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- PDB-6gn5: CRYSTAL STRUCTURE OF HUMAN GRAMD1C START DOMAIN -

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Basic information

Entry
Database: PDB / ID: 6gn5
TitleCRYSTAL STRUCTURE OF HUMAN GRAMD1C START DOMAIN
ComponentsGRAM domain-containing protein 1C
KeywordsLIPID TRANSPORT / ALPHA/BETA HELIX GRIP FOLD / STEROL BINDING
Function / homology
Function and homology information


endoplasmic reticulum-plasma membrane contact site / cellular response to cholesterol / cholesterol transfer activity / cholesterol binding / membrane => GO:0016020 / endoplasmic reticulum membrane / plasma membrane
Similarity search - Function
VASt domain / VAD1 Analog of StAR-related lipid transfer domain / VASt domain profile. / domain in glucosyltransferases, myotubularins and other putative membrane-associated proteins / GRAM domain / GRAM domain / PH-like domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.41 Å
AuthorsFriese, A. / Vetter, I.R.
CitationJournal: Nat.Chem.Biol. / Year: 2019
Title: The cholesterol transfer protein GRAMD1A regulates autophagosome biogenesis.
Authors: Laraia, L. / Friese, A. / Corkery, D.P. / Konstantinidis, G. / Erwin, N. / Hofer, W. / Karatas, H. / Klewer, L. / Brockmeyer, A. / Metz, M. / Scholermann, B. / Dwivedi, M. / Li, L. / Rios- ...Authors: Laraia, L. / Friese, A. / Corkery, D.P. / Konstantinidis, G. / Erwin, N. / Hofer, W. / Karatas, H. / Klewer, L. / Brockmeyer, A. / Metz, M. / Scholermann, B. / Dwivedi, M. / Li, L. / Rios-Munoz, P. / Kohn, M. / Winter, R. / Vetter, I.R. / Ziegler, S. / Janning, P. / Wu, Y.W. / Waldmann, H.
History
DepositionMay 30, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 10, 2019Group: Data collection / Database references / Category: citation_author / pdbx_database_proc / Item: _citation_author.identifier_ORCID
Revision 1.3Dec 25, 2019Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GRAM domain-containing protein 1C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0346
Polymers22,4431
Non-polymers5915
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-72 kcal/mol
Surface area9720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.320, 73.850, 45.340
Angle α, β, γ (deg.)90.000, 99.310, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein GRAM domain-containing protein 1C


Mass: 22443.025 Da / Num. of mol.: 1 / Fragment: STEROL BINDING START DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GRAMD1C, UNQ2543/PRO6095 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8IYS0
#2: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 43.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 40% MPD 10% PEG8000 0.1M HEPES PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97793 Å / Relative weight: 1
ReflectionResolution: 1.41→44.7 Å / Num. obs: 39116 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6.69 % / Biso Wilson estimate: 25.653 Å2 / Rmerge(I) obs: 0.056 / Rrim(I) all: 0.061 / Net I/σ(I): 14.76
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRrim(I) all% possible all
1.41-1.456.380.8641.6828170.93897.6
1.45-1.490.6512.3328240.706100
1.49-1.530.5112.927120.556100
1.53-1.580.3933.7326820.42899.8
1.58-1.630.3135.0125710.338100
1.63-1.690.256.1724960.2799.6
1.69-1.750.1977.9924230.213100
1.75-1.820.15110.3323220.164100
1.82-1.90.12112.6521960.13199.6
1.9-1.990.09315.9521150.10299.8
1.99-2.10.07820.5220580.084100
2.1-2.230.06624.3819150.072100
2.23-2.380.06126.517970.066100
2.38-2.570.05928.2616720.06499.9
2.57-2.820.05328.8615500.05899.9
2.82-3.150.04534.7613990.04999.4
3.15-3.640.03937.7112360.042100
3.64-4.460.03439.1210610.03799.9
4.46-6.310.03738.468120.0499.1
6.31-44.70.03940.614580.04299.6

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIXrefinement
PDB_EXTRACT3.11data extraction
XSCALEdata scaling
CRANK2phasing
RefinementResolution: 1.41→38.267 Å / Occupancy max: 1 / Occupancy min: 0.28 / SU ML: 0.12 / σ(F): 1.37 / Phase error: 20.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2052 1948 4.98 %
Rwork0.1825 37141 -
obs0.1837 39089 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 67.09 Å2 / Biso mean: 24.4441 Å2 / Biso min: 10.21 Å2
Refinement stepCycle: LAST / Resolution: 1.41→38.267 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1464 0 40 108 1612
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4104-1.44570.27471320.27752593272598
1.4457-1.48480.25151390.24526432782100
1.4848-1.52850.24121360.223626172753100
1.5285-1.57780.26491400.211526712811100
1.5778-1.63420.22991430.202726532796100
1.6342-1.69960.21391320.197126452777100
1.6996-1.7770.21231420.177426292771100
1.777-1.87070.19671400.18726632803100
1.8707-1.98790.20371440.181226622806100
1.9879-2.14130.19821370.173826512788100
2.1413-2.35680.21191400.179726742814100
2.3568-2.69770.19521390.191726712810100
2.6977-3.39850.2171420.183126592801100
3.3985-38.28110.18561420.163927102852100

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