[English] 日本語
Yorodumi
- PDB-4k84: Crystal structure of human ceramide-1-phosphate transfer protein ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4k84
TitleCrystal structure of human ceramide-1-phosphate transfer protein (CPTP) in complex with 16:0 ceramide-1-phosphate (16:0-C1P)
ComponentsGlycolipid transfer protein domain-containing protein 1
KeywordsLIPID TRANSPORT / Lipid transfer protein / GLTP-fold / CPTP / C1P / Ceramide-1-phosphate / Protein-lipid complex / Eicosanoid
Function / homology
Function and homology information


ceramide 1-phosphate transport / ceramide transport / ceramide 1-phosphate binding / ceramide 1-phosphate transfer activity / Glycosphingolipid transport / intermembrane lipid transfer / negative regulation of NLRP3 inflammasome complex assembly / nuclear outer membrane / negative regulation of interleukin-1 beta production / negative regulation of autophagy ...ceramide 1-phosphate transport / ceramide transport / ceramide 1-phosphate binding / ceramide 1-phosphate transfer activity / Glycosphingolipid transport / intermembrane lipid transfer / negative regulation of NLRP3 inflammasome complex assembly / nuclear outer membrane / negative regulation of interleukin-1 beta production / negative regulation of autophagy / phospholipid binding / endosome membrane / Golgi apparatus / plasma membrane / cytosol
Similarity search - Function
Glycolipid transfer protein domain / Glycolipid transfer protein superfamily / Glycolipid transfer protein (GLTP) / Glycolipid transfer protein, GLTP / Glycolipid transfer protein / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-1PX / Ceramide-1-phosphate transfer protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.897 Å
AuthorsSimanshu, D.K. / Brown, R.E. / Patel, D.J.
CitationJournal: Nature / Year: 2013
Title: Non-vesicular trafficking by a ceramide-1-phosphate transfer protein regulates eicosanoids.
Authors: Simanshu, D.K. / Kamlekar, R.K. / Wijesinghe, D.S. / Zou, X. / Zhai, X. / Mishra, S.K. / Molotkovsky, J.G. / Malinina, L. / Hinchcliffe, E.H. / Chalfant, C.E. / Brown, R.E. / Patel, D.J.
History
DepositionApr 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glycolipid transfer protein domain-containing protein 1
B: Glycolipid transfer protein domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2044
Polymers48,9682
Non-polymers1,2362
Water7,909439
1
A: Glycolipid transfer protein domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1022
Polymers24,4841
Non-polymers6181
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glycolipid transfer protein domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1022
Polymers24,4841
Non-polymers6181
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.604, 50.291, 62.870
Angle α, β, γ (deg.)90.00, 100.11, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Glycolipid transfer protein domain-containing protein 1


Mass: 24484.154 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GLTPD1 / Plasmid: pET-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Star / References: UniProt: Q5TA50
#2: Chemical ChemComp-1PX / (2S,3R,4E)-2-(hexadecanoylamino)-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate


Mass: 617.881 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H68NO6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 439 / 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: 1.99 Å3/Da / Density % sol: 38.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1 M MMT buffer pH 5.0, 25% PEG1500, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.2398 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 8, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2398 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 30620 / % possible obs: 99.7 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 10
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.9-1.974.50.269196.8
1.97-2.0560.2261100
2.05-2.146.90.1841100
2.14-2.257.10.1651100
2.25-2.397.30.1241100
2.39-2.587.30.1051100
2.58-2.847.30.0891100
2.84-3.257.30.0761100
3.25-4.097.10.0621100
4.09-5070.047199.7

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
PHENIX1.5_2refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Human ceramide-1-phosphate transfer protein in complex with C2 Ceramide-1-phosphate (2:0 C1P)

Resolution: 1.897→40.278 Å / Occupancy max: 1 / Occupancy min: 0.36 / SU ML: 0.2 / σ(F): 0.11 / Phase error: 22.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2133 1515 5.06 %
Rwork0.1622 --
obs0.1647 29952 97.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.821 Å2 / ksol: 0.36 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.7468 Å2-0 Å2-0.9344 Å2
2---1.8039 Å20 Å2
3---2.5507 Å2
Refinement stepCycle: LAST / Resolution: 1.897→40.278 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3297 0 84 439 3820
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073501
X-RAY DIFFRACTIONf_angle_d0.9364739
X-RAY DIFFRACTIONf_dihedral_angle_d18.0081359
X-RAY DIFFRACTIONf_chiral_restr0.06527
X-RAY DIFFRACTIONf_plane_restr0.005599
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8968-1.9580.25911030.16622363X-RAY DIFFRACTION89
1.958-2.0280.2351390.16972517X-RAY DIFFRACTION95
2.028-2.10920.22421310.16292567X-RAY DIFFRACTION96
2.1092-2.20520.20791490.15382495X-RAY DIFFRACTION97
2.2052-2.32140.19971380.15272599X-RAY DIFFRACTION98
2.3214-2.46690.2221300.15692613X-RAY DIFFRACTION99
2.4669-2.65730.2251400.16032618X-RAY DIFFRACTION99
2.6573-2.92460.21931440.16612614X-RAY DIFFRACTION99
2.9246-3.34770.21371430.16442678X-RAY DIFFRACTION100
3.3477-4.2170.1951550.14562676X-RAY DIFFRACTION100
4.217-40.28710.20111430.17242697X-RAY DIFFRACTION99

+
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://pdbjlvh1.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