity (1)
#214 - Oct 2017
Chimeric Antigen Receptors
similarity (1)
#238 - Oct 2019
Ribonucleotide Reductase
similarity (1)
#43 - Jul 2003
Src Tyrosine Kinase
similarity (1)
#50 - Feb 2004
Glycolytic Enzymes
similarity (1)
#60 - Dec 2004
Ubiquitin
similarity (1)
#73 - Jan 2006
Topoisomerase
similarity (1)
#80 - Aug 2006
AAA+ Proteases
similarity (1)
#95 - Nov 2007
Multidrug Resistance Transporters
similarity (1)

Deposited unit

G: 5'-R(P*UP*C)-3'

H: 5'-R(P*UP*C)-3'

J: 5'-R(P*UP*C)-3'

K: 5'-R(P*UP*C)-3'

L: 5'-R(P*UP*C)-3'

A: Transcription termination factor rho

B: Transcription termination factor rho

C: Transcription termination factor rho

D: Transcription termination factor rho

E: Transcription termination factor rho

F: Transcription termination factor rho

hetero molecules

288 kDa, 11 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	119.249, 204.649, 147.788
Angle α, β, γ (deg.)	90.00, 96.54, 90.00
Int Tables number	5
Space group name H-M	C121

#1: RNA chain	5'-R(PUPC)-3' Mass: 566.390 Da / Num. of mol.: 5 / Source method: obtained synthetically
#2: Protein	Transcription termination factor rho Mass: 47070.168 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: RHO / Production host: Escherichia coli (E. coli) / References: UniProt: P0AG30
#3: Chemical	ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER Mass: 506.196 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₁₀H₁₇N₆O₁₂P₃ / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal

Density Matthews: 3.14 Å³/Da / Density % sol: 60.82 %

Crystal grow

Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 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

Components of the solutions

ID	Name	Crystal-ID	Sol-ID
1	CacodylateCacodylic acid	1	1
2	NaClSodium chloride	1	1
3	PEG	1	1
4	glycerol	1	1
5	n-Nonyl-beta-D-thiomaltoside	1	1
6	TCEP	1	1
7	H2O	1	1
8	CacodylateCacodylic acid	1	2
9	NaClSodium chloride	1	2
10	PEG	1	2
11	H2O	1	2

Crystal grow

*PLUS

Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop

Components of the solutions

*PLUS

ID	Conc.	Common name	Crystal-ID	Sol-ID	Details	Chemical formula
1	10 mM	Tris-HCl	1	drop	pH7.5
2	50 mM		1	drop		NaCl
3	100 mM	sodium cacodylate	1	reservoir	pH6.5
4	100 mM		1	reservoir		NaCl
5	5 %	PEG8000	1	reservoir
6	40 %	glycerol	1	reservoir
7	0.6 mM	n-Nonyl-beta-D-thiomaltoside	1	reservoir
8	2 mM	TCEP	1	reservoir
9			1
10			1
11			1

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Data collection

Diffraction	Mean temperature: 95 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 19, 2003 / Details: mirrors
Radiation	Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 3→50 Å / Num. all: 77507 / Num. obs: 64912 / % possible obs: 95.7 % / Observed criterion σ(F): 2.5 / Observed criterion σ(I): 2.5 / B_iso Wilson estimate: 92 Å² / R_merge(I) obs: 0.04 / R_sym value: 0.05 / Net I/σ(I): 15.3
Reflection shell	Resolution: 3→3.12 Å / Redundancy: 2.2 % / R_merge(I) obs: 0.274 / Mean I/σ(I) obs: 2.5 / R_sym value: 0.332 / % possible all: 95
Reflection	PLUS % possible obs: 96.1 % / Redundancy: 2.2 % / R_merge(I) obs*: 0.05
Reflection shell	PLUS % possible obs: 95 % / R_merge(I) obs*: 0.332

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Processing

Software

Name	Version	Classification
REFMAC	5.1.24	refinement
HKL-2000		data reduction
SCALEPACK		data scaling
AMoRE		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1PV4

1pv4

Resolution: 3→20 Å / Cor.coef. F_o:F_c: 0.902 / Cor.coef. F_o:F_c free: 0.861 / SU B: 20.152 / SU ML: 0.381 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R Free: 0.518 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.30369	3727	5 %	RANDOM
R_work	0.27084	-	-	-
obs	0.27381	70421	95.7 %	-
all	-	77507	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 61.251 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.57 Å²	0 Å²	-1.66 Å²
2-	-	1.42 Å²	0 Å²
3-	-	-	-2.37 Å²

Refinement step

Cycle: LAST / Resolution: 3→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	18846	200	186	14	19246

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.022	19525
X-RAY DIFFRACTION	r_angle_refined_deg	1.252	2.001	26361
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.096	5	2373
X-RAY DIFFRACTION	r_chiral_restr	0.107	0.2	3041
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	14236
X-RAY DIFFRACTION	r_nbd_refined	0.248	0.2	9511
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.165	0.2	699
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.225	0.2	52
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.06	0.2	2
X-RAY DIFFRACTION	r_mcbond_it	0.575	1.5	11903
X-RAY DIFFRACTION	r_mcangle_it	1.098	2	19211
X-RAY DIFFRACTION	r_scbond_it	1.43	3	7622
X-RAY DIFFRACTION	r_scangle_it	2.579	4.5	7150

