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- PDB-4wgk: Crystal structure of human neutral ceramidase with Zn-bound phosphate -

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Basic information

Entry
Database: PDB / ID: 4wgk
TitleCrystal structure of human neutral ceramidase with Zn-bound phosphate
ComponentsNeutral ceramidaseCeramidase
KeywordsHYDROLASE / ceramidase / amidase / zinc / phosphate
Function / homology
Function and homology information


Glycosphingolipid metabolism / sphingosine metabolic process / ceramidase / N-acylsphingosine amidohydrolase activity / ceramidase activity / lipid digestion / ceramide catabolic process / ceramide metabolic process / sphingosine biosynthetic process / ceramide biosynthetic process ...Glycosphingolipid metabolism / sphingosine metabolic process / ceramidase / N-acylsphingosine amidohydrolase activity / ceramidase activity / lipid digestion / ceramide catabolic process / ceramide metabolic process / sphingosine biosynthetic process / ceramide biosynthetic process / long-chain fatty acid biosynthetic process / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / plasma membrane => GO:0005886 / cellular response to cytokine stimulus / negative regulation of apoptotic signaling pathway / regulation of mitotic cell cycle / caveola / Golgi membrane / apoptotic process / calcium ion binding / Golgi apparatus / mitochondrion / extracellular exosome / zinc ion binding / extracellular region / plasma membrane
Similarity search - Function
Neutral/alkaline non-lysosomal ceramidase, C-terminal domain / Neutral/alkaline nonlysosomal ceramidase / Neutral/alkaline non-lysosomal ceramidase, N-terminal / Neutral/alkaline non-lysosomal ceramidase, C-terminal / Neutral ceramidase, C-terminal domain superfamily / Neutral/alkaline non-lysosomal ceramidase, N-terminal / Neutral/alkaline non-lysosomal ceramidase, C-terminal / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
CITRIC ACID / PHOSPHATE ION / Neutral ceramidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.582 Å
AuthorsAirola, M.V. / Pulkoski-Gross, M.J. / Obeid, L.M. / Hannun, Y.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA172517 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F32GM100679 United States
CitationJournal: Structure / Year: 2015
Title: Structural Basis for Ceramide Recognition and Hydrolysis by Human Neutral Ceramidase.
Authors: Airola, M.V. / Allen, W.J. / Pulkoski-Gross, M.J. / Obeid, L.M. / Rizzo, R.C. / Hannun, Y.A.
History
DepositionSep 18, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2015Group: Database references
Revision 1.2Aug 12, 2015Group: Database references
Revision 1.3Aug 19, 2015Group: Database references
Revision 1.4Sep 6, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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 / pdbx_validate_close_contact / struct_asym / struct_conn / struct_conn_type / 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 / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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 / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 2023Group: 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: Neutral ceramidase
B: Neutral ceramidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,83223
Polymers151,9612
Non-polymers3,87021
Water8,899494
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A: Neutral ceramidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,01910
Polymers75,9811
Non-polymers2,0389
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Neutral ceramidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,81313
Polymers75,9811
Non-polymers1,83212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.480, 156.630, 80.330
Angle α, β, γ (deg.)90.00, 108.04, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Neutral ceramidase / Ceramidase / NCDase / Acylsphingosine deacylase 2 / BCDase / LCDase / hCD / N-acylsphingosine amidohydrolase 2 / ...NCDase / Acylsphingosine deacylase 2 / BCDase / LCDase / hCD / N-acylsphingosine amidohydrolase 2 / Non-lysosomal ceramidase


Mass: 75980.609 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ASAH2, HNAC1 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9NR71, ceramidase

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Sugars , 3 types, 8 molecules

#2: 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.: 2 / Source method: obtained synthetically
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
#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.: 1 / 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
#6: 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.: 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 , 7 types, 507 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#7: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#8: Chemical
ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H8O7
#9: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#10: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 494 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.89 Å3/Da / Density % sol: 57.48 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 10% PEG 1000, 0.2M Lithium sulfate, 0.1M citrate phosphate buffer, pH 4.6

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Data collection

DiffractionMean temperature: 193 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.582→68.65 Å / Num. all: 90770 / Num. obs: 49612 / % possible obs: 91.63 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.08051 / Net I/σ(I): 7.47
Reflection shellResolution: 2.582→2.674 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.3726 / Mean I/σ(I) obs: 1.91 / % possible all: 87.4

