[English] 日本語
Yorodumi
- PDB-8tyv: Crystal structure of the SPX domain of XPR1 in complex with IP8 -

+
Open data


ID or keywords:

Loading...

-
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 transmembrane transporter activity / phosphate ion transport / intracellular phosphate ion homeostasis / cellular response to phosphate starvation / phosphate ion transmembrane transport / inositol hexakisphosphate binding / efflux transmembrane transporter activity / response to virus / virus receptor activity / plasma membrane
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: Cell Rep / Year: 2024
Title: Homeostatic coordination of cellular phosphate uptake and efflux requires an organelle-based receptor for the inositol pyrophosphate IP8.
Authors: Li, X. / Kirkpatrick, R.B. / Wang, X. / Tucker, C.J. / Shukla, A. / Jessen, H.J. / Wang, H. / Shears, S.B. / Gu, C.
History
DepositionAug 25, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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
Has protein modificationN

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more