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- PDB-4uex: Structure of human Saposin A at lysosomal pH -

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Basic information

Entry
Database: PDB / ID: 4uex
TitleStructure of human Saposin A at lysosomal pH
ComponentsPROSAPOSIN
KeywordsLIPID BINDING PROTEIN / SAPOSIN A / SAPOSIN / SAP / LIPID TRANSFER PROTEIN / SPHINGOLIPID ACTIVATOR PROTEIN
Function / homology
Function and homology information


positive regulation of beta-galactosidase activity / ganglioside GM1 transport to membrane / ganglioside GM2 binding / ganglioside GM3 binding / ganglioside GP1c binding / ganglioside GM1 binding / ganglioside GT1b binding / sphingolipid metabolic process / prostate gland growth / epithelial cell differentiation involved in prostate gland development ...positive regulation of beta-galactosidase activity / ganglioside GM1 transport to membrane / ganglioside GM2 binding / ganglioside GM3 binding / ganglioside GP1c binding / ganglioside GM1 binding / ganglioside GT1b binding / sphingolipid metabolic process / prostate gland growth / epithelial cell differentiation involved in prostate gland development / Glycosphingolipid catabolism / lysosomal transport / azurophil granule membrane / regulation of lipid metabolic process / enzyme activator activity / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / lysosomal lumen / Peptide ligand-binding receptors / regulation of autophagy / phospholipid binding / late endosome / Platelet degranulation / G alpha (i) signalling events / scaffold protein binding / collagen-containing extracellular matrix / protease binding / lysosome / lysosomal membrane / intracellular membrane-bounded organelle / Neutrophil degranulation / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Saposin, chordata / Saposin-like / NK-Lysin / Saposin A-type domain / Saposin / Saposin A-type domain / Saposin A-type domain profile. / Saposin/surfactant protein-B A-type DOMAIN / Saposin-like type B, region 1 / Saposin-like type B, region 1 ...Saposin, chordata / Saposin-like / NK-Lysin / Saposin A-type domain / Saposin / Saposin A-type domain / Saposin A-type domain profile. / Saposin/surfactant protein-B A-type DOMAIN / Saposin-like type B, region 1 / Saposin-like type B, region 1 / Saposin B type, region 2 / Saposin-like type B, region 2 / Saposin (B) Domains / Saposin B type domain / Saposin-like / Saposin B type domain profile. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHill, C.H. / Read, R.J. / Deane, J.E.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Structure of Human Saposin a at Lysosomal Ph.
Authors: Hill, C.H. / Read, R.J. / Deane, J.E.
History
DepositionDec 20, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1May 29, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROSAPOSIN
B: PROSAPOSIN


Theoretical massNumber of molelcules
Total (without water)18,6062
Polymers18,6062
Non-polymers00
Water46826
1
A: PROSAPOSIN


Theoretical massNumber of molelcules
Total (without water)9,3031
Polymers9,3031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PROSAPOSIN


Theoretical massNumber of molelcules
Total (without water)9,3031
Polymers9,3031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.170, 58.690, 35.160
Angle α, β, γ (deg.)90.00, 93.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PROSAPOSIN / PROACTIVATOR POLYPEPTIDE / PROTEIN A / CEREBROSIDE SULFATE AC TIVATOR / CSACT / DISPERSIN / ...PROACTIVATOR POLYPEPTIDE / PROTEIN A / CEREBROSIDE SULFATE AC TIVATOR / CSACT / DISPERSIN / SPHINGOLIPID ACTIVATOR PROTEIN 1 / SAP-1 / SULFATIDE/GM1 ACTIVATOR / A1 ACTIVATOR / CO-BETA-GLUCOSIDASE / GLUC OSYLCERAMIDASE ACTIVATOR / SPHINGOLIPID ACTIVATOR PROTEIN 2 / SAP-2 / COMPONENT C / PROTEIN C / SAPOSIN A


Mass: 9302.781 Da / Num. of mol.: 2 / Fragment: RESIDUES 60-142
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ORIGAMI / References: UniProt: P07602
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsUNIPROT REFERENCE IS TO THE POLYPROTEIN PRECURSOR PSAP ( PROSAPOSIN). THE SEQUENCE OF THE SAPOSIN A ...UNIPROT REFERENCE IS TO THE POLYPROTEIN PRECURSOR PSAP ( PROSAPOSIN). THE SEQUENCE OF THE SAPOSIN A PROTEIN IS 60- 142 IN THIS RECORD. AN ADDITIONAL MG IS PRESENT AT THE N- TERMINUS OF THE EXPRESSION CONSTRUCT AS A RESULT OF THE CLONING STRATEGY. THE C-TERMINAL SLQ ARE NOT MODELLED AS THEY ARE DISORDERED.

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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: 1.84 Å3/Da / Density % sol: 33.2 % / Description: NONE
Crystal growMethod: vapor diffusion, sitting drop / pH: 4.8
Details: SITTING-DROP VAPOUR DIFFUSION: 400 NL DROP (200 NL PROTEIN AT 19.6 MG/ML IN 150 MM NACL, 50 MM TRIS PH 7.4 MIXED WITH 200 NL RESERVOIR SOLUTION) WAS EQUILIBRATED AGAINST A 80 UL RESERVOIR OF ...Details: SITTING-DROP VAPOUR DIFFUSION: 400 NL DROP (200 NL PROTEIN AT 19.6 MG/ML IN 150 MM NACL, 50 MM TRIS PH 7.4 MIXED WITH 200 NL RESERVOIR SOLUTION) WAS EQUILIBRATED AGAINST A 80 UL RESERVOIR OF 0.2 M LITHIUM SULPHATE, 0.1 M SODIUM ACETATE PH 4.8 AND 25% W/V POLYETHYLENE GLYCOL 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 2, 2011
Details: KIRKPATRICK BAEZ BIMORPH MIRROR PAIR FOR HORIZONTAL AND VERTICAL FOCUSSING
RadiationMonochromator: SI (111) DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.8→34.12 Å / Num. obs: 12753 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.2
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 6.8 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 1.8 / % possible all: 97.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.9_1692)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2DOB

2dob


Resolution: 1.8→34.12 Å / SU ML: 0.2 / σ(F): 1.36 / Phase error: 25.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2098 612 4.8 %
Rwork0.1852 --
obs0.1864 12737 98.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→34.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1212 0 0 26 1238
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041338
X-RAY DIFFRACTIONf_angle_d0.8071821
X-RAY DIFFRACTIONf_dihedral_angle_d13.314517
X-RAY DIFFRACTIONf_chiral_restr0.032214
X-RAY DIFFRACTIONf_plane_restr0.004237
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.98110.28431370.23673000X-RAY DIFFRACTION98
1.9811-2.26780.22421530.17983021X-RAY DIFFRACTION99
2.2678-2.85690.21191630.17623019X-RAY DIFFRACTION99
2.8569-34.12610.19511590.18183085X-RAY DIFFRACTION99
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)
10.46160.0339-0.05760.72360.45941.4646-0.0646-0.10180.0892-0.1209-0.02690.024-0.06530.0319-0.00630.16130.0197-0.00940.1670.00540.1598-1.92358.0717-16.6722
20.34160.05570.24560.57180.38180.691-0.0409-0.00470.06480.0003-0.0270.14240.0098-0.0326-0.00080.1752-0.01560.00660.1772-0.0230.2053-7.672712.09120.7954
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B

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