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- PDB-1tjj: Human GM2 Activator Protein PAF complex -

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Basic information

Entry
Database: PDB / ID: 1tjj
TitleHuman GM2 Activator Protein PAF complex
ComponentsGanglioside GM2 activator
KeywordsSIGNALING PROTEIN / platelet activating factor / lipid binding pocket / beta-cup topology / protein dynamics
Function / homology
Function and homology information


sphingolipid activator protein activity / beta-N-acetylgalactosaminidase activity / glycosphingolipid catabolic process / lipid transporter activity / Glycosphingolipid catabolism / lipid storage / ganglioside catabolic process / oligosaccharide catabolic process / phospholipase activator activity / neuromuscular process controlling balance ...sphingolipid activator protein activity / beta-N-acetylgalactosaminidase activity / glycosphingolipid catabolic process / lipid transporter activity / Glycosphingolipid catabolism / lipid storage / ganglioside catabolic process / oligosaccharide catabolic process / phospholipase activator activity / neuromuscular process controlling balance / lipid transport / lysosomal lumen / cytoplasmic side of plasma membrane / azurophil granule lumen / basolateral plasma membrane / learning or memory / apical plasma membrane / intracellular membrane-bounded organelle / Neutrophil degranulation / extracellular exosome / extracellular region / cytosol
Similarity search - Function
Ganglioside M2 Activator Protein; Chain: A, / Ganglioside GM2 activator / Ganglioside GM2 activator / GM2-AP, lipid-recognition domain superfamily / ML domain / MD-2-related lipid-recognition domain / Domain involved in innate immunity and lipid metabolism. / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / LAURIC ACID / ISOPROPYL ALCOHOL / 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Chem-PFS / Ganglioside GM2 activator
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWright, C.S. / Mi, L.-Z. / Rastinejad, F.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Evidence for lipid packaging in the crystal structure of the GM2-activator complex with platelet activating factor
Authors: Wright, C.S. / Mi, L.-Z. / Rastinejad, F.
History
DepositionJun 4, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 16, 2013Group: Non-polymer description
Revision 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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: Ganglioside GM2 activator
B: Ganglioside GM2 activator
C: Ganglioside GM2 activator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,96525
Polymers53,4833
Non-polymers4,48222
Water10,233568
1
A: Ganglioside GM2 activator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3148
Polymers17,8281
Non-polymers1,4867
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ganglioside GM2 activator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2768
Polymers17,8281
Non-polymers1,4487
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Ganglioside GM2 activator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3759
Polymers17,8281
Non-polymers1,5478
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13170 Å2
ΔGint-92 kcal/mol
Surface area25520 Å2
MethodPISA
5
A: Ganglioside GM2 activator
hetero molecules

B: Ganglioside GM2 activator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,59016
Polymers35,6552
Non-polymers2,93514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_645-x+1,y-1/2,-z+1/21
Buried area7000 Å2
ΔGint-62 kcal/mol
Surface area19670 Å2
MethodPISA
6
B: Ganglioside GM2 activator
hetero molecules

A: Ganglioside GM2 activator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,59016
Polymers35,6552
Non-polymers2,93514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y+1/2,-z+1/21
Buried area6980 Å2
ΔGint-58 kcal/mol
Surface area19700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.470, 86.510, 120.470
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Ganglioside GM2 activator / GM2-AP / Cerebroside sulfate activator protein / Shingolipid activator protein 3 / SAP-3


Mass: 17827.557 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GM2A / Organ: liver,placenta,kidney,brain / Plasmid: pET16b(Novagen) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P17900

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Non-polymers , 8 types, 590 molecules

#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical ChemComp-PFS / (2R)-2-(acetyloxy)-3-(hexadecyloxy)propyl 2-(trimethylammonio)ethyl phosphate / PLATELET ACTIVATING FACTOR


Mass: 523.683 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C26H54NO7P
#6: Chemical ChemComp-LPE / 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE / LPC-ETHER


Mass: 510.708 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C26H57NO6P
#7: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O
#8: Chemical ChemComp-DAO / LAURIC ACID


Mass: 200.318 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H24O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 568 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.94 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: Peg4000, iso-propanol, Hepes buffer, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 123 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorDate: Aug 2, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 45517 / Num. obs: 44841 / % possible obs: 98.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.9 % / Biso Wilson estimate: 10.8 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 29.5
Reflection shellResolution: 2→2.07 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.104 / Mean I/σ(I) obs: 16 / Num. unique all: 4592 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1refinement
HKL-2000data reduction
CCP4(TRUNCATE)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→19.79 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1894751.39 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.234 3727 8.3 %RANDOM
Rwork0.189 ---
all0.193 45517 --
obs0.189 44841 99.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 63.5801 Å2 / ksol: 0.352261 e/Å3
Displacement parametersBiso mean: 30.1 Å2
Baniso -1Baniso -2Baniso -3
1-1.29 Å20 Å20 Å2
2---0.42 Å20 Å2
3----0.87 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.01 Å
Refinement stepCycle: LAST / Resolution: 2→19.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3716 0 294 568 4578
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d26.1
X-RAY DIFFRACTIONc_improper_angle_d1
X-RAY DIFFRACTIONc_mcbond_it2.641.5
X-RAY DIFFRACTIONc_mcangle_it3.612
X-RAY DIFFRACTIONc_scbond_it10.022
X-RAY DIFFRACTIONc_scangle_it7.12.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.24 570 8.3 %
Rwork0.184 6337 -
obs--92.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3SOLVENT_REP.PARAMSOLVENT.TOP
X-RAY DIFFRACTION4PAF_LPE_EPE_LAU.PARAMPAF_LPE_EPE_LAU.TOP

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