PDB-9ys1: Crystal structure of Cysteinyl-tRNA synthetase (CysRS) from Plasm...

ID or keywords:

Entry

Database: PDB / ID: 9ys1

Title

Crystal structure of Cysteinyl-tRNA synthetase (CysRS) from Plasmodium falciparum in complex with AMP and Cysteine

Components

Cysteine--tRNA ligase

Keywords

TRANSFERASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / Cysteinyl-tRNA synthetase / CysRS

Function / homology

Function and homology information

cysteine-tRNA ligase / cysteine-tRNA ligase activity / cysteinyl-tRNA aminoacylation / apicoplast / ATP binding / metal ion binding / cytoplasm / cytosol
Similarity search - Function

Biological species

Plasmodium falciparum 3D7 (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.34 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	75N93022C00036	United States
National Institutes of Health/Office of the Director	S10OD030394	United States

Citation

Journal: To be published
Title: Crystal structure of Cysteinyl-tRNA synthetase (CysRS) from Plasmodium falciparum in complex with AMP and Cysteine
Authors: Liu, L. / Lovell, S. / Battaile, K.P.

History

Deposition	Oct 17, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 5, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9ys1.cif.gz	369.9 KB	Display	PDBx/mmCIF format
PDB format	pdb9ys1.ent.gz	302.2 KB	Display	PDB format
PDBx/mmJSON format	9ys1.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9ys1_validation.pdf.gz	3.2 MB	Display	wwPDB validaton report
Full document	9ys1_full_validation.pdf.gz	3.2 MB	Display
Data in XML	9ys1_validation.xml.gz	36.6 KB	Display
Data in CIF	9ys1_validation.cif.gz	48 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ys/9ys1 ftp://data.pdbj.org/pub/pdb/validation_reports/ys/9ys1	HTTPS FTP

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Related structure data

Similar structure data	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	#16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (2) #111 - Mar 2009 Hydrogenase similarity (1) #149 - May 2012 Leptin similarity (1) #129 - Sep 2010 Isocitrate Dehydrogenase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #24 - Dec 2001 Glycogen Phosphorylase similarity (1) #55 - Jul 2004 DNA Ligase similarity (1)

Deposited unit

A: Cysteine--tRNA ligase

B: Cysteine--tRNA ligase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	119.835, 119.835, 365.780
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	178
Space group name H-M	P6₁22

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Protein , 1 types, 2 molecules AB

#1: Protein	Cysteine--tRNA ligase / Cysteinyl-tRNA synthetase Mass: 54533.195 Da / Num. of mol.: 2 / Fragment: residues 91-535 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: PF3D7_1015200.1 / Plasmid: PlfaA.00133.a.A3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8IJP3, cysteine-tRNA ligase

#1: Protein

Cysteine--tRNA ligase / Cysteinyl-tRNA synthetase

Mass: 54533.195 Da / Num. of mol.: 2 / Fragment: residues 91-535
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Plasmodium falciparum 3D7 (eukaryote) / Gene: PF3D7_1015200.1 / Plasmid: PlfaA.00133.a.A3 / Production host:

Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8IJP3, cysteine-tRNA ligase

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Non-polymers , 6 types, 123 molecules

#2: Chemical	ChemComp-CYS / CYSTEINE Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₇NO₂S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-AMP / ADENOSINE MONOPHOSPHATE Mass: 347.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₄N₅O₇P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#4: Chemical	ChemComp-MLI / MALONATE ION Mass: 102.046 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₂O₄
#5: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.48 Å³/Da / Density % sol: 64.61 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 1.53M Sodium Malonate, pH 7.0. PlfaA.00133.a.A3.PS38777 at 12.3 mg/mL. 24 hour soak with 10 mM AMP and Cysteine in 3.4M sodium malonate. plate Liu-S-192 G5 Puck: PSL-0209, Cryo: direct from soaking solution

