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- PDB-8tyv: Crystal structure of the SPX domain of XPR1 in complex with IP8 -

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Basic information

Entry
Database: PDB / ID: 8tyv
TitleCrystal structure of the SPX domain of XPR1 in complex with IP8
ComponentsSolute carrier family 53 member 1
KeywordsTRANSFERASE / Inositol diphosphoinositol pentakisphosphate kinase / Analog methylenebisphosphonate / PPIP5K ATP-grasp / Pyrophosphate Diphosphate
Function / homology
Function and homology information


: / phosphate ion transport / intracellular phosphate ion homeostasis / inositol hexakisphosphate binding / phosphate ion transmembrane transport / cellular response to phosphate starvation / efflux transmembrane transporter activity / response to virus / trans-Golgi network / virus receptor activity ...: / phosphate ion transport / intracellular phosphate ion homeostasis / inositol hexakisphosphate binding / phosphate ion transmembrane transport / cellular response to phosphate starvation / efflux transmembrane transporter activity / response to virus / trans-Golgi network / virus receptor activity / Golgi apparatus / plasma membrane / cytoplasm
Similarity search - Function
EXS, C-terminal / EXS family / EXS domain profile. / SPX domain / SPX domain / SPX domain profile.
Similarity search - Domain/homology
Chem-I8P / Solute carrier family 53 member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsWang, H. / Shears, S.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)1ZIAES080046 United States
CitationJournal: To Be Published
Title: Co-ordination of cellular phosphate uptake and efflux requires an organelle-based receptor for the inositol pyrophosphate, IP8
Authors: Wang, H. / Shears, S.
History
DepositionAug 25, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Solute carrier family 53 member 1
A: Solute carrier family 53 member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7973
Polymers41,9772
Non-polymers8201
Water4,035224
1
B: Solute carrier family 53 member 1


Theoretical massNumber of molelcules
Total (without water)20,9891
Polymers20,9891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Solute carrier family 53 member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8092
Polymers20,9891
Non-polymers8201
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.712, 47.754, 70.373
Angle α, β, γ (deg.)90.00, 104.21, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Solute carrier family 53 member 1 / Phosphate exporter SLC53A1 / Protein SYG1 homolog / Xenotropic and polytropic murine leukemia virus ...Phosphate exporter SLC53A1 / Protein SYG1 homolog / Xenotropic and polytropic murine leukemia virus receptor X3 / X-receptor / Xenotropic and polytropic retrovirus receptor 1


Mass: 20988.633 Da / Num. of mol.: 2 / Fragment: SPX domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: XPR1, SLC53A1, SYG1, X3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UBH6
#2: Chemical ChemComp-I8P / (1R,3S,4R,5S,6R)-2,4,5,6-tetrakis(phosphonooxy)cyclohexane-1,3-diyl bis[trihydrogen (diphosphate)] / 1D-myo-inositol 1,5-bisdiphosphate 2,3,4,6-tetrakisphosphate


Mass: 819.995 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H20O30P8 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.2 Å3/Da / Density % sol: 44.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 2mM IP8 soaked into crystals grown under 6% PEG 3350, 30% Ethylene Glycol, 0.1 M Sodium Citrate, 0.1 M MgCl2, pH 6.0 for 3 Days

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 30876 / % possible obs: 98.2 % / Redundancy: 7.3 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.018 / Rrim(I) all: 0.05 / Χ2: 0.922 / Net I/σ(I): 15.4 / Num. measured all: 225578
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.85-1.885.50.61113100.8270.9510.2680.670.90585.1
1.88-1.926.30.62914410.880.9680.260.6820.88892
1.92-1.956.60.53515180.9170.9780.2190.580.84496.6
1.95-1.996.90.48815130.940.9840.1950.5260.89798.9
1.99-2.047.20.37515450.970.9920.1490.4040.92799.6
2.04-2.087.40.27815720.9830.9960.1090.2990.9399.7
2.08-2.147.50.21115710.9890.9970.0820.2270.93999.8
2.14-2.197.60.17315600.990.9970.0670.1850.9699.9
2.19-2.267.60.14715460.9920.9980.0570.1580.96100
2.26-2.337.60.11915510.9940.9990.0460.1280.968100
2.33-2.417.60.09815910.9950.9990.0380.1060.992100
2.41-2.517.60.08715640.9960.9990.0340.0941.058100
2.51-2.637.60.07515700.9960.9990.0290.081.085100
2.63-2.767.60.06315640.9970.9990.0250.0680.994100
2.76-2.947.60.05615780.9970.9990.0220.060.955100
2.94-3.167.60.0515910.9980.9990.0190.0540.904100
3.16-3.487.60.05315580.9970.9990.020.0571.063100
3.48-3.997.60.04616040.99810.0180.0490.938100
3.99-5.027.50.03915810.99810.0150.0420.67999.3
5.02-507.10.03215480.99910.0130.0350.48893.8

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-2000data scaling
HKL-2000data reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→36.05 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 29.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2705 1446 5.09 %
Rwork0.2358 --
obs0.2376 28427 90.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→36.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2828 0 44 224 3096
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122932
X-RAY DIFFRACTIONf_angle_d1.9223962
X-RAY DIFFRACTIONf_dihedral_angle_d9.356388
X-RAY DIFFRACTIONf_chiral_restr0.096434
X-RAY DIFFRACTIONf_plane_restr0.008496
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.920.3676720.28651610X-RAY DIFFRACTION54
1.92-1.990.3515900.28852099X-RAY DIFFRACTION71
1.99-2.080.28311310.25862530X-RAY DIFFRACTION85
2.08-2.190.28871550.24842896X-RAY DIFFRACTION97
2.19-2.330.29051740.24572924X-RAY DIFFRACTION100
2.33-2.510.25271580.24222999X-RAY DIFFRACTION100
2.51-2.760.23831640.22882968X-RAY DIFFRACTION100
2.76-3.160.27811640.24393006X-RAY DIFFRACTION100
3.16-3.980.24061720.21172987X-RAY DIFFRACTION100
3.98-36.050.28271660.22672962X-RAY DIFFRACTION96
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)
12.1177-0.47460.08842.5738-0.40282.23230.03710.1608-0.07110.1922-0.2077-0.1037-0.1275-0.23890.1030.17380.1325-0.04010.0032-0.12980.0865-28.0227.4258.822
22.6826-0.33130.01392.0086-0.31362.683-0.09560.22930.33870.5470.54390.4017-0.4316-0.7069-0.25590.35590.14710.21580.2890.29750.23732.73524.07343.094
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 2:205 )A2 - 205
2X-RAY DIFFRACTION2( CHAIN B AND RESID 2:205 )B2 - 205

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