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- PDB-5nxb: Mouse galactocerebrosidase in complex with saposin A -

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Basic information

Entry
Database: PDB / ID: 5nxb
TitleMouse galactocerebrosidase in complex with saposin A
Components
  • GalactocerebrosidaseGalactosylceramidase
  • Prosaposin
KeywordsHYDROLASE / Krabbe Disease / galactocerebroside / galactosylceramide / GALC / SapA
Function / homology
Function and homology information


corneocyte development / membrane lipid metabolic process / glycolipid metabolic process / glucosylceramide metabolic process / inclusion body assembly / walking behavior / cornified envelope assembly / Glycosphingolipid catabolism / lipid antigen binding / galactosylceramide catabolic process ...corneocyte development / membrane lipid metabolic process / glycolipid metabolic process / glucosylceramide metabolic process / inclusion body assembly / walking behavior / cornified envelope assembly / Glycosphingolipid catabolism / lipid antigen binding / galactosylceramide catabolic process / micturition / Peptide ligand-binding receptors / cerebellar Purkinje cell differentiation / lysosomal protein catabolic process / galactosylceramidase / galactosylceramidase activity / ceramide metabolic process / G alpha (i) signalling events / Platelet degranulation / NK T cell differentiation / sphingolipid metabolic process / prostate gland growth / epithelial cell differentiation involved in prostate gland development / nervous system process / aggresome / lysosomal transport / : / cochlea development / regulation of MAPK cascade / neuromuscular process controlling balance / regulation of lipid metabolic process / protein secretion / antigen processing and presentation / developmental growth / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / myelination / Neutrophil degranulation / G protein-coupled receptor binding / sensory perception of sound / intracellular protein transport / cellular response to reactive oxygen species / late endosome / gene expression / protease binding / positive regulation of MAPK cascade / lysosome / mitochondrion / extracellular space / extracellular region / identical protein binding / cytoplasm
Similarity search - Function
Glycosyl hydrolase family 59, central domain / : / : / Glycosyl hydrolase family 59 central domain / Galactocerebrosidase, C-terminal lectin domain / Glycoside hydrolase, family 59 / Glycosyl hydrolase family 59 / Saposin, chordata / Saposin-like / NK-Lysin ...Glycosyl hydrolase family 59, central domain / : / : / Glycosyl hydrolase family 59 central domain / Galactocerebrosidase, C-terminal lectin domain / Glycoside hydrolase, family 59 / Glycosyl hydrolase family 59 / 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. / Exo-inulinase; domain 1 / Glycosidases / Aldolase class I / Aldolase-type TIM barrel / Glycoside hydrolase superfamily / Jelly Rolls / TIM Barrel / Alpha-Beta Barrel / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Galactocerebrosidase / Prosaposin
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsGraham, S.C. / Hill, C.H. / Deane, J.E.
CitationJournal: Nat Commun / Year: 2018
Title: The mechanism of glycosphingolipid degradation revealed by a GALC-SapA complex structure.
Authors: Hill, C.H. / Cook, G.M. / Spratley, S.J. / Fawke, S. / Graham, S.C. / Deane, J.E.
History
DepositionMay 9, 2017Deposition site: PDBE / Processing site: PDBE
SupersessionMay 24, 2017ID: 5N8K
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Galactocerebrosidase
B: Galactocerebrosidase
C: Prosaposin
D: Prosaposin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,72714
Polymers168,3334
Non-polymers3,39310
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10840 Å2
ΔGint-22 kcal/mol
Surface area55140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)187.183, 187.183, 360.240
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein Galactocerebrosidase / Galactosylceramidase / GALCERase / Galactocerebroside beta-galactosidase / Galactosylceramidase / Galactosylceramide beta- ...GALCERase / Galactocerebroside beta-galactosidase / Galactosylceramidase / Galactosylceramide beta-galactosidase


Mass: 74596.750 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: FRAGMENT CORRESPONDS TO RESIDUES 25-668 BASED ON NUMBERING STARTING AT SECOND UNIPROT INITIATION SITE
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Galc / Plasmid: pSecTag2B-mGALC / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: P54818, galactosylceramidase
#2: Protein Prosaposin / / Sulfated glycoprotein 1 / SGP-1


Mass: 9569.935 Da / Num. of mol.: 2 / Fragment: UNP residues 59-143
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Psap, Sgp1 / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Variant (production host): Origami / References: UniProt: Q61207

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Sugars , 3 types, 8 molecules