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
Detector	Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Sep 20, 2025
Radiation	Monochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9786 Å / Relative weight: 1
Reflection	Resolution: 2.34→47.75 Å / Num. obs: 66622 / % possible obs: 100 % / Redundancy: 19.7 % / CC_1/2: 0.999 / R_merge(I) obs: 0.14 / R_pim(I) all: 0.032 / R_rim(I) all: 0.143 / Χ²: 1.16 / Net I/σ(I): 20.4 / Num. measured all: 1315411
Reflection shell	Resolution: 2.34→2.4 Å / % possible obs: 100 % / Redundancy: 18.9 % / R_merge(I) obs: 2.141 / Num. measured all: 91507 / Num. unique obs: 4842 / CC_1/2: 0.803 / R_pim(I) all: 0.505 / R_rim(I) all: 2.2 / Χ²: 0.97 / Net I/σ(I) obs: 1.5

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Processing

Software

Name	Version	Classification
PHENIX	(2.0_5765: ???)	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing
PDB_EXTRACT		data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.34→47.75 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.64 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2155	3316	4.99 %
R_work	0.188	-	-
obs	0.1894	66466	99.95 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.34→47.75 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7088	0	133	108	7329

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	7420
X-RAY DIFFRACTION	f_angle_d	0.974	10046
X-RAY DIFFRACTION	f_dihedral_angle_d	14.032	2687
X-RAY DIFFRACTION	f_chiral_restr	0.049	1069
X-RAY DIFFRACTION	f_plane_restr	0.006	1254

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 (%)
2.34-2.37	0.3617	132	0.2874	2564	X-RAY DIFFRACTION	100
2.37-2.41	0.3004	146	0.2791	2590	X-RAY DIFFRACTION	100
2.41-2.45	0.3081	153	0.2634	2557	X-RAY DIFFRACTION	100
2.45-2.49	0.2817	138	0.2513	2560	X-RAY DIFFRACTION	100
2.49-2.53	0.2776	131	0.2331	2590	X-RAY DIFFRACTION	100
2.53-2.58	0.2885	118	0.2503	2590	X-RAY DIFFRACTION	100
2.58-2.63	0.2834	113	0.2511	2602	X-RAY DIFFRACTION	100
2.63-2.68	0.323	139	0.2651	2584	X-RAY DIFFRACTION	100
2.68-2.74	0.3167	136	0.2885	2612	X-RAY DIFFRACTION	100
2.74-2.8	0.3084	159	0.2606	2558	X-RAY DIFFRACTION	100
2.8-2.87	0.2881	147	0.251	2591	X-RAY DIFFRACTION	100
2.87-2.95	0.2746	120	0.2314	2606	X-RAY DIFFRACTION	100
2.95-3.03	0.2457	136	0.2163	2600	X-RAY DIFFRACTION	100
3.03-3.13	0.2631	135	0.2134	2623	X-RAY DIFFRACTION	100
3.13-3.24	0.2344	135	0.2095	2639	X-RAY DIFFRACTION	100
3.24-3.37	0.2064	135	0.2029	2615	X-RAY DIFFRACTION	100
3.37-3.53	0.2046	139	0.1796	2649	X-RAY DIFFRACTION	100
3.53-3.71	0.2049	139	0.1533	2612	X-RAY DIFFRACTION	100
3.71-3.95	0.1727	126	0.1421	2653	X-RAY DIFFRACTION	100
3.95-4.25	0.1553	138	0.1337	2682	X-RAY DIFFRACTION	100
4.25-4.68	0.1304	141	0.126	2669	X-RAY DIFFRACTION	100
4.68-5.35	0.17	159	0.1404	2693	X-RAY DIFFRACTION	100
5.36-6.74	0.2275	148	0.1957	2766	X-RAY DIFFRACTION	100
6.74-47.75	0.2232	153	0.2088	2945	X-RAY DIFFRACTION	100

