[English] 日本語
Yorodumi
- PDB-8hqu: Crystal structure of the major sperm protein domain of SCS2 from ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8hqu
TitleCrystal structure of the major sperm protein domain of SCS2 from saccharomyces cerevisiae
ComponentsVesicle-associated membrane protein-associated protein SCS2
KeywordsCELL ADHESION / MSP (Major sperm protein) domain
Function / homology
Function and homology information


endoplasmic reticulum polarization / regulation of intracellular lipid transport / FFAT motif binding / endoplasmic reticulum-plasma membrane tethering / RHOC GTPase cycle / endoplasmic reticulum membrane organization / endoplasmic reticulum inheritance / regulation of phosphatidylinositol dephosphorylation / nucleus-vacuole junction / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane ...endoplasmic reticulum polarization / regulation of intracellular lipid transport / FFAT motif binding / endoplasmic reticulum-plasma membrane tethering / RHOC GTPase cycle / endoplasmic reticulum membrane organization / endoplasmic reticulum inheritance / regulation of phosphatidylinositol dephosphorylation / nucleus-vacuole junction / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / cellular bud tip / phospholipid biosynthetic process / cellular bud neck / reticulophagy / negative regulation of protein import into nucleus / subtelomeric heterochromatin formation / protein-membrane adaptor activity / Neutrophil degranulation / phosphatidylinositol binding / nuclear envelope / nuclear membrane / chromosome, telomeric region / endoplasmic reticulum membrane / endoplasmic reticulum / plasma membrane
Similarity search - Function
Vesicle-associated membrane-protein-associated protein / Major sperm protein (MSP) domain / MSP (Major sperm protein) domain / Major sperm protein (MSP) domain profile. / PapD-like superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Vesicle-associated membrane protein-associated protein SCS2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWang, C.C.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: To Be Published
Title: Structural insights into the major sperm protein domain of SCS2 from saccharomyces cerevisiae
Authors: Xu, T. / Wang, C.C.
History
DepositionDec 14, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Vesicle-associated membrane protein-associated protein SCS2


Theoretical massNumber of molelcules
Total (without water)15,1241
Polymers15,1241
Non-polymers00
Water1,18966
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7300 Å2
Unit cell
Length a, b, c (Å)68.507, 68.507, 56.237
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

-
Components

#1: Protein Vesicle-associated membrane protein-associated protein SCS2 / VAMP-associated protein SCS2 / Choline sensitivity suppressor protein 2 / VAP homolog 1


Mass: 15124.235 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SCS2, YER120W / Production host: Escherichia coli (E. coli) / References: UniProt: P40075
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.78 Å3/Da / Density % sol: 55.72 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / Details: 25% PEG 3350, 0.1 mM tris-bis (pH 5.5)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 10613 / % possible obs: 99.88 % / Redundancy: 19.3 % / Biso Wilson estimate: 38.34 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.0766 / Rpim(I) all: 0.0179 / Rrim(I) all: 0.0787 / Net I/σ(I): 28.32
Reflection shellResolution: 2→2.2 Å / Redundancy: 19.5 % / Rmerge(I) obs: 0.9656 / Mean I/σ(I) obs: 3.38 / Num. unique obs: 2607 / CC1/2: 0.94 / CC star: 0.98 / Rpim(I) all: 0.2236 / Rrim(I) all: 0.9915 / % possible all: 99.81

-
Processing

Software
NameVersionClassification
Cootmodel building
PHENIXdev_4778refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 2→40.81 Å / SU ML: 0.2243 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.9958
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2554 491 4.63 %
Rwork0.2177 10124 -
obs0.2195 10613 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.69 Å2
Refinement stepCycle: LAST / Resolution: 2→40.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms966 0 0 66 1032
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037986
X-RAY DIFFRACTIONf_angle_d0.78291342
X-RAY DIFFRACTIONf_chiral_restr0.0528159
X-RAY DIFFRACTIONf_plane_restr0.0046170
X-RAY DIFFRACTIONf_dihedral_angle_d15.1816364
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.20.32391310.28712477X-RAY DIFFRACTION99.85
2.2-2.520.324950.24152512X-RAY DIFFRACTION99.77
2.52-3.170.28771330.25852513X-RAY DIFFRACTION100
3.18-40.810.2231320.18932622X-RAY DIFFRACTION99.96

+
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