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- PDB-5u7z: Human acid ceramidase (ASAH1, aCDase) self-activated -

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Basic information

Entry
Database: PDB / ID: 5u7z
TitleHuman acid ceramidase (ASAH1, aCDase) self-activated
Components(Acid ceramidase) x 2
KeywordsHYDROLASE / ceramidase / ceramide / ntn-hydrolase
Function / homology
Function and homology information


regulation of programmed necrotic cell death / : / Glycosphingolipid metabolism / ceramidase / N-acylsphingosine amidohydrolase activity / : / ceramide catabolic process / fatty acid amide hydrolase activity / regulation of steroid biosynthetic process / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides ...regulation of programmed necrotic cell death / : / Glycosphingolipid metabolism / ceramidase / N-acylsphingosine amidohydrolase activity / : / ceramide catabolic process / fatty acid amide hydrolase activity / regulation of steroid biosynthetic process / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / sphingosine biosynthetic process / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / ceramide biosynthetic process / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / keratinocyte differentiation / lysosomal lumen / fatty acid metabolic process / nuclear receptor binding / transcription corepressor activity / tertiary granule lumen / cellular response to tumor necrosis factor / ficolin-1-rich granule lumen / lysosome / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / nucleus
Similarity search - Function
Acid ceramidase-like / Acid ceramidase, N-terminal / beta subunit of N-acylethanolamine-hydrolyzing acid amidase / Choloylglycine hydrolase/NAAA C-terminal / Linear amide C-N hydrolases, choloylglycine hydrolase family
Similarity search - Domain/homology
Ceramidase / Acid ceramidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsGebai, A. / Gorelik, A. / Illes, K. / Nagar, B.
CitationJournal: Nat Commun / Year: 2018
Title: Structural basis for the activation of acid ceramidase.
Authors: Gebai, A. / Gorelik, A. / Li, Z. / Illes, K. / Nagar, B.
History
DepositionDec 13, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2018Provider: repository / Type: Initial release
Revision 1.1May 2, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 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 / 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.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acid ceramidase
B: Acid ceramidase
C: Acid ceramidase
D: Acid ceramidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,67324
Polymers88,1454
Non-polymers3,52820
Water59433
1
A: Acid ceramidase
B: Acid ceramidase
hetero molecules

C: Acid ceramidase
D: Acid ceramidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,67324
Polymers88,1454
Non-polymers3,52820
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_545x+1/2,y-1/2,z1
Buried area18920 Å2
ΔGint-237 kcal/mol
Surface area29750 Å2
MethodPISA
2
A: Acid ceramidase
B: Acid ceramidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,77412
Polymers44,0732
Non-polymers1,70110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8820 Å2
ΔGint-117 kcal/mol
Surface area15480 Å2
MethodPISA
3
C: Acid ceramidase
D: Acid ceramidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,89912
Polymers44,0732
Non-polymers1,82710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8990 Å2
ΔGint-102 kcal/mol
Surface area15370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.667, 68.312, 97.805
Angle α, β, γ (deg.)90.00, 120.72, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein Acid ceramidase


Mass: 14865.188 Da / Num. of mol.: 2 / Fragment: UNP residues 22-140
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A8K0B6, UniProt: Q13510*PLUS
#2: Protein Acid ceramidase


Mass: 29207.396 Da / Num. of mol.: 2 / Fragment: UNP residues 141-395
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A8K0B6, UniProt: Q13510*PLUS

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Sugars , 2 types, 7 molecules

#3: 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: obtained synthetically
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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5 / Source method: obtained synthetically / 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 , 2 types, 46 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.5 Å3/Da / Density % sol: 50.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG 1000 sodium phosphate-citrate lithium sulfate / PH range: 4.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Nov 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.5→48.389 Å / Num. obs: 26671 / % possible obs: 99 % / Redundancy: 3.7 % / Net I/σ(I): 10.8