LS refinement shell

Resolution: 3→3.124 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.523	245
R_work	0.418	4648

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	18.3452	0.0916	-5.6818	6.198	6.0057	14.7909	-0.35	0.2727	-0.4099	0.403	0.7996	-0.4715	0.6415	0.5178	-0.4496	0.9772	-0.1184	-0.1275	0.6667	-0.1293	1.1918	-12.714	-57.3051	-10.1492
2	12.8544	6.3878	4.6283	17.5026	-1.542	13.6791	-0.3018	0.3198	-0.1606	0.5614	0.4904	0.7982	0.1662	0.2928	-0.1885	0.1593	0.4163	0.1195	1.1968	-0.0031	1.0068	-51.8988	13.8401	28.0707
3	9.5764	4.4378	-3.866	7.7585	-2.1386	6.7375	0.0048	0.414	0.9175	-0.0717	-0.0224	0.2735	-0.3631	-0.1095	0.0176	1.1852	0.3134	0.0449	0.9867	0.2716	1.1927	-15.8076	47.3571	21.1748
4	8.4092	2.191	0.2874	7.5431	0.1106	5.0602	0.4589	-0.1054	0.3404	-0.5528	-0.1042	0.0043	0.1183	0.4467	-0.3547	1.0852	-0.0156	0.173	1.1373	0.2225	1.0944	30.7518	34.1666	8.9709
5	6.0815	1.8712	0.6289	19.4162	2.0755	1.7629	-0.0847	0.3371	0.0194	-0.5744	0.5159	-1.2847	0.5502	0.3103	-0.4312	1.105	0.2124	0.0738	1.1713	-0.2381	0.919	45.7488	-13.129	10.56
6	0.4518	0.3458	0.4036	2.5669	1.5969	5.468	-0.2109	0.1668	-0.1348	-0.0592	0.0458	0.3758	0.1556	-0.2397	0.1651	1.0439	-0.0528	-0.0806	0.9453	0.047	1.2454	-24.8223	-44.1173	6.4076
7	1.7637	1.3878	-0.4694	5.3257	0.9333	0.0852	-0.2091	0.5383	-0.1107	-0.7221	-0.0768	1.7854	-0.2754	-0.2485	0.2859	0.6904	0.1258	-0.1547	1.3264	-0.2043	1.6006	-46.9654	-12.6505	25.5564
8	2.6608	0.572	1.268	2.0579	0.1347	4.9278	-0.1085	0.2441	0.1411	-0.198	0.3017	0.4466	-0.3647	-0.4795	-0.1932	0.9577	0.3589	0.0606	1.2177	0.0853	1.1239	-34.293	28.4561	27.778
9	3.0198	-1.0316	1.3026	1.3401	-1.3256	3.624	0.026	0.752	0.4087	-0.162	-0.0218	-0.2254	-0.4533	-0.012	-0.0042	1.2296	0.021	0.0707	1.1296	0.1187	1.2246	6.0355	41.3414	18.589
10	1.9553	-0.2515	1.58	3.2455	-0.7549	4.8609	0.228	0.1686	0.1859	-0.8363	0.0321	-0.0618	0.1853	0.1616	-0.26	1.0387	0.0636	0.1638	1.2182	0.0409	1.127	38.4273	13.2777	12.2627
11	2.1257	1.1401	3.4975	1.6368	-0.1359	8.7357	-0.0347	0.2161	-0.2034	-0.2663	0.4256	-0.1122	0.6545	-0.107	-0.3909	1.2654	0.2626	-0.1499	0.8215	-0.1614	1.0419	35.5427	-28.8135	23.4428
12	3.0159	-0.8353	-0.3211	3.1948	0.9804	4.9186	-0.0484	-0.1597	0.1288	0.1909	0.3332	-0.4108	0.1304	0.7277	-0.2848	0.972	0.1166	-0.085	1.0333	-0.0906	1.2397	-8.7027	-33.6274	24.9587
13	0.9543	-0.2002	0.1387	3.4394	0.86	2.764	0.0669	0.0595	-0.1028	0.4695	-0.0247	0.2403	0.3426	0.0045	-0.0422	1.0696	0.0433	0.1213	1.1043	0.0105	1.1812	-26.4178	-12.3561	41.689
14	1.5936	0.744	0.078	2.3752	0.9641	2.2002	0.0517	-0.1054	-0.1731	0.2206	-0.0025	0.0452	0.0969	-0.0788	-0.0492	1.1297	0.1772	0.1141	1.2133	0.0403	1.1106	-18.3405	18.304	46.5307
15	2.6975	-0.3004	0.2817	1.7355	0.5218	0.9645	-0.0698	-0.2503	0.0867	0.2528	0.1897	-0.2021	-0.0493	-0.0208	-0.1199	1.2644	0.1136	0.0219	1.1824	-0.0496	1.2256	11.3544	30.0336	41.9178
16	1.9134	-0.4844	0.6657	1.743	-0.2209	1.4468	-0.0459	-0.1011	0.2209	0.2181	0.0702	-0.1486	-0.0491	0.0517	-0.0243	1.1327	0.0473	0.0117	1.2503	-0.0882	1.2911	37.8334	11.9757	38.6535
17	1.5255	-0.036	0.8438	1.8876	-0.4568	3.0046	0.2147	-0.1522	-0.0011	0.1748	-0.0632	0.0197	0.3624	-0.0579	-0.1515	1.3199	0.107	-0.1287	1.0893	-0.0585	1.0238	39.5292	-18.7288	47.6973
18	-7.7218	-3.6013	-1.7503	12.2542	-11.5735	33.7283	1.2275	-0.9568	-0.6587	1.4084	-1.228	1.1809	0.0066	-0.192	0.0005	1.2593	0.001	0.0001	1.2599	0.0002	1.2594	0.8124	-47.0499	47.3241
19	10.816	5.4119	-12.301	7.5716	0.6049	51.047	0.1549	-1.0662	3.709	0.6931	-0.3353	-0.6814	-1.3661	0.7173	0.1804	1.2596	-0.0001	0.0002	1.2598	0.0003	1.2592	-25.9709	-18.6046	68.8482
20	-1.1434	-18.956	10.4713	-47.2272	-1.7524	23.4104	-1.0631	-0.7842	-0.0146	0.7703	0.4604	1.1218	-0.2295	1.1485	0.6026	1.2622	0.0362	0.0061	1.2635	0.0345	1.2624	-19.0529	25.9561	72.689
21	-20.3058	8.0728	8.2034	28.2662	0.4217	13.3394	1.6178	1.5301	-0.9123	1.4449	-1.8541	-1.0186	-1.0696	1.1132	0.2363	1.2599	-0.0007	-0.002	1.2588	-0.0017	1.2603	20.6666	43.1965	64.1563
22	21.783	-6.4053	12.7407	8.4624	-7.623	5.7864	-0.3994	-0.8305	0.0409	-0.9046	-0.9735	-0.3512	1.1819	0.3481	1.373	1.2595	-0.0001	-0.0008	1.2597	-0.0002	1.2598	58.0078	19.9327	55.512
23	2.5339	6.4391	24.3223	-13.8103	-10.7286	20.1439	0.1736	-0.6478	-0.4632	-0.8175	0.1147	-1.1249	0.4504	-0.2377	-0.2883	1.2598	0.0001	-0.0001	1.2599	-0.0002	1.2595	60.8263	-23.2621	63.5315

