[English] 日本語
Yorodumi
- PDB-7y10: Crystal structure of AtSFH5-Sec14 in complex with DPPA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7y10
TitleCrystal structure of AtSFH5-Sec14 in complex with DPPA
ComponentsPhosphatidylinositol/phosphatidylcholine transfer protein SFH5
KeywordsLIPID TRANSPORT / Sec14p homolog protein (SFH) / Arabidopsis thaliana / chloroplast / phosphatidic acid (PA)
Function / homology
Function and homology information


phosphatidylinositol transfer activity / post-Golgi vesicle-mediated transport / phosphatidic acid binding / plasmodesma / chloroplast / protein transport / Golgi membrane / endoplasmic reticulum / plasma membrane
Similarity search - Function
: / N-terminal domain of phosphatidylinositol transfer protein sec14p / Phosphatidylinositol Transfer Protein Sec14p / CRAL-TRIO lipid binding 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) ...: / N-terminal domain of phosphatidylinositol transfer protein sec14p / Phosphatidylinositol Transfer Protein Sec14p / CRAL-TRIO lipid binding 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 / Helicase, Ruva Protein; domain 3 / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / 1,2-DIPALMITOYL-SN-GLYCERO-3-PHOSPHATE / Phosphatidylinositol/phosphatidylcholine transfer protein SFH5
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLu, Y.Q. / Wang, X.Q. / Luo, Z.P. / Wu, J.W.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)91754201 China
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2023
Title: Arabidopsis Sec14 proteins (SFH5 and SFH7) mediate interorganelle transport of phosphatidic acid and regulate chloroplast development.
Authors: Yao, H.Y. / Lu, Y.Q. / Yang, X.L. / Wang, X.Q. / Luo, Z. / Lin, D.L. / Wu, J.W. / Xue, H.W.
History
DepositionJun 6, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phosphatidylinositol/phosphatidylcholine transfer protein SFH5
B: Phosphatidylinositol/phosphatidylcholine transfer protein SFH5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,7688
Polymers69,2382
Non-polymers1,5316
Water6,467359
1
A: Phosphatidylinositol/phosphatidylcholine transfer protein SFH5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3844
Polymers34,6191
Non-polymers7653
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint-4 kcal/mol
Surface area14800 Å2
MethodPISA
2
B: Phosphatidylinositol/phosphatidylcholine transfer protein SFH5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3844
Polymers34,6191
Non-polymers7653
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-3 kcal/mol
Surface area14060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.693, 114.551, 111.836
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-710-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: _ / Auth seq-ID: 77 - 351 / Label seq-ID: 3 - 277

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

#1: Protein Phosphatidylinositol/phosphatidylcholine transfer protein SFH5 / Protein SEC FOURTEEN HOMOLOGS 5 / AtSFH5 / AtSFH5-Sec14


Mass: 34618.797 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: ...Details: MSLTIEDIHDVEELRAVDEFRNLLVSENLLPPTLDDYHIMLRFLKARKFDIGKTKLMWSNMIKWRKDFGTDTIFEDFEFEEFDEVLKYYPHGYHGVDKEGRPVYIERLGLVDPAKLMQVTTVERFIRYHVREFEKTVNIKLPACCIAAKRHIDSSTTILDVQGVGFKNFSKPARDLIIQLQKIDNDNYPETLHRMFIINGGSGFKLVWATVKQFLDPKTVTKIHVIGNKYQNKLLEIIDASQLPDFLGGTCTCADRGGCMRSDKGPWNDPEILKMLQSGGPLCRHNSALNSLEHHHHHH
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SFH5, At1g75370, F1B16.10 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8GXC6
#2: Chemical ChemComp-PX6 / 1,2-DIPALMITOYL-SN-GLYCERO-3-PHOSPHATE


Mass: 647.883 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C35H68O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 359 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.66 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.1 M MES pH 6.0, 20% PEG6000, 0.2 M NaCl

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS3 R 200K-A / Detector: PIXEL / Date: Mar 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 37354 / % possible obs: 99.2 % / Redundancy: 6.4 % / CC1/2: 0.991 / Rmerge(I) obs: 0.157 / Rpim(I) all: 0.067 / Rrim(I) all: 0.171 / Χ2: 1.123 / Net I/σ(I): 11.9
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 5 % / Rmerge(I) obs: 0.837 / Mean I/σ(I) obs: 1.84 / Num. unique obs: 3480 / CC1/2: 0.525 / Rpim(I) all: 0.402 / Rrim(I) all: 0.933 / Χ2: 1.017 / % possible all: 93.4

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AUA

1aua


Resolution: 2.1→21.44 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.917 / SU B: 6.096 / SU ML: 0.153 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.278 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2473 1819 4.9 %RANDOM
Rwork0.2251 ---
obs0.2262 35459 98.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 146.85 Å2 / Biso mean: 33.322 Å2 / Biso min: 7.46 Å2
Baniso -1Baniso -2Baniso -3
1-0.77 Å2-0 Å20 Å2
2---1.14 Å20 Å2
3---0.37 Å2
Refinement stepCycle: final / Resolution: 2.1→21.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4608 0 92 359 5059
Biso mean--67.87 35.51 -
Num. residues----567
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0134813
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174673
X-RAY DIFFRACTIONr_angle_refined_deg1.4971.6486458
X-RAY DIFFRACTIONr_angle_other_deg1.3091.58610792
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.095565
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.20322.364258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.03915866
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.3341531
X-RAY DIFFRACTIONr_chiral_restr0.0750.2608
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025257
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021087
Refine LS restraints NCS

Ens-ID: 1 / Number: 8839 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.1→2.154 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 107 -
Rwork0.315 2354 -
all-2461 -
obs--90.48 %

+
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