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→48.389 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2709 1335 5.01 %
Rwork0.2335 --
obs0.2354 26667 87.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→48.389 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5882 0 213 33 6128
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036247
X-RAY DIFFRACTIONf_angle_d0.6758504
X-RAY DIFFRACTIONf_dihedral_angle_d12.6973658
X-RAY DIFFRACTIONf_chiral_restr0.042955
X-RAY DIFFRACTIONf_plane_restr0.0031052
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5001-2.58950.3112710.3141333X-RAY DIFFRACTION47
2.5895-2.69310.3457950.29281817X-RAY DIFFRACTION63
2.6931-2.81570.3261170.29422214X-RAY DIFFRACTION77
2.8157-2.96410.32351380.28342614X-RAY DIFFRACTION91
2.9641-3.14980.31081490.27562844X-RAY DIFFRACTION99
3.1498-3.3930.25581520.23822882X-RAY DIFFRACTION100
3.393-3.73430.25351510.22272861X-RAY DIFFRACTION100
3.7343-4.27440.23791520.20022909X-RAY DIFFRACTION100
4.2744-5.38410.22311530.19262890X-RAY DIFFRACTION100
5.3841-48.39770.30131570.2372968X-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)
10.62530.00450.3559-0.001-0.00810.2504-0.03450.3812-0.0932-0.2645-0.38640.47680.1818-0.35090.20510.39980.0879-0.05920.4888-0.1570.410369.8126-38.6069191.4086
20.50820.12410.06210.76830.2421.7559-0.23990.10750.165-0.1977-0.48230.3115-0.0442-0.45520.1854-0.1830.7326-0.3590.33380.19780.201174.1162-18.01190.7428
31.99211.1768-0.88742.33610.28572.94710.3025-0.11040.6294-0.1674-0.6392-0.1194-0.1625-0.39220.15970.26320.10780.00060.2420.06340.527684.1992-10.3514201.2975
45.60210.04790.11912.00751.99985.18460.2099-0.66810.31440.1997-0.2471-0.0865-0.0796-0.27540.11770.3325-0.05980.07610.24250.0280.391996.9664-10.3446212.7705
52.05850.1917-0.47591.15971.20682.89280.28390.08930.5594-0.3306-0.1043-0.1397-0.2264-0.0301-0.11510.2650.03370.0460.22040.05610.310593.1171-11.1978199.4529
61.27460.0596-0.4651.4169-0.19421.03750.08980.40770.1333-0.3113-0.1090.0387-0.1405-0.21970.00430.29250.0951-0.0960.32790.04430.221682.4957-24.0897191.447
71.58921.42110.0522.18930.69710.37570.1764-0.08030.09510.0145-0.1087-0.2838-0.11150.04580.02140.24970.1037-0.03220.34630.09930.3056101.7396-23.1757196.4953
82.68210.73690.21932.68360.2862.17660.05660.329-0.1876-0.5554-0.2862-0.24320.22020.04050.10080.38250.1477-0.02210.3088-0.00930.152295.6387-32.2248185.8951
91.7101-0.1056-0.43550.3007-0.03971.5342-0.06060.3595-0.4147-0.2182-0.07910.30310.216-0.4786-0.03260.32860.1029-0.15060.3733-0.1150.288777.8216-35.7535189.6931
101.23120.40890.01621.9505-0.07531.21140.22670.6762-0.2028-0.281-0.6241-0.71560.03680.97010.1050.24690.35040.17460.2797-0.16360.295758.1454-19.452190.6244
112.91590.42050.12562.5951-0.82471.76220.1999-0.1224-0.35880.1941-0.2347-0.02510.22640.10770.040.2824-0.0119-0.02250.16970.00950.340244.007-29.5796205.2401
120.84110.35370.43691.22970.16810.96510.07710.3154-0.1841-0.2169-0.1022-0.06130.18580.21310.01980.25330.12740.0690.3261-0.02230.24852.2505-17.1182191.9884
131.15891.752-0.38562.7899-0.60560.09610.538-0.13940.28970.2342-0.23170.5273-0.2338-0.1095-0.08350.37520.1160.0870.3449-0.02330.219332.8945-18.1059196.5799
141.99740.8568-0.38882.6474-0.24381.67020.06760.25040.095-0.3072-0.11530.0787-0.11560.05260.03930.31050.089-0.01250.28920.01750.169639.1474-9.011186.17
151.5307-0.26250.24690.96160.23461.3730.00310.38720.0924-0.2613-0.1104-0.3332-0.1960.3636-0.04320.28840.10230.10880.36330.0170.255856.8994-5.4252190.3622
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 28 through 42 )
2X-RAY DIFFRACTION2chain 'A' and (resid 43 through 52 )
3X-RAY DIFFRACTION3chain 'A' and (resid 53 through 87 )
4X-RAY DIFFRACTION4chain 'A' and (resid 88 through 105 )
5X-RAY DIFFRACTION5chain 'A' and (resid 106 through 140 )
6X-RAY DIFFRACTION6chain 'B' and (resid 143 through 218 )
7X-RAY DIFFRACTION7chain 'B' and (resid 219 through 248 )
8X-RAY DIFFRACTION8chain 'B' and (resid 249 through 332 )
9X-RAY DIFFRACTION9chain 'B' and (resid 333 through 395 )
10X-RAY DIFFRACTION10chain 'C' and (resid 28 through 62 )
11X-RAY DIFFRACTION11chain 'C' and (resid 63 through 140 )
12X-RAY DIFFRACTION12chain 'D' and (resid 143 through 218 )
13X-RAY DIFFRACTION13chain 'D' and (resid 219 through 248 )
14X-RAY DIFFRACTION14chain 'D' and (resid 249 through 332 )
15X-RAY DIFFRACTION15chain 'D' and (resid 333 through 395 )

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