[English] 日本語
Yorodumi
- PDB-4fmm: Dimeric Sec14 family homolog 3 from Saccharomyces cerevisiae pres... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4fmm
TitleDimeric Sec14 family homolog 3 from Saccharomyces cerevisiae presents some novel features of structure that lead to a surprising "dimer-monomer" state change induced by substrate binding
ComponentsPhosphatidylinositol transfer protein PDR16
KeywordsLIPID BINDING PROTEIN / Sec14 domain / Phosphatidylinositol binding / signaling protein
Function / homology
Function and homology information


negative regulation of sexual sporulation resulting in formation of a cellular spore / phosphatidylinositol transporter complex / phosphatidylinositol transfer activity / nucleus-vacuole junction / sterol binding / sterol biosynthetic process / phospholipid biosynthetic process / phospholipid transport / lipid droplet / cell periphery ...negative regulation of sexual sporulation resulting in formation of a cellular spore / phosphatidylinositol transporter complex / phosphatidylinositol transfer activity / nucleus-vacuole junction / sterol binding / sterol biosynthetic process / phospholipid biosynthetic process / phospholipid transport / lipid droplet / cell periphery / response to xenobiotic stimulus / endoplasmic reticulum membrane / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Phosphatidylinositol Transfer Protein Sec14p / CRAL-TRIO lipid binding domain / CRAL/TRIO, N-terminal domain / CRAL/TRIO, N-terminal domain / CRAL/TRIO, N-terminal domain / CRAL/TRIO, N-terminal domain superfamily / CRAL/TRIO domain / CRAL-TRIO lipid binding domain profile. / Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p) / CRAL-TRIO lipid binding domain ...Phosphatidylinositol Transfer Protein Sec14p / CRAL-TRIO lipid binding domain / CRAL/TRIO, N-terminal domain / CRAL/TRIO, N-terminal domain / CRAL/TRIO, N-terminal domain / CRAL/TRIO, N-terminal domain superfamily / CRAL/TRIO domain / CRAL-TRIO lipid binding domain profile. / Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p) / CRAL-TRIO lipid binding domain / CRAL-TRIO lipid binding domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Phosphatidylinositol transfer protein PDR16
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.34 Å
AuthorsYuan, Y. / Zhao, W. / Wang, X. / Gao, Y. / Niu, L. / Teng, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Dimeric Sfh3 has structural changes in its binding pocket that are associated with a dimer-monomer state transformation induced by substrate binding.
Authors: Yuan, Y. / Zhao, W. / Wang, X. / Gao, Y. / Niu, L. / Teng, M.
History
DepositionJun 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phosphatidylinositol transfer protein PDR16
B: Phosphatidylinositol transfer protein PDR16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,87814
Polymers83,9762
Non-polymers90212
Water4,864270
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5150 Å2
ΔGint-59 kcal/mol
Surface area29550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.177, 76.914, 294.956
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-610-

HOH

-
Components

#1: Protein Phosphatidylinositol transfer protein PDR16 / SEC14 homolog 3 / PITP / Pleiotropic drug resistance protein 16


Mass: 41988.230 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: N1158, PDR16, SFH3, YNL231C / Plasmid: pET-22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P53860
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 270 / 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: 2.57 Å3/Da / Density % sol: 52.18 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.2 M magnesium acetate tetrahydrate, 0.1 M sodium cacodylate trihydrate, pH 6.0, 20% w/v PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 7, 2011
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.34→147.48 Å / Num. obs: 37249 / % possible obs: 95.7 % / Observed criterion σ(F): 5 / Redundancy: 6.4 % / Rmerge(I) obs: 0.057
Reflection shellResolution: 2.34→2.38 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.105 / Num. unique all: 1407 / % possible all: 76

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.34→47.414 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.884 / SU B: 6.853 / SU ML: 0.169 / Cross valid method: THROUGHOUT / ESU R: 0.355 / ESU R Free: 0.257 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.26363 1781 5 %RANDOM
Rwork0.21445 ---
obs0.21696 33809 95.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.122 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20 Å20 Å2
2--1.8 Å20 Å2
3----2.21 Å2
Refinement stepCycle: LAST / Resolution: 2.34→47.414 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5182 0 57 270 5509
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0225372
X-RAY DIFFRACTIONr_angle_refined_deg1.0951.977275
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8655647
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.74623.739238
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.73915901
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9061531
X-RAY DIFFRACTIONr_chiral_restr0.070.2795
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214020
X-RAY DIFFRACTIONr_mcbond_it0.4461.53252
X-RAY DIFFRACTIONr_mcangle_it0.83325263
X-RAY DIFFRACTIONr_scbond_it1.07832120
X-RAY DIFFRACTIONr_scangle_it1.8074.52012
LS refinement shellResolution: 2.34→2.398 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 99 -
Rwork0.249 1960 -
obs--76.6 %

+
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