[English] 日本語
Yorodumi
- PDB-4xiz: Structure of a phospholipid trafficking complex with substrate -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4xiz
TitleStructure of a phospholipid trafficking complex with substrate
Components
  • Mitochondrial distribution and morphology protein 35
  • Protein UPS1, mitochondrial
KeywordsLIPID TRANSPORT/OXIDOREDUCTASE / phospholipid / LIPID TRANSPORT-OXIDOREDUCTASE complex
Function / homology
Function and homology information


TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / phosphatidic acid transfer activity / cardiolipin metabolic process / positive regulation of phosphatidylcholine biosynthetic process / mitochondrial respiratory chain complex assembly / phospholipid transport / phospholipid translocation / mitochondrion organization / mitochondrial intermembrane space / mitochondrial inner membrane ...TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / phosphatidic acid transfer activity / cardiolipin metabolic process / positive regulation of phosphatidylcholine biosynthetic process / mitochondrial respiratory chain complex assembly / phospholipid transport / phospholipid translocation / mitochondrion organization / mitochondrial intermembrane space / mitochondrial inner membrane / lipid binding / mitochondrion / nucleus / cytosol / cytoplasm
Similarity search - Function
PRELI/MSF1 domain / Slowmo/Ups family / PRELI-like family / PRELI/MSF1 domain profile. / Mitochondrial distribution/morphology family 35/apoptosis / Uncharacterised protein family (UPF0203) / Coiled coil-helix-coiled coil-helix (CHCH) domain profile.
Similarity search - Domain/homology
Chem-LPP / Mitochondrial distribution and morphology protein 35 / Protein UPS1, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsYu, F. / He, F. / Wang, C. / Zhang, P.
CitationJournal: Embo Rep. / Year: 2015
Title: Structural basis of intramitochondrial phosphatidic acid transport mediated by Ups1-Mdm35 complex
Authors: Yu, F. / He, F. / Yao, H. / Wang, C. / Wang, J. / Li, J. / Qi, X. / Xue, H. / Ding, J. / Zhang, P.
History
DepositionJan 8, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2015Group: Database references
Revision 1.2Aug 12, 2015Group: Refinement description
Revision 1.3Sep 16, 2015Group: Refinement description

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein UPS1, mitochondrial
B: Protein UPS1, mitochondrial
M: Mitochondrial distribution and morphology protein 35
N: Mitochondrial distribution and morphology protein 35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2366
Polymers54,9384
Non-polymers1,2982
Water6,846380
1
A: Protein UPS1, mitochondrial
N: Mitochondrial distribution and morphology protein 35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1183
Polymers27,4692
Non-polymers6491
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-29 kcal/mol
Surface area12230 Å2
MethodPISA
2
B: Protein UPS1, mitochondrial
M: Mitochondrial distribution and morphology protein 35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1183
Polymers27,4692
Non-polymers6491
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4290 Å2
ΔGint-30 kcal/mol
Surface area12210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.022, 74.123, 87.912
Angle α, β, γ (deg.)90.000, 95.140, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Protein UPS1, mitochondrial / Unprocessed MGM1 protein 1


Mass: 19493.252 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: UPS1, YLR193C / Production host: Escherichia coli (E. coli) / References: UniProt: Q05776
#2: Protein Mitochondrial distribution and morphology protein 35


Mass: 7975.900 Da / Num. of mol.: 2 / Fragment: UNP residues 6-75
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: MDM35, YKL053C-A / Production host: Escherichia coli (E. coli) / References: UniProt: O60200
#3: Chemical ChemComp-LPP / 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE / 1,2-DIPALMITOYL-SN-GLYCERO-3-PHOSPHATE / L-B,G-DIPALMITOYL-A-PHOSPHATIDIC ACID DISODIUM SALT / 3-SN-PHOSPHATIDIC ACID / 1,2-DIPALMITOYLDISODIUM SALT


Mass: 648.891 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C35H69O8P / Comment: phospholipid*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 380 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.63 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 2%(v/v)Tacsimate pH 6.0, 0.1M Bis-Tris pH 6.5, 20%(w/v) PEG3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 29, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 36740 / % possible obs: 99.4 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.116 / Χ2: 1.394 / Net I/av σ(I): 15.354 / Net I/σ(I): 10.7 / Num. measured all: 150394
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2-2.074.10.37536391.00499.9
2.07-2.154.10.30136951.02499.8
2.15-2.254.20.24137051.07499.9
2.25-2.374.20.18636621.11499.8
2.37-2.524.20.15436791.19299.8
2.52-2.714.20.12236571.21599.8
2.71-2.994.20.10636881.41199.9
2.99-3.424.10.10536951.96899.8
3.42-4.313.90.0936872.18298.8
4.31-503.90.08236331.88396

-
Processing

Software
NameVersionClassification
PHENIX1.9-1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2→34.13 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.24 1819 4.96 %
Rwork0.196 --
obs0.2018 36723 99.2 %
Displacement parametersBiso max: 137.57 Å2 / Biso mean: 43.322 Å2 / Biso min: 16.54 Å2
Refinement stepCycle: LAST / Resolution: 2→34.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3855 0 88 380 4323

+
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