PDB-4zc7: Paromomycin bound to a leishmanial ribosomal A-site

ID or keywords:

Entry

Database: PDB / ID: 4zc7

Title

Paromomycin bound to a leishmanial ribosomal A-site

Components

RNA duplex

Keywords

RNA / A-site / ribosome / paromomycin / Leishmania

Function / homology

PAROMOMYCIN / RNA / RNA (> 10)

Function and homology information

Biological species

synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 3.041 Å

Authors

Shalev, M. / Rozenberg, H. / Jaffe, C.L. / Adir, N. / Baasov, T.

Funding support

United States,

Germany, 2items

Citation

Journal: Nucleic Acids Res. / Year: 2015
Title: Structural basis for selective targeting of leishmanial ribosomes: aminoglycoside derivatives as promising therapeutics.
Authors: Shalev, M. / Rozenberg, H. / Smolkin, B. / Nasereddin, A. / Kopelyanskiy, D. / Belakhov, V. / Schrepfer, T. / Schacht, J. / Jaffe, C.L. / Adir, N. / Baasov, T.

History

Deposition	Apr 15, 2015	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Aug 26, 2015	Provider: repository / Type: Initial release
Revision 1.1	Oct 7, 2015	Group: Database references
Revision 1.2	Oct 11, 2017	Group: Data collection / Category: reflns_shell Item: _reflns_shell.d_res_low / _reflns_shell.percent_possible_all
Revision 1.3	Jan 31, 2018	Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / struct_conn / Item: _pdbx_audit_support.funding_organization
Revision 1.4	Jan 10, 2024	Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4zc7.cif.gz	109.5 KB	Display	PDBx/mmCIF format
PDB format	pdb4zc7.ent.gz	83.6 KB	Display	PDB format
PDBx/mmJSON format	4zc7.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4zc7_validation.pdf.gz	1 MB	Display	wwPDB validaton report
Full document	4zc7_full_validation.pdf.gz	1 MB	Display
Data in XML	4zc7_validation.xml.gz	6.3 KB	Display
Data in CIF	4zc7_validation.cif.gz	7.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zc/4zc7 ftp://data.pdbj.org/pub/pdb/validation_reports/zc/4zc7	HTTPS FTP

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Related structure data

Related structure data	1j7tS S: Starting model for refinement
Similar structure data	4e48-1 2o3y-d 4g78-d 3td0-d 1n8x-d 2o3w-d 2o3v-d 2et4-d 2g5k-d 2f4u-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#121 - Jan 2010 70S Ribosomes similarity (2) #130 - Oct 2010 Riboswitches similarity (1) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1) #157 - Jan 2013 Transfer-Messenger RNA similarity (1) #229 - Jan 2019 Fluorescent RNA Aptamers similarity (1) #181 - Jan 2015 Cascade and CRISPR similarity (1) #253 - Jan 2021 Expressome similarity (1) #260 - Aug 2021 Ribonuclease P similarity (1) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (2) #10 - Oct 2000 Ribosome similarity (3) #15 - Mar 2001 Transfer RNA similarity (1) #249 - Sep 2020 SARS-CoV-2 RNA-dependent RNA Polymerase similarity (1) #210 - Jun 2017 Adenine Riboswitch in Action similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #226 - Oct 2018 Aminoglycoside Antibiotics and Resistance similarity (2) #245 - May 2020 Spliceosomes similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #65 - May 2005 Self-splicing RNA similarity (1) #98 - Feb 2008 Small Interfering RNA similarity (1) #105 - Sep 2008 Ribonuclease A similarity (1) #230 - Feb 2019 Initiation Factor eIF4E similarity (1) #161 - May 2013 Ricin similarity (1) #143 - Nov 2011 Toll-like Receptors similarity (1) #106 - Oct 2008 Poly(A) Polymerase similarity (1) #266 - Feb 2022 Oligosaccharyltransferase similarity (1) #81 - Sep 2006 Elongation Factors similarity (1) #104 - Aug 2008 Selenocysteine Synthase similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1) #227 - Nov 2018 Telomerase similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#121 - Jan 2010
70S Ribosomes
similarity (2)
#130 - Oct 2010
Riboswitches
similarity (1)
#16 - Apr 2001
Aminoacyl-tRNA Synthetases
similarity (1)
#157 - Jan 2013
Transfer-Messenger RNA
similarity (1)
#229 - Jan 2019
Fluorescent RNA Aptamers
similarity (1)
#181 - Jan 2015
Cascade and CRISPR
similarity (1)
#253 - Jan 2021
Expressome
similarity (1)
#260 - Aug 2021
Ribonuclease P
similarity (1)
#146 - Feb 2012
Aminoglycoside Antibiotics
similarity (2)
#10 - Oct 2000
Ribosome
similarity (3)
#15 - Mar 2001
Transfer RNA
similarity (1)
#249 - Sep 2020
SARS-CoV-2 RNA-dependent RNA Polymerase
similarity (1)
#210 - Jun 2017
Adenine Riboswitch in Action
similarity (1)
#87 - Mar 2007
Zinc Fingers
similarity (1)
#226 - Oct 2018
Aminoglycoside Antibiotics and Resistance
similarity (2)
#245 - May 2020
Spliceosomes
similarity (1)
#262 - Oct 2021
Fifty Years of Open Access to PDB Structures
similarity (1)
#65 - May 2005
Self-splicing RNA
similarity (1)
#98 - Feb 2008
Small Interfering RNA
similarity (1)
#105 - Sep 2008
Ribonuclease A
similarity (1)
#230 - Feb 2019
Initiation Factor eIF4E
similarity (1)
#161 - May 2013
Ricin
similarity (1)
#143 - Nov 2011
Toll-like Receptors
similarity (1)
#106 - Oct 2008
Poly(A) Polymerase
similarity (1)
#266 - Feb 2022
Oligosaccharyltransferase
similarity (1)
#81 - Sep 2006
Elongation Factors
similarity (1)
#104 - Aug 2008
Selenocysteine Synthase
similarity (1)
#89 - May 2007
Aconitase and Iron Regulatory Protein 1
similarity (1)
#227 - Nov 2018
Telomerase
similarity (1)
#241 - Jan 2020
Twenty Years of Molecules
similarity (1)

