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- PDB-3h3t: Crystal structure of the CERT START domain in complex with HPA-16 -

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Basic information

Entry
Database: PDB / ID: 3h3t
TitleCrystal structure of the CERT START domain in complex with HPA-16
ComponentsGoodpasture antigen binding protein
KeywordsLIPID TRANSPORT / LIPID TRANSFER PROTEIN / CERT / CERAMIDE TRANSFER
Function / homology
Function and homology information


intermembrane sphingolipid transfer / ceramide transfer activity / endoplasmic reticulum-trans-Golgi network membrane contact site / ER to Golgi ceramide transport / ceramide 1-phosphate transfer activity / ceramide 1-phosphate binding / sphingomyelin biosynthetic process / ceramide metabolic process / intermembrane lipid transfer / lipid transfer activity ...intermembrane sphingolipid transfer / ceramide transfer activity / endoplasmic reticulum-trans-Golgi network membrane contact site / ER to Golgi ceramide transport / ceramide 1-phosphate transfer activity / ceramide 1-phosphate binding / sphingomyelin biosynthetic process / ceramide metabolic process / intermembrane lipid transfer / lipid transfer activity / ceramide binding / Sphingolipid de novo biosynthesis / sphingolipid biosynthetic process / phosphatidylinositol-4-phosphate binding / kinase activity / immune response / endoplasmic reticulum membrane / Golgi apparatus / mitochondrion / nucleoplasm / 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-16H / Ceramide transfer protein / Ceramide transfer protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 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)58,7034
Polymers57,8642
Non-polymers8392
Water63135
1
A: Goodpasture antigen binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3512
Polymers28,9321
Non-polymers4201
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Goodpasture antigen binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3512
Polymers28,9321
Non-polymers4201
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.340, 74.568, 78.021
Angle α, β, γ (deg.)90.000, 102.840, 90.000
Int Tables number4
Space group name H-MP1211
DetailsThere are 2 biological units in the asymmetric unit.

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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) / Plasmid: PGEX-5X1 (MODIFIED) / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: A8K7S2, UniProt: Q9Y5P4*PLUS
#2: Chemical ChemComp-16H / N-[(1R,3R)-3-hydroxy-1-(hydroxymethyl)-3-phenylpropyl]hexadecanamide


Mass: 419.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H45NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 40.73 % / Mosaicity: 0.964 °
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: vapor diffusion, temperature 293K, VAPOR DIFFUSION

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.9778 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 14, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 18692 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Redundancy: 5.1 % / Rmerge(I) obs: 0.074 / Χ2: 1.31 / Net I/σ(I): 26.082
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.4-2.494.90.3418600.81699.5
2.49-2.595.10.29318510.83499.9
2.59-2.75.10.23418580.896100
2.7-2.855.20.18218650.961100
2.85-3.025.20.13418621.135100
3.02-3.265.20.118811.279100
3.26-3.585.10.07318491.58599.9
3.58-4.15.10.0618661.81699.8
4.1-5.175.10.04618811.84199.6
5.17-505.10.04519191.89999.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
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: 2.4→20 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.916 / Occupancy max: 1 / Occupancy min: 0.35 / SU B: 9.304 / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.675 / ESU R Free: 0.302 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.264 948 5.1 %RANDOM
Rwork0.205 ---
obs0.208 18577 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 65.7 Å2 / Biso mean: 32.999 Å2 / Biso min: 11.62 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å20 Å21.5 Å2
2--0.31 Å20 Å2
3---0.69 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3778 0 60 35 3873
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223926
X-RAY DIFFRACTIONr_angle_refined_deg1.4691.9445334
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4765468
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.81824.346191
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.3215649
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1061526
X-RAY DIFFRACTIONr_chiral_restr0.1090.2593
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212986
X-RAY DIFFRACTIONr_mcbond_it0.7181.52351
X-RAY DIFFRACTIONr_mcangle_it1.38123840
X-RAY DIFFRACTIONr_scbond_it1.95731575
X-RAY DIFFRACTIONr_scangle_it3.3424.51494
LS refinement shellResolution: 2.4→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 67 -
Rwork0.248 1269 -
all-1336 -
obs--99.11 %

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