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- PDB-5lnc: Structure of SPX domain of the yeast inorganic polyphophate polym... -

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Basic information

Entry
Database: PDB / ID: 5lnc
TitleStructure of SPX domain of the yeast inorganic polyphophate polymerase Vtc4 crystallized by carrier-driven crystallization in fusion with the macro domain of human histone macroH2A1.1
ComponentsVacuolar transporter chaperone 4,Core histone macro-H2A.1
KeywordsHYDROLASE / macro domain / spx domain / inositol polyphosphate binding / carrier-driven crystallization
Function / homology
Function and homology information


vacuolar transporter chaperone complex / negative regulation of cell cycle G2/M phase transition / negative regulation of protein localization to chromosome, telomeric region / regulation of NAD metabolic process / ATP-polyphosphate phosphotransferase / positive regulation of response to oxidative stress / polyphosphate biosynthetic process / positive regulation of maintenance of mitotic sister chromatid cohesion / engulfment of target by autophagosome / negative regulation of response to oxidative stress ...vacuolar transporter chaperone complex / negative regulation of cell cycle G2/M phase transition / negative regulation of protein localization to chromosome, telomeric region / regulation of NAD metabolic process / ATP-polyphosphate phosphotransferase / positive regulation of response to oxidative stress / polyphosphate biosynthetic process / positive regulation of maintenance of mitotic sister chromatid cohesion / engulfment of target by autophagosome / negative regulation of response to oxidative stress / regulation of response to oxidative stress / Barr body / ADP-D-ribose binding / polyphosphate kinase activity / ADP-D-ribose modification-dependent protein binding / sex-chromosome dosage compensation / negative regulation of transcription of nucleolar large rRNA by RNA polymerase I / sex chromatin / vacuole fusion, non-autophagic / microautophagy / establishment of protein localization to chromatin / polyphosphate metabolic process / positive regulation of endodermal cell differentiation / double-stranded methylated DNA binding / vacuolar transport / rDNA binding / inositol hexakisphosphate binding / regulation of oxidative phosphorylation / negative regulation of protein serine/threonine kinase activity / poly-ADP-D-ribose modification-dependent protein binding / protein serine/threonine kinase inhibitor activity / positive regulation of keratinocyte differentiation / fungal-type vacuole membrane / vacuolar membrane / nucleosomal DNA binding / negative regulation of gene expression, epigenetic / nuclear chromosome / site of DNA damage / autophagosome membrane / regulation of lipid metabolic process / pericentric heterochromatin / epigenetic regulation of gene expression / condensed chromosome / transcription initiation-coupled chromatin remodeling / cell periphery / promoter-specific chromatin binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / chromatin DNA binding / nucleosome assembly / structural constituent of chromatin / nucleosome / cell cortex / cytoplasmic vesicle / chromosome, telomeric region / calmodulin binding / transcription cis-regulatory region binding / protein heterodimerization activity / DNA repair / chromatin / endoplasmic reticulum membrane / nucleolus / protein kinase binding / negative regulation of transcription by RNA polymerase II / enzyme binding / endoplasmic reticulum / DNA binding / extracellular exosome / nucleoplasm / membrane / nucleus
Similarity search - Function
VTC domain superfamily / Domain of unknown function DUF202 / VTC domain / Domain of unknown function (DUF202) / VTC domain / Core histone macro-H2A / Core histone macro-H2A, macro domain / SPX domain / SPX domain profile. / Histone H2A, C-terminal domain ...VTC domain superfamily / Domain of unknown function DUF202 / VTC domain / Domain of unknown function (DUF202) / VTC domain / Core histone macro-H2A / Core histone macro-H2A, macro domain / SPX domain / SPX domain profile. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Macro domain / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain-like
Similarity search - Domain/homology
Core histone macro-H2A.1 / Vacuolar transporter chaperone complex subunit 4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.29 Å
AuthorsWild, R. / Hothorn, M.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
European Research Council310856 Switzerland
CitationJournal: Protein Sci. / Year: 2017
Title: The macro domain as fusion tag for carrier-driven crystallization.
Authors: Wild, R. / Hothorn, M.
History
DepositionAug 3, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2017Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Vacuolar transporter chaperone 4,Core histone macro-H2A.1
B: Vacuolar transporter chaperone 4,Core histone macro-H2A.1


Theoretical massNumber of molelcules
Total (without water)84,4702
Polymers84,4702
Non-polymers00
Water0
1
A: Vacuolar transporter chaperone 4,Core histone macro-H2A.1


