PDB-7zkw: Crystal structure of cystinosin from Arabidopsis thaliana in comp...

ID or keywords:

Entry

Database: PDB / ID: 7zkw

Title

Crystal structure of cystinosin from Arabidopsis thaliana in complex with Cystine and sybody

Components

Cystinosin homolog
sybody

Keywords

MEMBRANE PROTEIN / Cystinosin / PQ-loop protein / proton coupling / cystine transport

Function / homology

Lysosomal cystine transporter / Repeated motif present between transmembrane helices in cystinosin, yeast ERS1p, mannose-P-dolichol utilization defect 1, and other hypothetical proteins. / PQ-loop repeat / PQ loop repeat / L-cystine transmembrane transporter activity / plant-type vacuole / lysosomal membrane / L-cystine / Cystinosin homolog

Function and homology information

Biological species

Arabidopsis thaliana (thale cress)
synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.372 Å

Authors

Parker, J.L. / Loebel, M. / Newstead, S.

Funding support

United Kingdom, 1items

Citation

Journal: Nat Commun / Year: 2022
Title: Structural basis for proton coupled cystine transport by cystinosin.
Authors: Lobel, M. / Salphati, S.P. / El Omari, K. / Wagner, A. / Tucker, S.J. / Parker, J.L. / Newstead, S.

History

Deposition	Apr 13, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 31, 2022	Provider: repository / Type: Initial release
Revision 1.1	Jan 31, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7zkw.cif.gz	713.4 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	7zkw_validation.pdf.gz	864 KB	Display	wwPDB validaton report
Full document	7zkw_full_validation.pdf.gz	891.1 KB	Display
Data in XML	7zkw_validation.xml.gz	29.4 KB	Display
Data in CIF	7zkw_validation.cif.gz	38.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zk/7zkw ftp://data.pdbj.org/pub/pdb/validation_reports/zk/7zkw	HTTPS FTP

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Related structure data

Related structure data	7zk1SC 7zkzC S: Starting model for refinement C: citing same article (ref.)
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	#21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

A: Cystinosin homolog

B: Cystinosin homolog

C: sybody

D: sybody

hetero molecules

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

1

A: Cystinosin homolog

C: sybody

hetero molecules

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

2

B: Cystinosin homolog

D: sybody

hetero molecules

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

Unit cell

Length a, b, c (Å)	283.372, 64.065, 55.443
Angle α, β, γ (deg.)	90.000, 99.946, 90.000
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	A
3	2	A
4	2	A

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Auth asym-ID	Auth seq-ID
1	1	1	A	3 - 245
2	1	1	A	3 - 245
3	2	2	A	1 - 121
4	2	2	A	1 - 121

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4

#1: Protein	Cystinosin homolog Mass: 31902.965 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At5g40670, MNF13.23 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Variant (production host): BJ5460 / References: UniProt: P57758
#2: Antibody	sybody Mass: 13651.062 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli MC1061 (bacteria)
#3: Chemical	ChemComp-IYY / L-cystine / (2R)-2-azanyl-3-[[(2R)-2-azanyl-3-oxidanyl-3-oxidanylidene-propyl]disulfanyl]propanoic acid Mass: 240.300 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₁₂N₂O₄S₂ / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.97 Å³/Da / Density % sol: 58.56 %
Crystal grow	Temperature: 293 K / Method: lipidic cubic phase / pH: 5.5 Details: 28% PEG 500DME, 100 mM MES-NaOH, pH 5.50, 150 mM K-formate

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

Diamond

/ Beamline: I24 / Wavelength: 0.9762 Å

Detector

Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 5, 2020

Radiation

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

Radiation wavelength

Wavelength: 0.9762 Å / Relative weight: 1

Reflection twin

Type	Crystal-ID	ID	Operator	Domain-ID	Fraction
pseudo-merohedral	1	1	H, K, L	1	0.676
pseudo-merohedral	2	2	-H-4/2L, -K, L	2	0.324

Reflection

Resolution: 3.37→69.78 Å / Num. obs: 13144 / % possible obs: 99.95 % / Redundancy: 6.1 % / CC_1/2: 0.79 / R_pim(I) all: 0.15 / Net I/σ(I): 2

Reflection shell

Resolution: 3.37→3.52 Å / Mean I/σ(I) obs: 0.6 / Num. unique obs: 3643 / CC_1/2: 0.1

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0350	refinement
DIALS		data reduction
DIALS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7ZK1

7zk1

Resolution: 3.372→69.778 Å / Cor.coef. F_o:F_c: 0.823 / Cor.coef. F_o:F_c free: 0.802 / WR_factor R_free: 0.276 / WR_factor R_work: 0.238 / SU B: 27.489 / SU ML: 0.22 / Average fsc free: 0.9804 / Average fsc work: 0.9851 / Cross valid method: THROUGHOUT / ESU R Free: 0.144
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2795	631	4.833 %
R_work	0.2495	12426	-
all	0.251	-	-
obs	-	13057	92.774 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 68.309 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-4.757 Å²	0 Å²	-2.371 Å²
2-	-	-8.223 Å²	-0 Å²
3-	-	-	12.98 Å²

Refinement step

Cycle: LAST / Resolution: 3.372→69.778 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5898	0	28	0	5926