#3: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 1 types, 2 molecules

#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca

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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: 5.41 Å3/Da / Density % sol: 77.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 800 nL of protein (90 uM GALC plus 180 uM SapA) was mixed with 800 nL of reservoir solution (75 mM Sodium citrate pH 5.6, 11% PEG 3350) and equilibrated against 200 uL reservoirs at 20C.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92818 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 5, 2015 / Details: Toroidal mirrors
RadiationMonochromator: SI(111) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92818 Å / Relative weight: 1
ReflectionResolution: 3.6→180.12 Å / Num. obs: 44024 / % possible obs: 100 % / Redundancy: 25.6 % / Biso Wilson estimate: 61.93 Å2 / CC1/2: 0.945 / Rmerge(I) obs: 0.386 / Net I/σ(I): 9.3
Reflection shellResolution: 3.6→3.7 Å / Redundancy: 25.2 % / Rmerge(I) obs: 2.946 / Num. unique obs: 3316 / CC1/2: 0.677 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CCE, 4DDJ

4cce

4ddj


Resolution: 3.6→162.11 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.892 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.422
Details: Refined using LSSR restraints to target structure 4CCE
RfactorNum. reflection% reflectionSelection details
Rfree0.231 2138 4.88 %RANDOM
Rwork0.217 ---
obs0.218 43825 99.7 %-
Displacement parametersBiso mean: 101.63 Å2
Baniso -1Baniso -2Baniso -3
1--0.463 Å20 Å20 Å2
2---0.463 Å20 Å2
3---0.9261 Å2
Refine analyzeLuzzati coordinate error obs: 0.49 Å
Refinement stepCycle: 1 / Resolution: 3.6→162.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11522 0 220 0 11742
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00812110HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9416542HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4012SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes262HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1760HARMONIC5
X-RAY DIFFRACTIONt_it12110HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.38
X-RAY DIFFRACTIONt_other_torsion16.39
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1586SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance8HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact13279SEMIHARMONIC4
LS refinement shellResolution: 3.6→3.69 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 158 5.07 %
Rwork0.305 2958 -
all0.305 3116 -
obs--98.82 %
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)
14.3111-0.0791-0.13911.7432-0.07682.1878-0.1411-0.27060.04480.18850.0052-0.64080.09060.77620.13590.61470.12630.0290.66730.0770.180686.5091134.207942.386
23.40080.16171.7138-0.9469-0.88025.0412-0.00030.0136-0.0898-0.01520.0537-0.3247-0.03020.0927-0.05340.4445-0.13920.143-0.06410.14370.031271.3662158.232221.4844
30.9922-0.74520.63392.4195-0.60632.8383-0.2385-0.30260.18530.00090.3375-0.1093-0.0547-0.072-0.0990.64880.03010.09590.17420.0404-0.18357.3835144.084936.1678
42.8156-0.51440.62523.9777-1.29873.26220.03750.14370.0354-0.5059-0.04240.037-0.0293-0.27020.00490.6250.02920.0678-0.05520.1566-0.449146.8155152.061111.3348
52.7774-0.42950.14983.1082-0.72523.64760.23740.63020.3969-0.3868-0.05860.5382-0.2579-0.4867-0.17880.70770.08950.030.3480.16990.233749.8002106.79662.8972
61.91720.1604-0.0843-0.45380.93011.70560.09290.0103-0.0629-0.1532-0.0681-0.0643-0.09570.0178-0.02480.2959-0.00290.22720.22150.0697-0.105681.715592.02860.4006
72.1936-0.1887-0.22161.5477-0.2661.91780.228-0.0249-0.2554-0.1397-0.17410.15670.15670.2935-0.05390.6052-0.00670.08470.09120.0252-0.000668.982790.422421.5376
84.7016-0.68310.05982.80181.10993.05610.1308-0.036-0.0320.0301-0.1447-0.5732-0.0730.64780.0140.28250.04230.14830.39580.1446-0.08296.986891.897922.8463
93.77330.68180.5535.1156-0.14753.09870.0819-0.07080.16640.0586-0.07460.05780.0680.0018-0.0073-0.167-0.03510.1742-0.6708-0.1158-0.536553.9968110.476935.0155
103.92640.2076-1.18342.98790.06913.76990.00730.008-0.12020.0731-0.1350.11320.16-0.08790.12770.10120.14390.019-0.65650.0848-0.732159.2148116.172941.2751
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|472 - A|668 }
2X-RAY DIFFRACTION2{ A|453 - A|471 }
3X-RAY DIFFRACTION3{ A|41 - A|337 }
4X-RAY DIFFRACTION4tls4completeA
5X-RAY DIFFRACTION5{ B|472 - B|668 }
6X-RAY DIFFRACTION6{ B|453 - B|471 }
7X-RAY DIFFRACTION7{ B|41 - B|337 }
8X-RAY DIFFRACTION8tls4completeB
9X-RAY DIFFRACTION9{ C|* }
10X-RAY DIFFRACTION10{ D|* }

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