[English] 日本語
Yorodumi
- PDB-6tqr: The crystal structure of the MSP domain of human VAP-A in complex... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6tqr
TitleThe crystal structure of the MSP domain of human VAP-A in complex with the Phospho-FFAT motif of STARD3.
Components
  • StAR-related lipid transfer protein 3
  • Vesicle-associated membrane protein-associated protein A
KeywordsPROTEIN BINDING / Membrane contact sites / FFAT motif / MSP domain / Endoplasmic reticulum
Function / homology
Function and homology information


vesicle tethering to endoplasmic reticulum / progesterone biosynthetic process / endoplasmic reticulum-endosome membrane contact site / FFAT motif binding / endoplasmic reticulum-plasma membrane tethering / sphingomyelin biosynthetic process / organelle membrane contact site / ceramide transport / COPII-coated vesicle budding / host-mediated suppression of viral genome replication ...vesicle tethering to endoplasmic reticulum / progesterone biosynthetic process / endoplasmic reticulum-endosome membrane contact site / FFAT motif binding / endoplasmic reticulum-plasma membrane tethering / sphingomyelin biosynthetic process / organelle membrane contact site / ceramide transport / COPII-coated vesicle budding / host-mediated suppression of viral genome replication / sterol transport / host-mediated activation of viral genome replication / protein localization to endoplasmic reticulum / Sphingolipid de novo biosynthesis / Pregnenolone biosynthesis / phospholipid transport / cholesterol transfer activity / cholesterol transport / azurophil granule membrane / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / cholesterol binding / mitochondrial transport / steroid metabolic process / viral release from host cell / bicellular tight junction / endoplasmic reticulum to Golgi vesicle-mediated transport / cholesterol metabolic process / protein-membrane adaptor activity / lipid metabolic process / neuron projection development / late endosome membrane / microtubule cytoskeleton / nuclear membrane / microtubule binding / vesicle / membrane fusion / positive regulation of canonical NF-kappaB signal transduction / endosome / cadherin binding / protein heterodimerization activity / Golgi membrane / protein domain specific binding / lysosomal membrane / Neutrophil degranulation / endoplasmic reticulum membrane / endoplasmic reticulum / protein homodimerization activity / mitochondrion / nucleoplasm / plasma membrane / cytoplasm / cytosol
Similarity search - Function
MENTAL domain / StAR-related lipid transfer protein 3, C-terminal / Cholesterol-capturing domain / MENTAL domain profile. / Steroidogenic acute regulatory protein-like / : / Vesicle-associated membrane-protein-associated protein / Major sperm protein (MSP) domain / MSP (Major sperm protein) domain / Major sperm protein (MSP) domain profile. ...MENTAL domain / StAR-related lipid transfer protein 3, C-terminal / Cholesterol-capturing domain / MENTAL domain profile. / Steroidogenic acute regulatory protein-like / : / Vesicle-associated membrane-protein-associated protein / Major sperm protein (MSP) domain / MSP (Major sperm protein) domain / Major sperm protein (MSP) domain profile. / in StAR and phosphatidylcholine transfer protein / START domain / START domain / START domain profile. / PapD-like superfamily / START-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
StAR-related lipid transfer protein 3 / Vesicle-associated membrane protein-associated protein A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Vesicle-associated membrane protein-associated protein A
B: Vesicle-associated membrane protein-associated protein A
C: Vesicle-associated membrane protein-associated protein A
D: Vesicle-associated membrane protein-associated protein A
E: StAR-related lipid transfer protein 3
F: StAR-related lipid transfer protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,12813
Polymers101,8806
Non-polymers2487
Water5,170287
1
A: Vesicle-associated membrane protein-associated protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5854
Polymers24,4781
Non-polymers1063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-19 kcal/mol
Surface area7740 Å2
MethodPISA
2
B: Vesicle-associated membrane protein-associated protein A
E: StAR-related lipid transfer protein 3


Theoretical massNumber of molelcules
Total (without water)26,4622
Polymers26,4622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-22 kcal/mol
Surface area8750 Å2
MethodPISA
3
C: Vesicle-associated membrane protein-associated protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5493
Polymers24,4781
Non-polymers712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-9 kcal/mol
Surface area7860 Å2
MethodPISA
4
D: Vesicle-associated membrane protein-associated protein A
F: StAR-related lipid transfer protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5334
Polymers26,4622
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-23 kcal/mol
Surface area8120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.140, 43.780, 83.640
Angle α, β, γ (deg.)89.460, 92.910, 105.130
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Vesicle-associated membrane protein-associated protein A / VAP-A / 33 kDa VAMP-associated protein / VAP-33