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	0.35	0.4366	0.1321	0.5842	0.1063	0.1122	-0.1754	0.3419	0.0775	-0.4887	0.0308	-0.0043	0.0641	0.0604	0	0.8969	-0.0083	-0.0487	0.4952	-0.0146	0.5327	29.303	-44.737	-13.729
2	0.6911	-0.1022	-0.4175	0.4732	-0.1713	0.4759	0.0843	0.1377	0.1604	-0.1101	-0.069	-0.1839	-0.0631	0.076	-0	0.6393	-0.0011	-0.0615	0.3526	0.0459	0.5178	29.914	-27.038	3.969
3	0.6778	-0.0479	0.0523	0.6921	-0.0034	0.01	0.2412	0.4688	-0.0491	-0.5043	-0.0599	-0.3418	-0.1696	-0.1367	0.0497	1.0041	-0.0141	0.0339	0.6108	0.1752	0.5566	27.697	-19.571	-20.746
4	0.3101	-0.0614	-0.2449	0.1832	-0.1519	0.3915	0.0123	0.0911	0.1758	-0.033	-0.0332	-0.4809	-0.1853	0.1037	0.0032	0.9	0.0312	-0	0.4348	0.1393	0.5175	27.77	-13.12	-11.405
5	0.4994	-0.2294	0.5169	0.6066	-0.1027	0.5432	-0.054	0.0426	0.0572	-0.2541	-0.0548	0.1045	-0.0573	-0.1945	-0.0005	0.6339	-0.0092	-0.0987	0.3893	0.0473	0.4736	20.689	-32.471	0.661
6	1.0347	-0.8624	-0.2135	0.8821	-0.0147	0.2576	-0.1443	-0.1967	-0.2487	-0.0524	0.1979	0.2022	0.1235	-0.1742	-0	0.5933	-0.0253	-0.0289	0.4077	0.0689	0.5369	29.048	-57.519	17.422
7	6.924	2.593	3.3997	2.2462	2.2638	2.4391	-0.1784	-0.827	1.1518	-0.2418	0.4565	-0.3346	0.246	0.7466	-0.2485	0.7455	0.0176	0.0734	0.549	0.1806	0.5481	23.868	-23.213	-1.727
8	0.7664	0.1335	-0.4513	0.4732	-0.0376	0.8688	-0.1097	0.0321	-0.0752	-0.1145	0.0534	0.0056	0.1115	0.0716	0	0.5602	0.0507	0.0512	0.3879	0.0411	0.4863	50.605	-67.026	15.402
9	1.5103	-0.5278	0.3561	0.8334	0.2148	0.2501	-0.008	0.1476	-0.324	-0.1215	0.1688	-0.0325	0.2409	0.0205	0.0002	0.7942	0.0583	0.1002	0.3461	-0.0139	0.6583	53.685	-90.362	13.196
10	0.1212	-0.2048	-0.0509	0.3597	-0.0879	0.5108	-0.094	0.044	-0.2053	-0.1497	0.0508	-0.0724	0.1747	0.1378	-0	0.6474	0.0596	0.1013	0.3997	0.0268	0.4998	55.638	-74.06	12.746
11	0.9019	-0.6304	0.4846	0.8794	-0.5205	0.5159	-0.078	0.0667	0.2498	-0.0867	-0.0099	-0.3521	-0.1244	0.1633	-0	0.5654	-0.0529	0.0371	0.4385	0.0538	0.6294	54.036	-39.873	11.401
12	9.5344	1.115	-0.8813	3.318	3.126	3.3526	-0.4106	-1.1053	0.7487	-0.2719	-0.0853	0.7353	-0.129	-0.568	0.9224	0.6885	0.006	0.0302	0.3017	-0.0988	0.6998	56.358	-73.58	19.391

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN A AND RESID 13:42 )	A	13 - 42
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 43:146 )	A	43 - 146
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 147:193 )	A	147 - 193
4	X-RAY DIFFRACTION	4	( CHAIN A AND RESID 194:256 )	A	194 - 256
5	X-RAY DIFFRACTION	5	( CHAIN A AND RESID 257:350 )	A	257 - 350
6	X-RAY DIFFRACTION	6	( CHAIN A AND RESID 351:458 )	A	351 - 458
7	X-RAY DIFFRACTION	7	( CHAIN A AND RESID 501:501 )	A	501
8	X-RAY DIFFRACTION	8	( CHAIN B AND RESID 12:146 )	B	12 - 146
9	X-RAY DIFFRACTION	9	( CHAIN B AND RESID 147:239 )	B	147 - 239
10	X-RAY DIFFRACTION	10	( CHAIN B AND RESID 240:316 )	B	240 - 316
11	X-RAY DIFFRACTION	11	( CHAIN B AND RESID 317:458 )	B	317 - 458
12	X-RAY DIFFRACTION	12	( CHAIN B AND RESID 502:502 )	B	502

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