[English] 日本語
Yorodumi
- PDB-5lnc: Structure of SPX domain of the yeast inorganic polyphophate polym... -

+
Open data


ID or keywords:

Loading...

-
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 / ATP-polyphosphate phosphotransferase / regulation of NAD metabolic process / positive regulation of response to oxidative stress / polyphosphate biosynthetic process / engulfment of target by autophagosome / positive regulation of maintenance of mitotic sister chromatid cohesion / 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 / ATP-polyphosphate phosphotransferase / regulation of NAD metabolic process / positive regulation of response to oxidative stress / polyphosphate biosynthetic process / engulfment of target by autophagosome / positive regulation of maintenance of mitotic sister chromatid cohesion / regulation of response to oxidative stress / ADP-D-ribose binding / polyphosphate kinase activity / ADP-D-ribose modification-dependent protein binding / negative regulation of transcription of nucleolar large rRNA by RNA polymerase I / microautophagy / sex chromatin / vacuole fusion, non-autophagic / sex-chromosome dosage compensation / polyphosphate metabolic process / positive regulation of endodermal cell differentiation / establishment of protein localization to chromatin / double-stranded methylated DNA binding / poly-ADP-D-ribose modification-dependent protein binding / Barr body / rDNA binding / vacuolar transport / inositol hexakisphosphate binding / negative regulation of protein serine/threonine kinase activity / regulation of oxidative phosphorylation / positive regulation of keratinocyte differentiation / fungal-type vacuole membrane / protein serine/threonine kinase inhibitor activity / negative regulation of response to oxidative stress / vacuolar membrane / nuclear chromosome / negative regulation of gene expression, epigenetic / site of DNA damage / autophagosome membrane / regulation of lipid metabolic process / pericentric heterochromatin / condensed chromosome / nucleosomal DNA binding / epigenetic regulation of gene expression / transcription initiation-coupled chromatin remodeling / cell periphery / promoter-specific chromatin binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / chromatin DNA binding / heterochromatin formation / structural constituent of chromatin / nucleosome / nucleosome assembly / cell cortex / cytoplasmic vesicle / chromosome, telomeric region / transcription cis-regulatory region binding / calmodulin binding / protein heterodimerization activity / DNA repair / endoplasmic reticulum membrane / chromatin / nucleolus / protein kinase binding / negative regulation of transcription by RNA polymerase II / enzyme binding / endoplasmic reticulum / DNA binding / extracellular exosome / nucleoplasm / nucleus
Similarity search - Function
Domain of unknown function DUF202 / VTC domain / VTC domain superfamily / : / Domain of unknown function (DUF202) / VTC domain / Core histone macro-H2A / Core histone macro-H2A, macro domain / SPX domain / SPX domain profile. ...Domain of unknown function DUF202 / VTC domain / VTC domain superfamily / : / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water00
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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}

+
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