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- PDB-3h3q: Crystal structure of the CERT START domain in complex with HPA-13 -

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Basic information

Entry
Database: PDB / ID: 3h3q
TitleCrystal structure of the CERT START domain in complex with HPA-13
ComponentsGoodpasture antigen binding protein
KeywordsLIPID TRANSPORT / LIPID TRANSFER PROTEIN / CERT / CERAMIDE TRANSFER / Collagen
Function / homology
Function and homology information


intermembrane sphingolipid transfer / ceramide transfer activity / ER to Golgi ceramide transport / ceramide 1-phosphate transfer activity / ceramide 1-phosphate binding / ceramide transport / ceramide metabolic process / ceramide binding / intermembrane lipid transfer / Sphingolipid de novo biosynthesis ...intermembrane sphingolipid transfer / ceramide transfer activity / ER to Golgi ceramide transport / ceramide 1-phosphate transfer activity / ceramide 1-phosphate binding / ceramide transport / ceramide metabolic process / ceramide binding / intermembrane lipid transfer / Sphingolipid de novo biosynthesis / endoplasmic reticulum organization / phosphatidylinositol-4-phosphate binding / lipid homeostasis / heart morphogenesis / muscle contraction / response to endoplasmic reticulum stress / mitochondrion organization / cell morphogenesis / kinase activity / in utero embryonic development / cell population proliferation / immune response / endoplasmic reticulum membrane / Golgi apparatus / signal transduction / mitochondrion / nucleoplasm / identical protein binding / cytosol
Similarity search - Function
STARD11, START domain / : / in StAR and phosphatidylcholine transfer protein / START domain / START domain / START domain profile. / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / PH domain ...STARD11, START domain / : / in StAR and phosphatidylcholine transfer protein / START domain / START domain / START domain profile. / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-H13 / Ceramide transfer protein / Ceramide transfer protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsKudo, N. / Wakatsuki, S. / Kato, R.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Crystal structures of the CERT START domain with inhibitors provide insights into the mechanism of ceramide transfer.
Authors: Kudo, N. / Kumagai, K. / Matsubara, R. / Kobayashi, S. / Hanada, K. / Wakatsuki, S. / Kato, R.
History
DepositionApr 17, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Goodpasture antigen binding protein
B: Goodpasture antigen binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6194
Polymers57,8642
Non-polymers7552
Water1,17165
1
A: Goodpasture antigen binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3092
Polymers28,9321
Non-polymers3781
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Goodpasture antigen binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3092
Polymers28,9321
Non-polymers3781
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.480, 74.706, 77.605
Angle α, β, γ (deg.)90.000, 102.640, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Goodpasture antigen binding protein / cDNA FLJ77923 / highly similar to Homo sapiens collagen / type IV / alpha 3 (Goodpasture antigen) ...cDNA FLJ77923 / highly similar to Homo sapiens collagen / type IV / alpha 3 (Goodpasture antigen) binding protein / COL4A3BP / transcript variant 2 / mRNA / Collagen / type IV / alpha 3 (Goodpasture antigen) binding protein / isoform CRA_a


Mass: 28931.764 Da / Num. of mol.: 2 / Fragment: CERT START DOMAIN (RESIDUES 347-598)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CERT, COL4A3BP, hCG_18817 / Plasmid: PGEX-5X1 (MODIFIED) / Production host: Escherichia coli (E. coli) / Strain (production host): DH5ALPHA / References: UniProt: A8K7S2, UniProt: Q9Y5P4*PLUS
#2: Chemical ChemComp-H13 / N-[(1R,3R)-3-hydroxy-1-(hydroxymethyl)-3-phenylpropyl]tridecanamide


Mass: 377.561 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H39NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 2.08 Å3/Da / Density % sol: 40.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 15, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 32043 / % possible obs: 94 % / Observed criterion σ(F): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.093
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.499 / Num. unique all: 2326 / % possible all: 73.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.341 / Cor.coef. Fo:Fc: 0.776
Highest resolutionLowest resolution
Rotation3 Å41.45 Å
Translation3 Å41.45 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RESOLVEphasing
REFMAC5.4.0069refinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2E3N

2e3n


Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.921 / Occupancy max: 1 / Occupancy min: 0.35 / SU B: 5.562 / SU ML: 0.157 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.246 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.282 1507 5 %RANDOM
Rwork0.216 ---
obs0.219 30090 93.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 66.74 Å2 / Biso mean: 36.067 Å2 / Biso min: 18.46 Å2
Baniso -1Baniso -2Baniso -3
1-2.12 Å20 Å20.47 Å2
2---0.97 Å20 Å2
3----0.95 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3782 0 54 65 3901
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223924
X-RAY DIFFRACTIONr_angle_refined_deg1.5761.9435335
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8795468
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.04824.346191
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.8515650
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.211526
X-RAY DIFFRACTIONr_chiral_restr0.1450.2596
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212986
X-RAY DIFFRACTIONr_mcbond_it0.8991.52352
X-RAY DIFFRACTIONr_mcangle_it1.66923845
X-RAY DIFFRACTIONr_scbond_it2.50431572
X-RAY DIFFRACTIONr_scangle_it4.0674.51490
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 86 -
Rwork0.264 1580 -
all-1666 -
obs--71.78 %

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