Theoretical massNumber of molelcules
Total (without water)42,2351
Polymers42,2351
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Vacuolar transporter chaperone 4,Core histone macro-H2A.1


Theoretical massNumber of molelcules
Total (without water)42,2351
Polymers42,2351
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.020, 130.050, 158.330
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121

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Components

#1: Protein Vacuolar transporter chaperone 4,Core histone macro-H2A.1 / Phosphate metabolism protein 3 / mH2A1 / Histone H2A.y / H2A/y / Medulloblastoma antigen MU-MB-50.205


Mass: 42234.934 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast), (gene. exp.) Homo sapiens (human)
Gene: VTC4, PHM3, YJL012C, J1345, H2AFY, MACROH2A1 / Organ: vacuole / Plasmid: pMH-macroHC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): DE3 RIL / References: UniProt: P47075, UniProt: O75367

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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: 3.47 Å3/Da / Density % sol: 65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 8.75% PEG 6000, 2.75M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97963 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 5, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97963 Å / Relative weight: 1
ReflectionResolution: 3.29→48.9 Å / Num. obs: 17957 / % possible obs: 98.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 192.94 Å2 / CC1/2: 1 / Rsym value: 0.07 / Net I/σ(I): 15.37
Reflection shellResolution: 3.29→3.38 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 0.6 / CC1/2: 0.253 / % possible all: 82.3

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1yd9

1yd9


Resolution: 3.29→48.9 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.92 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.496
RfactorNum. reflection% reflectionSelection details
Rfree0.302 909 5.06 %RANDOM
Rwork0.279 ---
obs0.28 17956 98.4 %-
Displacement parametersBiso mean: 179.49 Å2
Baniso -1Baniso -2Baniso -3
1-49.6938 Å20 Å20 Å2
2---74.8976 Å20 Å2
3---25.2038 Å2
Refine analyzeLuzzati coordinate error obs: 1.02 Å
Refinement stepCycle: 1 / Resolution: 3.29→48.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4673 0 0 0 4673
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0114746HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.136523HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1312SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes85HARMONIC2
X-RAY DIFFRACTIONt_gen_planes787HARMONIC5
X-RAY DIFFRACTIONt_it4746HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.54
X-RAY DIFFRACTIONt_other_torsion18.22
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion733SEMIHARMONIC5
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_contact5488SEMIHARMONIC4
LS refinement shellResolution: 3.29→3.49 Å / Rfactor Rfree error: 0 / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.446 144 5.46 %
Rwork0.377 2492 -
all0.381 2636 -
obs--90.57 %
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)
11.80370.29832.1864.19711.62730.6086-0.0518-0.1087-0.2087-0.21180.0136-0.09760.2560.10780.03810.2955-0.1517-0.01560.1624-0.1109-0.30454.1821-82.78429.0779
202.91040.88491.9853-0.60643.19410.05220.007-0.0050.14650.40840.2035-0.2005-0.1094-0.46070.1744-0.152-0.1441-0.13280.0312-0.282436.0038-66.028810.3698
38.3147-1.03372.91048.3155-2.91048.11120.0866-0.1090.5442-0.1713-0.05020.0206-0.5442-0.2963-0.0363-0.29930.1520.0998-0.02320.1520.13215.1236-27.774232.7189
46.5176-0.53642.76685.5839-2.91047.0934-0.0527-0.09920.1270.45160.1592-0.0283-0.02160.1045-0.1065-0.2784-0.00910.14970.11630.1520.036226.4935-35.968936.9831
56.29732.4782-1.82013.2537-2.54317.76740.13430.1567-0.23-0.1458-0.12780.03880.054-0.3561-0.0065-0.1550.1025-0.0673-0.19370.152-0.128610.8901-52.350860.9117
61.6714-0.5944-2.91040.97930.79227.8418-0.1513-0.25270.16140.38280.3861-0.0748-0.1913-0.2872-0.23490.1862-0.05320.03110.13150.152-0.220932.4955-44.073743.2392
74.56242.9104-0.89197.3466-0.9078.30910.02820.2947-0.1497-0.4380.4879-0.1990.5301-0.2104-0.5161-0.0874-0.152-0.05170.00490.0091-0.301450.6758-45.63317.9924
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|2 - 69}
2X-RAY DIFFRACTION2{A|70 - 190}
3X-RAY DIFFRACTION3{A|191 - 321}
4X-RAY DIFFRACTION4{A|322 - 371}
5X-RAY DIFFRACTION5{B|3 - 149}
6X-RAY DIFFRACTION6{B|150 - 212}
7X-RAY DIFFRACTION7{B|213 - 369}

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