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

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Basic information

Entry
Database: PDB / ID: 5iit
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
Keywordsinositol phosphate binding protein / helical bundle / alpha-helical hairpin / protein-protein interaction / chaperone
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 / transcription cis-regulatory region binding / calmodulin 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: 2.134 Å
AuthorsWild, R. / Hothorn, M.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
European Research Council310856 Switzerland
CitationJournal: Science / Year: 2016
Title: Control of eukaryotic phosphate homeostasis by inositol polyphosphate sensor domains.
Authors: Wild, R. / Gerasimaite, R. / Jung, J.Y. / Truffault, V. / Pavlovic, I. / Schmidt, A. / Saiardi, A. / Jessen, H.J. / Poirier, Y. / Hothorn, M. / Mayer, A.
History
DepositionMar 1, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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
C: Vacuolar transporter chaperone 4,Core histone macro-H2A.1
D: Vacuolar transporter chaperone 4,Core histone macro-H2A.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,46419
Polymers168,9404
Non-polymers1,52415
Water3,315184
1
A: Vacuolar transporter chaperone 4,Core histone macro-H2A.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6505
Polymers42,2351
Non-polymers4154
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Vacuolar transporter chaperone 4,Core histone macro-H2A.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6135
Polymers42,2351
Non-polymers3784
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Vacuolar transporter chaperone 4,Core histone macro-H2A.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6756
Polymers42,2351
Non-polymers4405
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Vacuolar transporter chaperone 4,Core histone macro-H2A.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5263
Polymers42,2351
Non-polymers2912
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.640, 67.922, 129.677
Angle α, β, γ (deg.)90.00, 93.32, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#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.: 4
Source method: isolated from a genetically manipulated source
Details: Artificial fusion between the SPX domain (residues 1-178) to the macro domain of human histone macroH2A1.1 connected by a AGS linker.
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast), (gene. exp.) Homo sapiens (human)
Strain: ATCC 204508 / S288c / Gene: VTC4, PHM3, YJL012C, J1345, H2AFY, MACROH2A1 / Plasmid: pMH-macroHC / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: P47075, UniProt: O75367

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Non-polymers , 5 types, 199 molecules

#2: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 184 / Source method: isolated from a natural source / Formula: H2O

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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: 2.75 Å3/Da / Density % sol: 55.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 19% PEG 3350, 0.1M AmSO4, 0.1M MES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976251 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976251 Å / Relative weight: 1
ReflectionResolution: 2.13→50 Å / Num. obs: 101489 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Biso Wilson estimate: 51 Å2 / CC1/2: 0.999 / Rsym value: 0.079 / Net I/σ(I): 15.5
Reflection shellResolution: 2.13→2.26 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 1.9 / % possible all: 96.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1zr3

