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- PDB-5jjd: crystal structure of the ceramide transfer protein PH and START d... -

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Basic information

Entry
Database: PDB / ID: 5jjd
Titlecrystal structure of the ceramide transfer protein PH and START domain complex
Components(Collagen type IV alpha-3-binding protein) x 2
KeywordsLIPID TRANSPORT / CERT / PH / START / complex
Function / homology
Function and homology information


intermembrane sphingolipid transfer / ceramide transfer activity / ceramide transport / ceramide 1-phosphate binding / ceramide 1-phosphate transfer activity / ER to Golgi ceramide transport / ceramide binding / intermembrane lipid transfer / ceramide metabolic process / Sphingolipid de novo biosynthesis ...intermembrane sphingolipid transfer / ceramide transfer activity / ceramide transport / ceramide 1-phosphate binding / ceramide 1-phosphate transfer activity / ER to Golgi ceramide transport / ceramide binding / intermembrane lipid transfer / ceramide metabolic process / Sphingolipid de novo biosynthesis / endoplasmic reticulum organization / phosphatidylinositol-4-phosphate binding / lipid homeostasis / heart morphogenesis / response to endoplasmic reticulum stress / mitochondrion organization / muscle contraction / 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 / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like ...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 / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Ceramide transfer protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.403 Å
AuthorsPrashek, J. / Bouyain, S. / Yao, X.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1 R15 GM113200-01 United States
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Interaction between the PH and START domains of ceramide transfer protein competes with phosphatidylinositol 4-phosphate binding by the PH domain.
Authors: Prashek, J. / Bouyain, S. / Fu, M. / Li, Y. / Berkes, D. / Yao, X.
History
DepositionApr 23, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 16, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Collagen type IV alpha-3-binding protein
B: Collagen type IV alpha-3-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8526
Polymers40,3832
Non-polymers4694
Water1,40578
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.761, 60.914, 95.804
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Collagen type IV alpha-3-binding protein / Ceramide transfer protein / hCERT / Goodpasture antigen-binding protein / GPBP / START domain- ...Ceramide transfer protein / hCERT / Goodpasture antigen-binding protein / GPBP / START domain-containing protein 11 / StARD11 / StAR-related lipid transfer protein 11


Mass: 12345.551 Da / Num. of mol.: 1 / Fragment: UNP residues 148-250
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COL4A3BP, CERT, STARD11 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y5P4
#2: Protein Collagen type IV alpha-3-binding protein / Ceramide transfer protein / hCERT / Goodpasture antigen-binding protein / GPBP / START domain- ...Ceramide transfer protein / hCERT / Goodpasture antigen-binding protein / GPBP / START domain-containing protein 11 / StARD11 / StAR-related lipid transfer protein 11


Mass: 28037.914 Da / Num. of mol.: 1 / Fragment: UNP residues 359-598
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COL4A3BP, CERT, STARD11 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y5P4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.16 Å3/Da / Density % sol: 43.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M MES bis-tris (pH 6.0), 6% (w/v) polyethylene glycol 10,000, and 10 micro molar calcium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→38.97 Å / Num. obs: 13860 / % possible obs: 97.74 % / Redundancy: 6.7 % / Net I/σ(I): 19.9