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	F	1 - 46	1 - 46
2	X-RAY DIFFRACTION	2	C	H	1 - 46	1 - 46
3	X-RAY DIFFRACTION	3	D	I	1 - 46	1 - 46
4	X-RAY DIFFRACTION	4	E	J	1 - 46	1 - 46
5	X-RAY DIFFRACTION	5	F	K	1 - 46	1 - 46
6	X-RAY DIFFRACTION	6	A	F	47 - 155	47 - 155
7	X-RAY DIFFRACTION	7	B	G	51 - 155	51 - 155
8	X-RAY DIFFRACTION	8	C	H	47 - 155	47 - 155
9	X-RAY DIFFRACTION	9	D	I	47 - 155	47 - 155
10	X-RAY DIFFRACTION	10	E	J	47 - 155	47 - 155
11	X-RAY DIFFRACTION	11	F	K	47 - 155	47 - 155
12	X-RAY DIFFRACTION	12	A	F	156 - 400	156 - 400
13	X-RAY DIFFRACTION	13	B	G	156 - 400	156 - 400
14	X-RAY DIFFRACTION	14	C	H	156 - 400	156 - 400
15	X-RAY DIFFRACTION	15	D	I	156 - 400	156 - 400
16	X-RAY DIFFRACTION	16	E	J	156 - 400	156 - 400
17	X-RAY DIFFRACTION	17	F	K	156 - 400	156 - 400
18	X-RAY DIFFRACTION	18	A	F	401 - 417	401 - 417
19	X-RAY DIFFRACTION	19	B	G	401 - 417	401 - 417
20	X-RAY DIFFRACTION	20	C	H	401 - 417	401 - 417
21	X-RAY DIFFRACTION	21	D	I	401 - 417	401 - 417
22	X-RAY DIFFRACTION	22	E	J	401 - 417	401 - 417
23	X-RAY DIFFRACTION	23	F	K	401 - 417	401 - 417

Refinement

*PLUS

Highest resolution: 3 Å / Lowest resolution: 20 Å / % reflection R_free: 5 % / R_factor R_free: 0.303 / R_factor R_work: 0.27

Solvent computation

*PLUS

Displacement parameters

*PLUS

Refine LS restraints

*PLUS

Refine-ID	Type	Dev ideal
X-RAY DIFFRACTION	r_bond_d	0.01
X-RAY DIFFRACTION	r_angle_d
X-RAY DIFFRACTION	r_angle_deg	1.25

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About Yorodumi

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Yorodumi