[English] 日本語
Yorodumi
- PDB-5zym: Crystal structure of CERT START domain in complex with compound E25B -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5zym
TitleCrystal structure of CERT START domain in complex with compound E25B
ComponentsLIPID-TRANSFER PROTEIN CERT
KeywordsLIPID TRANSPORT / CERT / PH / START / COMPLEX
Function / homology
Function and homology information


intermembrane sphingolipid transfer / ceramide transfer activity / ER to Golgi ceramide transport / ceramide 1-phosphate transfer activity / ceramide transport / ceramide 1-phosphate binding / ceramide metabolic process / intermembrane lipid transfer / ceramide binding / Sphingolipid de novo biosynthesis ...intermembrane sphingolipid transfer / ceramide transfer activity / ER to Golgi ceramide transport / ceramide 1-phosphate transfer activity / ceramide transport / ceramide 1-phosphate binding / ceramide metabolic process / intermembrane lipid transfer / ceramide binding / Sphingolipid de novo biosynthesis / endoplasmic reticulum organization / phosphatidylinositol-4-phosphate binding / lipid homeostasis / heart morphogenesis / muscle contraction / response to endoplasmic reticulum stress / mitochondrion organization / cell morphogenesis / kinase activity / in utero embryonic development / cell population proliferation / immune response / endoplasmic reticulum membrane / Golgi apparatus / signal transduction / mitochondrion / nucleoplasm / identical protein binding / cytosol
Similarity search - Function
STARD11, START domain / : / in StAR and phosphatidylcholine transfer protein / START domain / START domain / START domain profile. / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / PH domain ...STARD11, START domain / : / in StAR and phosphatidylcholine transfer protein / START domain / START domain / START domain profile. / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-9M6 / Ceramide transfer protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsSuzuki, M. / Nakao, N. / Ueno, M. / Sakai, S. / Egawa, D. / Hanzawa, H. / Kawasaki, S. / Kumagai, K. / Kobayashi, S. / Hanada, K.
CitationJournal: Commun Chem / Year: 2019
Title: Natural ligand-nonmimetic inhibitors of the lipid-transfer protein CERT
Authors: Nakao, N. / Ueno, M. / Sakai, S. / Egawa, D. / Hanzawa, H. / Kawasaki, S. / Kumagai, K. / Suzuki, M. / Kobayashi, S. / Hanada, K.
History
DepositionMay 25, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN
Revision 1.2Mar 27, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2
Item: _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: LIPID-TRANSFER PROTEIN CERT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5963
Polymers27,0571
Non-polymers5402
Water4,378243
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-0 kcal/mol
Surface area12020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.868, 59.868, 153.757
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein LIPID-TRANSFER PROTEIN CERT / Ceramide transfer protein / hCERT / StAR-related lipid transfer protein 11


Mass: 27056.781 Da / Num. of mol.: 1 / Fragment: UNP residues 364-598
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CERT / Plasmid: pET28b-His-3C-CERT START / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y5P4
#2: Chemical ChemComp-9M6 / 2-[4-[4-cyclopentyl-3-[(1~{R},2~{S})-2-pyridin-2-ylcyclopropyl]phenyl]phenyl]sulfonylethanol


Mass: 447.589 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H29NO3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTwo residues GLY362A and PRO363A are originated from protease site after N-terminal affinity tag. ...Two residues GLY362A and PRO363A are originated from protease site after N-terminal affinity tag. THIS SEQUENCE CORRESPONDS TO THE ISOFORM 2 FOUND IN UNP Q9Y5P4.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.9
Details: 0.1M trisodium citrate/HCl buffer, pH 5.9, containing 24% PEG3350 and 0.2% n-octyl-beta-D-glucoside

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5406 Å
DetectorType: RIGAKU / Detector: AREA DETECTOR / Date: Oct 4, 2017
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 1.9→28.46 Å / Num. obs: 22919 / % possible obs: 99.9 % / Redundancy: 6.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.041 / Rrim(I) all: 0.11 / Net I/σ(I): 11.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.9-1.944.90.44415220.7750.2230.599.6
8.91-28.464.70.052720.9940.0250.05795.7

-
Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
REFMAC5.8.0189refinement
PDB_EXTRACT3.24data extraction
CrysalisProdata reduction
REFMACphasing
RefinementResolution: 1.9→25 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.926 / SU B: 3.197 / SU ML: 0.094 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.143 / ESU R Free: 0.14 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2284 1189 5.2 %RANDOM
Rwork0.1797 ---
obs0.1823 21667 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 83.45 Å2 / Biso mean: 20.107 Å2 / Biso min: 6.15 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å2-0 Å2-0 Å2
2--0.1 Å2-0 Å2
3----0.2 Å2
Refinement stepCycle: final / Resolution: 1.9→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1886 0 38 243 2167
Biso mean--31.41 28.23 -
Num. residues----235
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0191988
X-RAY DIFFRACTIONr_angle_refined_deg2.1131.9512709
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1095236
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.7824.43397
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.02515331
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2811513
X-RAY DIFFRACTIONr_chiral_restr0.1560.2302
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211514
LS refinement shellResolution: 1.9→1.966 Å / Rfactor Rfree error: 0 / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.235 105 -
Rwork0.198 2089 -
all-2194 -
obs--99.41 %

+
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