Mass: 24478.170 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: MSP domain / Source: (gene. exp.) Homo sapiens (human) / Gene: VAPA, VAP33 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9P0L0
#2: Protein/peptide StAR-related lipid transfer protein 3 / Metastatic lymph node gene 64 protein / MLN 64 / Protein CAB1 / START domain-containing protein 3 / StARD3


Mass: 1983.762 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: phospho-FFAT motif / Source: (synth.) Homo sapiens (human) / References: UniProt: Q14849
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 25% PEG 2000 MME, 0.1 M HEPES pH 7.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 25, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.85→42.26 Å / Num. obs: 42485 / % possible obs: 92.8 % / Redundancy: 3.338 % / Biso Wilson estimate: 38.514 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.208 / Rpim(I) all: 0.133 / Rrim(I) all: 0.248 / Χ2: 1.116 / Net I/σ(I): 4.57
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2% possible allRmerge(I) obsMean I/σ(I) obsRrim(I) all
1.85-1.92.45619360.79357.1
1.9-1.952.47825240.78875.91.4710.41.872
1.95-2.012.84531020.12197.14.3570.275.4
2.01-2.073.00830550.16297.72.5680.523.141
2.07-2.143.26729610.28998.61.9590.742.349
2.14-2.213.57729070.43298.91.8240.862.141
2.21-2.293.1823140.62280.9
2.29-2.393.70426580.62999.41.1281.381.318
2.39-2.493.56325560.71398.80.8831.71.039
2.49-2.613.6125070.83498.90.652.420.761
2.61-2.763.54123410.89199.20.4443.410.522
2.76-2.923.71222020.94499.50.3344.620.389
2.92-3.133.61320990.97299.60.2126.750.249
3.13-3.383.70619520.98699.30.1389.610.162
3.38-3.73.42616640.98393.50.13410.770.158
3.7-4.133.56416230.9999.40.09314.330.109
4.13-4.773.65114290.99499.50.06518.570.076
4.77-5.853.45312110.99599.30.06218.750.074
5.85-8.273.6569320.99499.70.06418.290.075
8.27-42.263.495120.9971000.04325.580.051

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXdev-3699refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Z9O

1z9o


Resolution: 1.85→42.26 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.92 / Phase error: 34.68
RfactorNum. reflection% reflection
Rfree0.2543 1237 5.05 %
Rwork0.2043 --
obs0.2068 24512 53.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 149.49 Å2 / Biso mean: 36.8225 Å2 / Biso min: 8.91 Å2
Refinement stepCycle: final / Resolution: 1.85→42.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4129 0 7 289 4425
Biso mean--45.82 36.41 -
Num. residues----522
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-1.930.4167100.38882152254
1.93-2.010.3407330.328345048310
2.01-2.120.3412470.309786591218
2.12-2.250.3476660.31751505157131
2.25-2.430.31471290.29772512264152
2.43-2.670.29812130.28093617383076
2.67-3.060.29072490.25754601485096
3.06-3.850.25272570.18944694495197
3.85-42.260.19972330.14574816504999
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.75290.7684-0.28961.6985-0.02540.99230.00490.01-0.33950.0136-0.0043-0.04790.0292-0.0689-00.189-0.00150.00140.1630.01240.1863-4.8552-25.33694.0723
22.23750.8948-0.26711.30460.82572.4138-0.102-0.29460.04970.04-0.0652-0.1151-0.0165-0.1234-0.03460.22250.00650.03230.1474-0.00870.1538.8871-14.337423.0312
32.74910.3367-0.15360.8539-0.13930.9855-0.0116-0.3994-0.05050.08530.00820.07530.0617-0.02550.00350.1476-0.0079-0.00820.216-0.02640.13920.36962.997566.1222
42.0852-0.20121.29511.88081.5042.3032-0.07970.0605-0.16630.0221-0.0129-0.00230.03430.17710.00140.18180.01960.02880.23740.03140.15497.8169-5.079644.4827
51.32630.06170.62870.2372-0.32590.83660.1943-0.428-0.02340.10220.30580.18260.031-0.08033.0060.09730.05360.06170.3482-0.00930.6108-1.5359-24.202523.3679
61.35810.6232-0.82040.2934-0.34160.9766-0.70370.2906-0.83560.45990.2778-0.08030.2890.29670.00350.44610.0120.06770.59130.12370.367915.8374-12.59546.7826
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' )A0
2X-RAY DIFFRACTION2(chain 'B' )B0
3X-RAY DIFFRACTION3(chain 'C' )C0
4X-RAY DIFFRACTION4(chain 'D' )D0
5X-RAY DIFFRACTION5(chain 'E' )E0
6X-RAY DIFFRACTION6(chain 'F' )F0

+
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