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2E3M, 4HHV

2e3m

4hhv


Resolution: 2.403→38.97 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.28
RfactorNum. reflection% reflection
Rfree0.2452 690 4.98 %
Rwork0.2011 --
obs0.2033 13855 97.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.403→38.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2695 0 31 78 2804
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032801
X-RAY DIFFRACTIONf_angle_d0.4833800
X-RAY DIFFRACTIONf_dihedral_angle_d10.4471663
X-RAY DIFFRACTIONf_chiral_restr0.045412
X-RAY DIFFRACTIONf_plane_restr0.003489
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.403-2.58820.26811210.26242366X-RAY DIFFRACTION89
2.5882-2.84860.28231410.24282627X-RAY DIFFRACTION99
2.8486-3.26060.27251360.22862659X-RAY DIFFRACTION100
3.2606-4.10730.26591410.18552694X-RAY DIFFRACTION100
4.1073-38.97560.20031510.17212819X-RAY DIFFRACTION100
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)
13.25430.77420.67837.54843.29916.9177-0.3275-0.7622-0.0582-0.056-0.07860.2771-0.13630.07750.41630.16660.0669-0.00170.2752-0.00740.1991-42.8645-4.3716-29.3075
24.99650.46230.32053.6859-0.98986.036-0.02250.6444-0.0457-0.56190.1297-0.4834-0.45730.8146-0.16950.3386-0.0452-0.01410.3882-0.03920.255-39.5332.674-31.7796
39.3360.08160.59428.85920.24172.75660.1127-0.3179-0.19730.4660.02560.9825-0.3772-0.5481-0.18910.24680.05630.02480.357-0.03980.2729-49.8786-2.6228-21.9285
43.7174-1.82451.43025.3474-6.84248.9558-0.3155-0.24380.40251.39180.4833-0.0787-1.1178-0.5026-0.09760.44410.02240.01720.3976-0.1070.3536-42.88676.2163-17.1548
54.7635-1.1332-0.961.4073-1.86476.5005-0.27820.45790.3108-0.1944-0.1479-0.5351-0.15840.54020.42850.3187-0.07920.07690.36770.08580.4058-59.81970.4397-59.5287
63.93110.8925-1.71566.47450.68476.9458-0.0685-0.62550.31711.03540.0923-0.6532-1.00330.1451-0.06190.60220.0251-0.07830.4918-0.06070.4147-69.685610.1296-39.3614
75.43932.20082.61883.7386-3.1467.4556-0.23230.52530.73460.26220.16230.7857-2.5510.10630.2120.81660.057-0.0560.3699-0.08720.5804-74.331516.9247-54.0529
84.3465-1.97121.37174.0018-4.19485.08590.1265-0.43710.05940.8856-0.1515-0.2127-0.7941-0.0393-0.12160.2826-0.06460.02680.1918-0.04970.1994-67.7164-1.6212-38.1112
93.12460.27371.78622.4584-0.80373.8665-0.1840.1280.0026-0.1070.0860.1693-0.2139-0.070.05780.1998-0.02430.00890.1851-0.02290.2307-75.4367-7.1656-54.5414
100.4870.1082-0.78231.74080.69481.823-0.12420.38350.1753-0.19460.0698-0.053-0.31940.64230.0650.2208-0.0476-0.00510.26570.01360.2603-66.969-2.0524-54.0688
113.2106-1.7466-0.77054.12825.17578.0549-0.4769-1.3254-0.70371.36790.43290.47171.25430.08620.10330.38150.0475-0.02870.4767-0.00920.3708-54.3129-15.4031-26.4517
122.6024-0.05080.32953.3569-1.28534.8303-0.2291-0.15190.40080.0870.19640.1498-0.6964-0.34280.19950.2543-0.0080.02260.1855-0.02440.2125-71.25551.5601-45.4399
134.2618-3.35830.89288.114-1.72494.8898-0.2133-0.4837-0.08240.27920.46460.9669-0.6247-0.6777-0.22740.2302-0.00460.03460.416-0.05810.2522-75.7759-4.4104-41.2371
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 24 through 39 )
2X-RAY DIFFRACTION2chain 'A' and (resid 40 through 74 )
3X-RAY DIFFRACTION3chain 'A' and (resid 75 through 101 )
4X-RAY DIFFRACTION4chain 'A' and (resid 102 through 120 )
5X-RAY DIFFRACTION5chain 'B' and (resid 364 through 381 )
6X-RAY DIFFRACTION6chain 'B' and (resid 382 through 405 )
7X-RAY DIFFRACTION7chain 'B' and (resid 406 through 417 )
8X-RAY DIFFRACTION8chain 'B' and (resid 418 through 428 )
9X-RAY DIFFRACTION9chain 'B' and (resid 429 through 489 )
10X-RAY DIFFRACTION10chain 'B' and (resid 490 through 533 )
11X-RAY DIFFRACTION11chain 'B' and (resid 534 through 543 )
12X-RAY DIFFRACTION12chain 'B' and (resid 544 through 564 )
13X-RAY DIFFRACTION13chain 'B' and (resid 565 through 598 )

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