[English] 日本語
Yorodumi
- PDB-6tqt: The crystal structure of the MSP domain of human MOSPD2. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6tqt
TitleThe crystal structure of the MSP domain of human MOSPD2.
ComponentsMotile sperm domain-containing protein 2
KeywordsPROTEIN BINDING / Membrane contact sites / FFAT motif / MSP domain / Endoplasmic reticulum
Function / homology
Function and homology information


endoplasmic reticulum-endosome membrane contact site / FFAT motif binding / lipid droplet formation / organelle membrane contact site / RHOD GTPase cycle / positive regulation of monocyte chemotaxis / positive regulation of neutrophil chemotaxis / endomembrane system / specific granule membrane / protein homooligomerization ...endoplasmic reticulum-endosome membrane contact site / FFAT motif binding / lipid droplet formation / organelle membrane contact site / RHOD GTPase cycle / positive regulation of monocyte chemotaxis / positive regulation of neutrophil chemotaxis / endomembrane system / specific granule membrane / protein homooligomerization / chemotaxis / Neutrophil degranulation / endoplasmic reticulum membrane / endoplasmic reticulum / membrane / plasma membrane
Similarity search - Function
Major sperm protein (MSP) domain / MSP (Major sperm protein) domain / Major sperm protein (MSP) domain profile. / CRAL/TRIO, N-terminal domain superfamily / CRAL/TRIO domain / PapD-like superfamily / 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 / Immunoglobulin-like fold
Similarity search - Domain/homology
PHOSPHATE ION / Motile sperm domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsMcEwen, A.G. / Poussin-Courmontagne, P. / Di Mattia, T. / Wendling, C. / Cavarelli, J. / Tomasetto, C. / Alpy, F.
Funding support France, 4items
OrganizationGrant numberCountry
French National Research AgencyANR-19-CE44-0003 France
French National Research AgencyANR-10-INSB-05-01 France
French National Research AgencyANR-10-LABX-0030-INRT France
French National Research AgencyANR-10-IDEX-0002-02. France
CitationJournal: Embo J. / Year: 2020
Title: FFAT motif phosphorylation controls formation and lipid transfer function of inter-organelle contacts.
Authors: Di Mattia, T. / Martinet, A. / Ikhlef, S. / McEwen, A.G. / Nomine, Y. / Wendling, C. / Poussin-Courmontagne, P. / Voilquin, L. / Eberling, P. / Ruffenach, F. / Cavarelli, J. / Slee, J. / ...Authors: Di Mattia, T. / Martinet, A. / Ikhlef, S. / McEwen, A.G. / Nomine, Y. / Wendling, C. / Poussin-Courmontagne, P. / Voilquin, L. / Eberling, P. / Ruffenach, F. / Cavarelli, J. / Slee, J. / Levine, T.P. / Drin, G. / Tomasetto, C. / Alpy, F.
History
DepositionDec 17, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2020Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Motile sperm domain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5214
Polymers24,2691
Non-polymers2523
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, SEC-MALS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area580 Å2
ΔGint-6 kcal/mol
Surface area7660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.114, 51.216, 78.799
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Motile sperm domain-containing protein 2


Mass: 24268.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: MSP domain / Source: (gene. exp.) Homo sapiens (human) / Gene: MOSPD2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8NHP6
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.97 Å3/Da / Density % sol: 37.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2 / Details: 40% PEG 300, 0.1 M Sodium Phosphate Citrate pH 4.2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.54178 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Jul 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.5→78.8 Å / Num. obs: 18679 / % possible obs: 98.5 % / Redundancy: 6.6 % / CC1/2: 0.995 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.046 / Rrim(I) all: 0.137 / Net I/σ(I): 9.8 / Num. measured all: 124110 / Scaling rejects: 20
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.5-1.531.80.36413297200.7250.3160.4841.880.5
8.22-78.87.40.08611501550.9990.0320.09313.899.5

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.5 Å31.23 Å
Translation1.5 Å31.23 Å

-
Processing

Software
NameVersionClassification
PHENIXdev-3699refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.2phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6TQS

6tqs


Resolution: 1.5→31.23 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 17.42
RfactorNum. reflection% reflection
Rfree0.1826 962 5.16 %
Rwork0.1335 --
obs0.136 18627 98.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 62.63 Å2 / Biso mean: 25.9414 Å2 / Biso min: 11.28 Å2
Refinement stepCycle: final / Resolution: 1.5→31.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1008 0 20 162 1190
Biso mean--51.88 38.57 -
Num. residues----131
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.580.24641080.1432268237689
1.58-1.680.18891520.112224902642100
1.68-1.810.17011520.099424892641100
1.81-1.990.16411130.095725692682100
1.99-2.280.16181410.105425402681100
2.28-2.870.1831520.14725972749100
2.87-31.230.1891440.151227122856100

+
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