[English] 日本語
Yorodumi
- PDB-2rkk: Crystal Structure of S.cerevisiae Vta1 N-terminal domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2rkk
TitleCrystal Structure of S.cerevisiae Vta1 N-terminal domain
ComponentsVacuolar protein sorting-associated protein VTA1
KeywordsLIPID TRANSPORT / MIT motif / Cytoplasm / Endosome / Membrane / Protein transport / Transport
Function / homology
Function and homology information


ESCRT IV complex / Endosomal Sorting Complex Required For Transport (ESCRT) / late endosome to vacuole transport via multivesicular body sorting pathway / late endosome to vacuole transport / lipid transport / ATPase activator activity / multivesicular body / protein transport / protein-macromolecule adaptor activity / endosome
Similarity search - Function
Vacuolar protein sorting-associated protein vta1 / Vta1/Callose synthase, N-terminal domain superfamily / Vta1/callose synthase, N-terminal / Vta1, C-terminal / Vacuolar protein sorting-associated protein Vta1-like / Vta1 like / Vta1 C-terminal domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Vacuolar protein sorting-associated protein VTA1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.9 Å
AuthorsXiao, J. / Xia, H. / Zhou, J. / Xu, Z.
CitationJournal: Dev.Cell / Year: 2008
Title: Structural basis of vta1 function in the multivesicular body sorting pathway.
Authors: Xiao, J. / Xia, H. / Zhou, J. / Azmi, I.F. / Davies, B.A. / Katzmann, D.J. / Xu, Z.
History
DepositionOct 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Vacuolar protein sorting-associated protein VTA1
B: Vacuolar protein sorting-associated protein VTA1


Theoretical massNumber of molelcules
Total (without water)38,2982
Polymers38,2982
Non-polymers00
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.169, 126.169, 70.252
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4

-
Components

#1: Protein Vacuolar protein sorting-associated protein VTA1 / VPS20-associated protein 1


Mass: 19149.123 Da / Num. of mol.: 2 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: VTA1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q06263
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.65 Å3/Da / Density % sol: 66.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: Sodium Formate, vapor diffusion, temperature 293K, pH 7, VAPOR DIFFUSION

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å
DetectorDetector: CCD / Date: Feb 8, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 9.7 % / Av σ(I) over netI: 11 / Number: 101963 / Rmerge(I) obs: 0.081 / Χ2: 2.13 / D res high: 3 Å / D res low: 50 Å / Num. obs: 10527 / % possible obs: 95.2
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.465099.610.0557.6759.8
5.136.4610010.0793.10910.1
4.485.1310010.0622.11210.2
4.074.4810010.0791.66410.2
3.784.0710010.1031.310.2
3.563.7810010.1450.95910.1
3.383.5697.810.2050.859.8
3.233.3894.910.3320.829.4
3.113.2385.710.4140.768.8
33.117310.4870.7397.4
ReflectionResolution: 2.9→50 Å / Num. obs: 12169 / % possible obs: 99.5 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.062 / Χ2: 1.325 / Net I/σ(I): 11.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.9-370.41811640.61696.7
3-3.127.50.30111960.67499.3
3.12-3.277.70.21712280.801100
3.27-3.447.60.14912080.908100
3.44-3.657.60.10712111.212100
3.65-3.947.50.08212201.546100
3.94-4.337.30.06712301.992100
4.33-4.967.20.05612172.13299.9
4.96-6.247.50.04912361.61100
6.24-507.10.03312591.74699.3

-
Phasing

PhasingMethod: SIRAS

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
DMphasing
CNSrefinement
PDB_EXTRACT3data extraction
RefinementMethod to determine structure: SIRAS / Resolution: 2.9→50 Å / FOM work R set: 0.79 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.26 602 4.9 %
Rwork0.215 --
obs-11746 94.8 %
Solvent computationBsol: 64.107 Å2
Displacement parametersBiso mean: 81.482 Å2
Baniso -1Baniso -2Baniso -3
1--11.795 Å20 Å20 Å2
2---11.795 Å20 Å2
3---23.591 Å2
Refinement stepCycle: LAST / Resolution: 2.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2518 0 0 11 2529
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_d1.108
X-RAY DIFFRACTIONc_mcbond_it1.4941.5
X-RAY DIFFRACTIONc_scbond_it1.8572
X-RAY DIFFRACTIONc_mcangle_it2.6912
X-RAY DIFFRACTIONc_scangle_it3.0822.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

+
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