Deposited unit

A: RNA duplex

B: RNA duplex

C: RNA duplex

D: RNA duplex

hetero molecules

119 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: RNA duplex

B: RNA duplex

hetero molecules

defined by software
59.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: RNA duplex

D: RNA duplex

hetero molecules

defined by software
59.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	31.690, 57.180, 47.700
Angle α, β, γ (deg.)	78.920, 109.440, 123.610
Int Tables number	1
Space group name H-M	P1

#1: RNA chain	RNA duplex Mass: 29560.441 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical	ChemComp-PAR / PAROMOMYCIN / PAROMOMYCIN I / AMMINOSIDIN / CATENULIN / CRESTOMYCIN / MONOMYCIN A / NEOMYCIN E Mass: 615.628 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₃H₄₅N₅O₁₄ / Comment: Antimicrobial, medication*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 4 / 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 grow	Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Sodium cacodylate pH 7.0, spermine tetrahydrochloride, 2-methyl-2,4-pentanediol (MPD), MgSO4, KCl.

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: ID14-4 / Wavelength: 0.9394 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 28, 2013

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9394 Å / Relative weight: 1

Reflection

Resolution: 3.04→45 Å / Num. all: 5004 / Num. obs: 5004 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / B_iso Wilson estimate: 68.87 Å² / R_merge F obs: 0.998 / R_merge(I) obs: 0.09 / R_rim(I) all: 0.106 / Χ²: 0.904 / Net I/σ(I): 7.05 / Num. measured all: 15718

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Redundancy (%)	R_merge F obs	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	R_rim(I) all	% possible all
3.04-3.12	3.1	0.959	0.283	2.13	1212	381	382	0.339	100
3.12-3.21		0.995	0.137	2.99	1214	391	380	0.163	97.2
3.21-3.3		0.971	0.198	3.45	1000	308	311	0.235	100
3.3-3.4		0.98	0.179	3.65	1182	377	373	0.213	98.9
3.4-3.51		0.986	0.162	3.9	1029	323	319	0.191	98.8
3.51-3.63		0.982	0.143	4.59	1058	335	329	0.169	98.2
3.63-3.77		0.994	0.118	5.22	916	290	292	0.139	100
3.77-3.93		0.989	0.129	6.06	961	316	308	0.152	97.5
3.93-4.1		0.987	0.117	7.25	919	292	285	0.138	97.6
4.1-4.3		0.989	0.118	7.16	838	262	269	0.141	100
4.3-4.53		0.99	0.105	8.67	798	267	257	0.124	96.3
4.53-4.81		0.986	0.099	10.72	858	267	264	0.116	98.9
4.81-5.14		0.986	0.099	11.28	683	214	217	0.117	100
5.14-5.55		0.995	0.085	11.48	616	211	203	0.101	96.2
5.55-6.08		0.988	0.084	12.41	631	211	210	0.098	99.5
6.08-6.8		0.991	0.083	12.6	543	189	179	0.098	94.7
6.8-7.85		0.996	0.061	14.13	459	151	150	0.072	99.3
7.85-9.62		0.994	0.077	13.87	423	140	137	0.09	97.9
9.62-13.6		0.998	0.049	14.81	261	96	93	0.059	96.9
13.6-45		0.998	0.033	14.46	117	57	46	0.04	80.7

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
PHASER		phasing
PHENIX		refinement
Coot		model building
PDB_EXTRACT	3.15	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1J7T

1j7t

Resolution: 3.041→44.979 Å / SU ML: 0.31 / Cross valid method: NONE / σ(F): 1.98 / Phase error: 31.87 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2614	991	10 %	Random selection
R_work	0.1828	8818	-	-
obs	0.1912	5004	96.87 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 188.91 Å² / B_iso mean: 97.5302 Å² / B_iso min: 50.26 Å²

