[English] 日本語
Yorodumi
- PDB-5agc: Crystallographic forms of the Vps75 tetramer -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5agc
TitleCrystallographic forms of the Vps75 tetramer
ComponentsVACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 75
KeywordsTRANSPORT PROTEIN / VPS75 / VACUOLAR PROTEIN SORTING 75 / HISTONE CHAPERONE / NAP1 / CHROMATIN
Function / homology
Function and homology information


H3 histone acetyltransferase complex / acetyltransferase activator activity / protein modification process / double-strand break repair via nonhomologous end joining / protein transport / nucleosome assembly / histone binding / chromatin binding / chromatin / identical protein binding ...H3 histone acetyltransferase complex / acetyltransferase activator activity / protein modification process / double-strand break repair via nonhomologous end joining / protein transport / nucleosome assembly / histone binding / chromatin binding / chromatin / identical protein binding / nucleus / cytosol
Similarity search - Function
Nucleosome assembly protein (NAP) / NAP-like superfamily / Nucleosome assembly protein (NAP)
Similarity search - Domain/homology
Vacuolar protein sorting-associated protein 75
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 Å
AuthorsHammond, C.M. / Sundaramoorthy, R. / Owen-Hughes, T.
Citation
Journal: Nucleic Acids Res. / Year: 2016
Title: The Histone Chaperone Vps75 Forms Multiple Oligomeric Assemblies Capable of Mediating Exchange between Histone H3-H4 Tetramers and Asf1-H3-H4 Complexes.
Authors: Hammond, C.M. / Sundaramoorthy, R. / Larance, M. / Lamond, A. / Stevens, M.A. / El-Mkami, H. / Norman, D.G. / Owen-Hughes, T.
#1: Journal: Nucleic Acids Res. / Year: 2014
Title: The Histone Chaperones Vps75 and Nap1 Form Ring-Like, Tetrameric Structures in Solution.
Authors: Bowman, A. / Hammond, C.M. / Stirling, A. / Ward, R. / Shang, W. / El-Mkami, H. / Robinson, D.A. / Svergun, D.I. / Norman, D.G. / Owen-Hughes, T.
History
DepositionJan 29, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2016Group: Database references
Revision 1.2Aug 10, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 75
B: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 75
C: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 75
D: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 75


Theoretical massNumber of molelcules
Total (without water)122,6244
Polymers122,6244
Non-polymers00
Water00
1
C: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 75
D: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 75

C: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 75
D: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 75


Theoretical massNumber of molelcules
Total (without water)122,6244
Polymers122,6244
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
2
A: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 75

A: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 75

B: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 75

B: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 75


Theoretical massNumber of molelcules
Total (without water)122,6244
Polymers122,6244
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
crystal symmetry operation4_445-x-1/2,y-1/2,-z1
crystal symmetry operation3_545x+1/2,y-1/2,z1
3
B: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 75

B: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 75

A: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 75

A: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 75


Theoretical massNumber of molelcules
Total (without water)122,6244
Polymers122,6244
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,y,-z1
crystal symmetry operation4_455-x-1/2,y+1/2,-z1
crystal symmetry operation3_455x-1/2,y+1/2,z1
Unit cell
Length a, b, c (Å)82.750, 92.430, 160.750
Angle α, β, γ (deg.)90.00, 93.85, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.1485, -0.9667, 0.2084), (-0.9587, 0.0891, -0.27), (0.2424, -0.2399, -0.9401)-6.174, 3.872, 84.08
2given(-0.8552, -0.05984, -0.5147), (0.05607, -0.9982, 0.02289), (-0.5152, 0.009284, -0.857)-37.11, 13.24, -10.8
3given(0.149, 0.9583, 0.2439), (0.9586, -0.07943, -0.2736), (-0.2428, 0.2745, -0.9304)-28.04, 8.78, 76.43

-
Components

#1: Protein
VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 75


Mass: 30656.084 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: PET30A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA 2 / References: UniProt: P53853

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.7 % / Description: NONE
Crystal growpH: 6.5 / Details: 0.1M SODIUM CACODYLATE PH 6.5, 25% W/V PEG 4K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 4→50.06 Å / Num. obs: 9771 / % possible obs: 99 % / Observed criterion σ(I): 3 / Redundancy: 5.1 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 7
Reflection shellResolution: 4→4.22 Å / Redundancy: 5 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 3.4 / % possible all: 96.4

-
Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ZD7

2zd7


Resolution: 4→50.06 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.915 / SU B: 63.669 / SU ML: 0.829 / Cross valid method: THROUGHOUT / ESU R Free: 0.93 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26463 495 4.8 %RANDOM
Rwork0.22934 ---
obs0.23104 9771 98.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 122.949 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20.02 Å2
2---0.02 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 4→50.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7250 0 0 0 7250
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0197442
X-RAY DIFFRACTIONr_bond_other_d0.0070.025268
X-RAY DIFFRACTIONr_angle_refined_deg1.3971.9510025
X-RAY DIFFRACTIONr_angle_other_deg1.17312792
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7195865
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.09924.606393
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.752151363
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.1451536
X-RAY DIFFRACTIONr_chiral_restr0.0870.21013
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218203
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021589
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 4→4.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.412 42 -
Rwork0.389 657 -
obs--95.36 %

+
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