1zr3


Resolution: 2.134→46.859 Å / SU ML: 0.29 / σ(F): 1.35 / Phase error: 30.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2471 5074 5 %
Rwork0.2109 --
obs0.2128 101454 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.134→46.859 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11278 0 90 184 11552
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00411658
X-RAY DIFFRACTIONf_angle_d0.74815745
X-RAY DIFFRACTIONf_dihedral_angle_d12.894362
X-RAY DIFFRACTIONf_chiral_restr0.0291769
X-RAY DIFFRACTIONf_plane_restr0.0032004
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1345-2.15880.3621500.36142849X-RAY DIFFRACTION88
2.1588-2.18410.3791680.33743179X-RAY DIFFRACTION99
2.1841-2.21080.3511660.31883166X-RAY DIFFRACTION99
2.2108-2.23880.35651670.3133170X-RAY DIFFRACTION99
2.2388-2.26820.34131690.30123210X-RAY DIFFRACTION99
2.2682-2.29930.31641680.28853181X-RAY DIFFRACTION99
2.2993-2.33210.32771690.28373205X-RAY DIFFRACTION99
2.3321-2.3670.33481690.27523216X-RAY DIFFRACTION99
2.367-2.40390.30011680.27013192X-RAY DIFFRACTION99
2.4039-2.44340.31931690.27183212X-RAY DIFFRACTION100
2.4434-2.48550.28961680.26573199X-RAY DIFFRACTION100
2.4855-2.53070.30681710.25333243X-RAY DIFFRACTION99
2.5307-2.57930.28241690.25643194X-RAY DIFFRACTION99
2.5793-2.6320.2961670.24143194X-RAY DIFFRACTION100
2.632-2.68920.27691690.24753209X-RAY DIFFRACTION99
2.6892-2.75180.26141680.24293205X-RAY DIFFRACTION99
2.7518-2.82060.281720.23063259X-RAY DIFFRACTION100
2.8206-2.89680.28081670.23533186X-RAY DIFFRACTION100
2.8968-2.9820.31211720.25463259X-RAY DIFFRACTION100
2.982-3.07830.28191700.24613236X-RAY DIFFRACTION100
3.0783-3.18830.28231700.24643232X-RAY DIFFRACTION100
3.1883-3.31590.29061700.22623227X-RAY DIFFRACTION100
3.3159-3.46680.25281700.2193215X-RAY DIFFRACTION100
3.4668-3.64950.23121710.20773253X-RAY DIFFRACTION100
3.6495-3.8780.22441690.19083225X-RAY DIFFRACTION100
3.878-4.17730.20421740.17373295X-RAY DIFFRACTION100
4.1773-4.59730.20281710.15163252X-RAY DIFFRACTION100
4.5973-5.26180.2061720.15553271X-RAY DIFFRACTION99
5.2618-6.62630.21721730.19843287X-RAY DIFFRACTION100
6.6263-46.870.18741780.16943359X-RAY DIFFRACTION99
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)
10.3162-0.20040.39860.166-0.56622.21830.04240.2902-0.05020.07810.1946-0.220.06530.43790.00090.2958-0.02390.0080.5013-0.09720.4156-73.620341.9723-19.1309
20.9890.84331.0061.12330.08550.8036-0.03430.3409-0.0483-0.20130.222-0.2063-0.20540.08560.00580.3111-0.0390.03820.6264-0.0730.3663-84.777735.597-31.6038
30.1913-0.21170.20370.3879-0.41410.69460.08930.54890.4967-0.1065-0.39660.7974-0.3666-0.64790.00020.431-0.04350.00550.7051-0.14150.5158-105.999437.7606-27.6116
42.9882-1.32880.76132.2885-1.48814.43050.0177-0.00440.26480.09320.036-0.083-0.5139-0.1753-0.00050.3725-0.01670.04050.2844-0.01330.3253-126.530732.5677-52.7079
51.0502-0.55311.2732.5449-0.67962.25940.0652-0.06360.0084-0.03730.16570.14330.2478-0.340.0010.3277-0.0295-0.03340.44360.02020.3356-125.892621.4919-46.9032
60.34470.0923-0.39480.0895-0.55851.7249-0.0204-0.18580.0171-0.08440.099-0.10220.04630.47900.3477-0.05330.00980.5964-0.07760.3821-71.9716-0.9703-42.2233