Refinement step

Cycle: final / Resolution: 3.041→44.979 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	0	1749	73	4	1826
B_iso mean	-	-	109.45	60.38	-
Num. residues	-	-	-	-	82

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	2027
X-RAY DIFFRACTION	f_angle_d	1.23	3142
X-RAY DIFFRACTION	f_chiral_restr	0.058	442
X-RAY DIFFRACTION	f_plane_restr	0.007	82
X-RAY DIFFRACTION	f_dihedral_angle_d	13.618	965

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
3.0406-3.2009	0.2573	144	0.2293	1281	X-RAY DIFFRACTION	96
3.2009-3.4014	0.2465	143	0.1972	1255	X-RAY DIFFRACTION	97
3.4014-3.6639	0.3298	140	0.2082	1286	X-RAY DIFFRACTION	98
3.6639-4.0324	0.2997	141	0.1844	1228	X-RAY DIFFRACTION	97
4.0324-4.6154	0.2943	147	0.192	1267	X-RAY DIFFRACTION	98
4.6154-5.8129	0.325	135	0.182	1266	X-RAY DIFFRACTION	97
5.8129-45	0.2065	141	0.1591	1235	X-RAY DIFFRACTION	95

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	3.6182	2.2596	-1.6839	5.5268	2.5299	3.8751	0.5333	-2.0599	1.7307	0.0095	-0.3799	-0.0451	-0.6819	-1.129	-0.3561	1.1614	0.1224	-0.3409	0.9476	0.0532	1.0658	16.7124	-34.2602	14.6121
2	0.7747	1.5311	2.3263	5.6173	5.2556	7.1089	-0.7222	0.0174	0.477	-0.2282	-1.0055	1.2566	-1.6817	-1.1074	-2.9966	0.7089	0.081	0.1698	0.4734	0.6257	0.9622	-7.8452	-3.8249	8.6166
3	3.3213	-2.9588	-1.0443	3.8965	3.587	5.9009	-0.5818	-0.1227	-0.7891	0.1652	0.5855	0.2094	0.5726	0.6549	0.0724	0.6449	0.1298	0.2265	1.0676	0.2131	0.6331	-6.3336	-4.2896	16.0553
4	4.4303	-1.7413	2.9387	4.4696	-3.0291	7.9806	0.2517	-0.4171	-0.8902	-0.1304	0.2142	-0.3692	0.9049	0.6105	-0.6577	0.8878	0.2564	0.0615	0.6993	-0.0568	0.7913	6.7594	-21.9721	16.3369
5	1.9941	0.3351	4.711	2.0041	3.4571	5.9678	-0.0147	1.3057	-0.1501	-0.0522	0.8694	2.9183	1.5973	1.1677	-0.2645	1.1403	0.2473	0.1565	0.6588	0.215	0.9352	11.6515	-39.7216	11.0806
6	4.2831	4.1177	2.4563	3.762	2.0932	1.7715	0.9385	-1.2167	0.0346	0.2015	-0.9972	0.207	-0.5333	0.4306	0.0073	1.609	-0.524	0.0937	1.0448	-0.0692	1.0453	9.0613	-9.0471	36.5781
7	4.4848	-0.1567	-2.7441	5.571	-0.9234	5.5987	-0.4039	0.4871	-0.7641	-0.4259	0.005	0.6427	0.3663	-0.253	0.2412	0.6833	-0.0149	-0.0718	0.4709	-0.07	0.7398	-2.7729	-32.5747	40.5514
8	1.7183	0.6509	-1.1366	3.0097	-0.6191	2.4628	-0.1787	0.8258	0.0968	0.6697	0.6038	1.748	1.0522	-0.1122	-0.2383	0.6693	-0.1236	-0.0345	0.7957	0.2383	0.7993	-2.0529	-29.5502	38.5118
9	4.5223	1.7146	1.9688	5.2439	2.4114	5.8455	-0.3277	-0.189	-0.2626	-0.7721	0.3819	0.509	-0.0584	-0.0844	0.0436	0.9571	-0.271	0.1012	0.6433	0.0598	0.837	9.8824	-6.1417	35.6091
10	4.7805	2.9912	-1.4771	4.7573	2.3241	8.3937	1.1723	1.0005	-1.2511	1.9955	-0.4993	0.4356	1.3497	2.0344	-0.2679	0.8692	0.2299	-0.1136	0.9121	0.0766	1.1306	3.5223	-18.3924	16.2553

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 7 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 17 through 23 )	A
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 26 through 31 )	B
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 32 through 40 )	B
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 42 through 46 )	B
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 3 through 12 )	C
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 13 through 23 )	C
8	X-RAY DIFFRACTION	8	chain 'D' and (resid 26 through 35 )	D
9	X-RAY DIFFRACTION	9	chain 'D' and (resid 36 through 46 )	D
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 8 through 16 )	A

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