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.011	6096
X-RAY DIFFRACTION	r_bond_other_d	0.044	0.016	5448
X-RAY DIFFRACTION	r_angle_refined_deg	2.006	1.624	8290
X-RAY DIFFRACTION	r_angle_other_deg	1.036	1.549	12600
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.72	5	724
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	5.578	10	26
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	20.495	10	962
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	17.383	10	280
X-RAY DIFFRACTION	r_chiral_restr	0.09	0.2	894
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	6862
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	1378
X-RAY DIFFRACTION	r_nbd_refined	0.248	0.2	1452
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.226	0.2	5654
X-RAY DIFFRACTION	r_nbtor_refined	0.195	0.2	2994
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.085	0.2	3209
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.209	0.2	104
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.108	0.2	5
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.396	0.2	70
X-RAY DIFFRACTION	r_nbd_other	0.441	0.2	149
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.434	0.2	7
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.163	0.2	2
X-RAY DIFFRACTION	r_mcbond_it	1.388	5.595	2908
X-RAY DIFFRACTION	r_mcbond_other	1.388	5.595	2908
X-RAY DIFFRACTION	r_mcangle_it	2.045	8.388	3630
X-RAY DIFFRACTION	r_mcangle_other	2.045	8.388	3631
X-RAY DIFFRACTION	r_scbond_it	1.179	5.681	3188
X-RAY DIFFRACTION	r_scbond_other	1.179	5.681	3187
X-RAY DIFFRACTION	r_scangle_it	1.814	8.492	4660
X-RAY DIFFRACTION	r_scangle_other	1.814	8.492	4660
X-RAY DIFFRACTION	r_lrange_it	2.628	108.348	25601
X-RAY DIFFRACTION	r_lrange_other	2.628	108.347	25600
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.149	0.05	8309
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.105	0.05	3636

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.14878	0.05008
1	2	A	X-RAY DIFFRACTION	Local ncs	0.14878	0.05008
2	3	A	X-RAY DIFFRACTION	Local ncs	0.10485	0.05009
2	4	A	X-RAY DIFFRACTION	Local ncs	0.10485	0.05009

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 (%)
3.372-3.46	0.527	2	0.277	97	X-RAY DIFFRACTION	20
3.46-3.554	0.283	54	0.266	926	X-RAY DIFFRACTION	96.9337
3.554-3.657	0.264	34	0.247	926	X-RAY DIFFRACTION	98.4615
3.657-3.77	0.23	38	0.225	882	X-RAY DIFFRACTION	97.4576
3.77-3.893	0.27	41	0.238	873	X-RAY DIFFRACTION	99.5643
3.893-4.03	0.24	38	0.2	865	X-RAY DIFFRACTION	100
4.03-4.182	0.267	40	0.243	816	X-RAY DIFFRACTION	100
4.182-4.353	0.262	44	0.254	781	X-RAY DIFFRACTION	99.3976
4.353-4.546	0.299	47	0.263	723	X-RAY DIFFRACTION	97.3451
4.546-4.767	0.27	37	0.246	740	X-RAY DIFFRACTION	100
4.767-5.025	0.263	37	0.234	698	X-RAY DIFFRACTION	99.3243
5.025-5.329	0.303	29	0.244	653	X-RAY DIFFRACTION	99.8536
5.329-5.697	0.392	48	0.256	594	X-RAY DIFFRACTION	99.3808
5.697-6.152	0.318	33	0.269	587	X-RAY DIFFRACTION	100
6.152-6.738	0.315	31	0.264	502	X-RAY DIFFRACTION	97.0856
6.738-7.531	0.27	28	0.233	492	X-RAY DIFFRACTION	100
7.531-8.692	0.351	10	0.224	443	X-RAY DIFFRACTION	99.5604
8-10	0.222	22	0.202	363	X-RAY DIFFRACTION	97.7157

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	0.1411	0.0357	0.1066	0.0469	-0.0386	0.2129	-0.0471	-0.0586	-0.0047	-0.0562	0.0413	0.029	0.0584	-0.1368	0.0058	0.107	0.0076	0.0164	0.258	-0.0162	0.2255	22.653	-2.9019	20.0297
2	0.1261	-0.0501	-0.0382	0.1312	0.0184	0.0148	-0.0216	0.1083	0.0203	-0.0386	0.0263	0.0342	-0.0042	-0.0527	-0.0048	0.0745	0.001	0.0382	0.3063	-0.0057	0.1803	18.8333	25.0799	43.4876
3	0.5853	-0.4637	-0.4769	0.7814	0.5949	0.5047	-0.0137	0.0421	0.0331	-0.1287	0.0853	-0.0877	-0.0642	0.0159	-0.0717	0.0484	-0.0292	0.0191	0.1198	0.0158	0.1969	59.3472	-6.4889	24.7671
4	0.6283	0.8527	0.5151	1.4259	1.0488	0.882	-0.0703	0.0925	0.0138	-0.0327	0.1377	-0.0295	0.0275	0.0679	-0.0675	0.0272	-0.0103	-0.0049	0.1141	0.0394	0.1591	54.1344	29.3161	54.1351

Refinement TLS group

Selection: ALL

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