71.0722-0.9208-0.94881.27090.31410.49-0.0543-0.25870.02660.13290.1337-0.0980.19430.05920.00020.3053-0.0665-0.02060.5454-0.05980.3051-84.85056.2143-30.6946
80.5056-0.1419-0.625-0.12190.05710.13960.01110.0657-0.52820.1707-0.15920.42840.20580.1996-0.00050.4778-0.0039-0.04780.6374-0.11220.5371-110.32496.2796-35.5288
93.29790.90770.37412.4452-0.71263.71170.09070.0474-0.2109-0.02360.078-0.05380.3409-0.06130.26220.27990.0113-0.06150.0179-0.02560.3172-129.37318.9512-13.4519
101.08520.1959-1.4682.321-0.58492.46840.03820.41660.1905-0.02810.13120.0115-0.3926-0.201700.2801-0.02470.03120.3029-00.3179-126.789520.701-20.5918
112.03631.5060.05441.9884-0.9821.72810.4086-0.22970.45540.1655-0.40671.0944-0.5826-0.1075-0.00770.4842-0.09080.14760.5251-0.18670.5811-110.499639.1574-13.9091
120.26430.20480.13380.17670.16010.3431-0.189-0.0106-0.90810.0676-0.27791.49660.094-0.2031-0.01190.3480.00250.01610.6398-0.02580.4819-94.36075.7464-20.4934
131.2757-0.2598-0.54811.20270.00440.74120.2891-0.25270.22930.1614-0.2134-0.0715-0.19120.07030.00030.3412-0.10940.00980.5988-0.09070.3067-93.549828.2377-16.23
143.6266-0.65281.58882.3501-0.4622.65420.1888-0.3836-0.0930.3226-0.0961-0.13130.0766-0.3830.00220.3952-0.1267-0.060.45750.05510.4315-54.35044.5694-13.7685
150.6749-0.52790.81672.1457-0.14281.07950.21210.2907-0.0161-0.1055-0.2199-0.35110.3761-0.1189-0.00010.4037-0.0353-0.02450.53820.03510.4583-54.76217.981-26.392
161.8718-1.32090.331.1957-0.91821.71940.43580.2413-0.4761-0.5999-0.29860.92510.6265-0.04570.00620.66360.049-0.21070.6872-0.17670.6135-108.28572.2913-51.9615
170.2829-0.181-0.14760.09460.15620.1951-0.18940.18240.877-0.1446-0.12171.7286-0.0992-0.1493-0.00240.493-0.0883-0.02520.6674-0.03940.5872-93.307235.2777-43.7608
181.01210.24670.61771.12180.06020.63940.30290.2889-0.178-0.2674-0.2277-0.09930.12760.08990.01940.41150.05450.00590.6366-0.09180.2873-91.519714.2585-47.0194
192.68131.6208-0.62163.219-0.90352.48160.19670.3390.2514-0.5561-0.1902-0.6076-0.2727-0.0463-0.01430.55230.0780.25140.53110.13770.7279-51.465236.9663-43.537
200.65851.0683-0.65082.051-0.53681.17370.3884-0.14730.3490.2196-0.3449-0.3435-0.5460.1180.00050.5033-0.05230.10740.53880.0340.6387-54.01133.5602-31.6777
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 12:73)
2X-RAY DIFFRACTION2(chain A and resseq 74:158)
3X-RAY DIFFRACTION3(chain A and resseq 159:178)
4X-RAY DIFFRACTION4(chain A and resseq 179:310)
5X-RAY DIFFRACTION5(chain A and resseq 311:367)
6X-RAY DIFFRACTION6(chain B and resseq 14:73)
7X-RAY DIFFRACTION7(chain B and resseq 74:158)
8X-RAY DIFFRACTION8(chain B and resseq 159:190)
9X-RAY DIFFRACTION9(chain B and resseq 191:310)
10X-RAY DIFFRACTION10(chain B and resseq 311:369)
11X-RAY DIFFRACTION11(chain C and resseq 13:67)
12X-RAY DIFFRACTION12(chain C and resseq 68:88)
13X-RAY DIFFRACTION13(chain C and resseq 89:177)
14X-RAY DIFFRACTION14(chain C and resseq 178:310)
15X-RAY DIFFRACTION15(chain C and resseq 311:369)
16X-RAY DIFFRACTION16(chain D and resseq 14:67)
17X-RAY DIFFRACTION17(chain D and resseq 68:86)
18X-RAY DIFFRACTION18(chain D and resseq 87:177)
19X-RAY DIFFRACTION19(chain D and resseq 178:310)
20X-RAY DIFFRACTION20(chain D and resseq 311:368)

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