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

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Basic information

Entry
Database: PDB / ID: 7zkz
TitleCrystal structure of cystinosin from Arabidopsis thaliana bound to two nanobodies
Components
  • Cystinosin homolog
  • Llama nanobody
  • nanobody
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.329 Å
AuthorsLoebel, M. / Newstead, S.
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 13, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 31, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cystinosin homolog
B: Llama nanobody
C: nanobody


Theoretical massNumber of molelcules
Total (without water)58,9493
Polymers58,9493
Non-polymers00
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3070 Å2
ΔGint-18 kcal/mol
Surface area22360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)210.281, 77.457, 46.303
Angle α, β, γ (deg.)90.000, 93.250, 90.000
Int Tables number5
Space group name H-MC121

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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) / Variant (production host): BJ5460 / References: UniProt: P57758
#2: Protein Llama 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 nanobody


Mass: 13157.398 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)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 3.24 Å3/Da / Density % sol: 62.04 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 5.75
Details: 28% PEG 500DME, 100 mM MES-NaOH, pH 5.75, 150 mM K-formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.329→104.76 Å / Num. obs: 31727 / % possible obs: 100 % / Redundancy: 6.4 % / Biso Wilson estimate: 61.36 Å2 / Rpim(I) all: 0.072 / Rrim(I) all: 0.185 / Net I/σ(I): 7.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) all% possible all
2.33-2.376.70.61035615540.9172.387100
6.32-104.876.433.71056616590.0260.06499.9

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Processing

Software
NameVersionClassification
xia2data scaling
BUSTER2.10.4 (20-OCT-2021)refinement
PDB_EXTRACT3.27data extraction
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7ZK1

7zk1


Resolution: 2.329→20.79 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.924 / SU R Cruickshank DPI: 0.269 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.26 / SU Rfree Blow DPI: 0.211 / SU Rfree Cruickshank DPI: 0.216
RfactorNum. reflection% reflectionSelection details
Rfree0.2649 1566 4.95 %RANDOM
Rwork0.2347 ---
obs0.2363 31641 99.3 %-
Displacement parametersBiso max: 131.19 Å2 / Biso mean: 66.88 Å2 / Biso min: 43.51 Å2
Baniso -1Baniso -2Baniso -3
1-7.7556 Å20 Å22.7636 Å2
2---8.4631 Å20 Å2
3---0.7075 Å2
Refine analyzeLuzzati coordinate error obs: 0.38 Å
Refinement stepCycle: final / Resolution: 2.329→20.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3773 0 0 108 3881
Biso mean---61.88 -
Num. residues----480
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1280SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes651HARMONIC5
X-RAY DIFFRACTIONt_it3885HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion502SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3148SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3885HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg5286HARMONIC20.97
X-RAY DIFFRACTIONt_omega_torsion3.12
X-RAY DIFFRACTIONt_other_torsion19.29
LS refinement shellResolution: 2.33→2.35 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.5489 38 6 %
Rwork0.4119 595 -
all0.4198 633 -
obs--77.22 %
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)
14.2158-0.70340.90541.7044-0.27592.7282-0.1106-0.2986-0.04070.050.10960.3904-0.0662-0.43230.001-0.28850.1644-0.0138-0.11380.0268-0.3853.3731-9.392714.0411
24.5241-1.7671.35724.7142-2.48044.5656-0.0456-0.030.00360.1321-0.0839-0.2252-0.15740.06990.1295-0.55690.0273-0.0562-0.1622-0.0659-0.503483.6406-20.08237.2676
38.5072-0.52650.02392.540.14033.32130.1475-0.4745-0.32450.0466-0.0847-0.31220.19230.0842-0.0628-0.1496-0.0029-0.08860.11630.052-0.068912.7242-5.81618.4032
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A2 - 244
2X-RAY DIFFRACTION2{ B|* }B1 - 127
3X-RAY DIFFRACTION3{ C|* }C1 - 122

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