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- PDB-7zk1: Crystal structure of cystinosin from Arabidopsis thaliana bound t... -

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Basic information

Entry
Database: PDB / ID: 7zk1
TitleCrystal structure of cystinosin from Arabidopsis thaliana bound to sybody and nanobody
Components
  • Cystinosin homolog
  • Llama derived nanobody
  • Synthetic nanobody (Sybody)
KeywordsMEMBRANE PROTEIN / Cystinosin / PQ-loop protein / proton coupling / cystine transport
Function / homology
Function and homology information


L-cystine transport / L-amino acid transmembrane transporter activity / plant-type vacuole / lysosomal membrane
Similarity search - Function
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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesArabidopsis thaliana (thale cress)
Lama glama (llama)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.65 Å
AuthorsLoebel, M. / Newstead, S. / Omari, K.E.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust215519/Z/19/Z United Kingdom
CitationJournal: 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
DepositionApr 12, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 31, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cystinosin homolog
B: Llama derived nanobody
C: Synthetic nanobody (Sybody)


Theoretical massNumber of molelcules
Total (without water)59,4433
Polymers59,4433
Non-polymers00
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint-17 kcal/mol
Surface area22830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.787, 319.962, 45.648
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Cystinosin homolog


Mass: 31902.965 Da / Num. of mol.: 1
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) / Strain (production host): BJ5460 / References: UniProt: P57758
#2: Protein Llama derived nanobody


Mass: 13888.493 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli MC1061 (bacteria)
#3: Antibody Synthetic nanobody (Sybody)


Mass: 13651.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.13 Å3/Da / Density % sol: 70.19 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 5.5
Details: 27.5% PEG 500DME, 100 mM MES-NaOH, pH 5.50, 100 mM K-formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.65→79.99 Å / Num. obs: 28079 / % possible obs: 99.9 % / Redundancy: 20 % / CC1/2: 0.996 / Rmerge(I) obs: 0.542 / Rpim(I) all: 0.114 / Rrim(I) all: 0.554 / Net I/σ(I): 5.9
Reflection shell

Diffraction-ID: 1 / % possible all: 99.9

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs
2.65-2.7913.67.0955437040120.3792.0117.380.5
8.37-79.99210.1342198410460.9960.0340.13917.9

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Processing

Software
NameVersionClassification
BUSTERrefinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
autoPROCdata reduction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.65→79.99 Å / SU R Cruickshank DPI: 0.391 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.391 / SU Rfree Blow DPI: 0.286 / SU Rfree Cruickshank DPI: 0.289
RfactorNum. reflection% reflectionSelection details
Rfree0.27 1331 -RANDOM
Rwork0.23 ---
obs-26170 93.4 %-
Displacement parametersBiso max: 131.86 Å2 / Biso mean: 84.8151 Å2 / Biso min: 33.68 Å2
Baniso -1Baniso -2Baniso -3
1--6.7123 Å20 Å20 Å2
2--23.4473 Å20 Å2
3----16.735 Å2
Refine analyzeLuzzati coordinate error obs: 0.49 Å
Refinement stepCycle: LAST / Resolution: 2.65→79.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3920 0 0 32 3952
LS refinement shellResolution: 2.65→2.68 Å
RfactorNum. reflection% reflection
Rfree0.43 24 4.58 %
Rwork0.32 524 -
obs--52.09 %
Refinement TLS params.

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

IDL11 (°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)
10.4985-0.04340.35043.40870.17170.67180.0289-0.05640.27180.0099-0.0746-0.07570.2014-0.07050.04570.304-0.00820.01530.03460.02470.16483.411635.7648-4.5806
22.5088-1.37130.21676.31132.09183.9251-0.23120.171-0.3537-0.01470.084-0.5169-0.248-0.00910.14720.304-0.02930.01360.0030.01540.109411.90953.191217.4456
32.64640.4144-0.36257.5323-0.5650.29270.16120.0829-0.00060.19480.0247-0.0719-0.0497-0.0002-0.18590.17050.0309-0.0663-0.0885-0.04620.3044.492372.7504-2.0436
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A3 - 245
2X-RAY DIFFRACTION2{ B|* }B1 - 127
3X-RAY DIFFRACTION3{ C|* }C1 - 121

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