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZWS

2zws


Resolution: 2.582→68.65 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2227 1998 4.03 %Random selection
Rwork0.1784 ---
obs0.1801 49606 91.62 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.582→68.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10401 0 240 494 11135
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310904
X-RAY DIFFRACTIONf_angle_d0.69114816
X-RAY DIFFRACTIONf_dihedral_angle_d13.3823935
X-RAY DIFFRACTIONf_chiral_restr0.0311645
X-RAY DIFFRACTIONf_plane_restr0.0031920
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.582-2.64660.35561350.26383202X-RAY DIFFRACTION87
2.6466-2.71820.26921390.24773321X-RAY DIFFRACTION89
2.7182-2.79810.28531380.22893303X-RAY DIFFRACTION89
2.7981-2.88850.28531380.21553278X-RAY DIFFRACTION89
2.8885-2.99170.26521390.21473292X-RAY DIFFRACTION89
2.9917-3.11150.26411380.20213285X-RAY DIFFRACTION89
3.1115-3.25310.25531370.19253274X-RAY DIFFRACTION89
3.2531-3.42460.23761390.18583294X-RAY DIFFRACTION89
3.4246-3.63910.20451400.16723383X-RAY DIFFRACTION91
3.6391-3.92010.20591490.1483547X-RAY DIFFRACTION95
3.9201-4.31450.17551510.1433598X-RAY DIFFRACTION97
4.3145-4.93870.17471520.13773606X-RAY DIFFRACTION97
4.9387-6.22160.20511520.16823615X-RAY DIFFRACTION97
6.2216-68.67720.18711510.1793610X-RAY DIFFRACTION96
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)
11.2770.56750.38841.08990.17420.91530.1158-0.0938-0.28040.0563-0.0535-0.01430.08930.0078-0.00190.20120.0052-0.0170.21380.02290.2173-15.346-21.2227119.9639
20.9429-0.08580.31761.4776-0.42770.1690.2304-0.0661-0.3511-0.2484-0.0217-0.34740.41050.09660.06550.2689-0.0161-0.07420.20430.03150.2335-8.9041-23.9306115.5597
30.93360.3410.29420.5804-0.10010.5217-0.0006-0.08020.2812-0.00590.04670.0087-0.14850.0165-0.00220.20060.00250.0130.1326-0.00130.1877-16.5018-4.0362110.0413
41.68580.4417-0.17220.84420.2180.7757-0.03980.0845-0.2022-0.04470.0151-0.03080.02660.00840.01740.14630.003-0.01290.13240.01260.18-23.7831-19.2392101.9627
50.9173-0.0153-0.16090.514-0.01360.944-0.0494-0.0588-0.18770.01920.0520.09260.06160.1058-0.07590.192-0.02610.00470.2362-0.00760.278314.8687-13.0685120.6634
60.9922-0.08130.25980.70970.85992.12440.0898-0.007-0.06920.06230.0237-0.150.132-0.2556-0.01350.1611-0.02170.03470.1977-0.00670.16345.492-8.0275127.9063
70.950.4042-0.13220.36510.17151.2698-0.1033-0.1313-0.0738-0.13250.08770.21420.00720.0075-0.04190.1737-0.0291-0.04040.2388-0.01360.202711.7352-9.3918125.5564
81.1354-0.1320.41010.62540.08491.15740.08290.4601-0.0324-0.1202-0.03570.00950.09520.00980.02040.1964-0.00330.01670.2416-0.02490.164-13.713219.5727139.9398
90.76520.0103-0.14990.00470.10510.93320.08270.28750.21-0.27260.0238-0.0594-0.17280.2575-0.02260.23670.02560.02890.3574-0.00630.2469-7.128724.8314137.9753
100.8688-0.0895-0.19380.70820.0410.64460.0068-0.1309-0.02780.055-0.016-0.04980.0638-0.01480.0060.1559-0.00380.00050.14490.02070.1394-13.936925.6318159.0815
110.7602-0.3867-0.03250.6318-0.09260.7117-0.03720.22620.1757-0.12850.05540.0883-0.1007-0.0030.05370.1678-0.0064-0.00950.240.04280.2481-22.042940.1953145.5144
121.35830.32770.82921.20630.01710.7498-0.06860.34150.2222-0.10050.0092-0.0777-0.0384-0.00190.0090.16070.01840.01060.20950.05520.2092-23.149638.7801142.5335
131.06150.0417-0.14551.11420.02110.9928-0.02040.01740.0977-0.0833-0.016-0.19670.08650.1271-0.03830.1723-0.0413-0.05130.17830.00310.222815.961718.4154147.6344
141.43040.3575-0.15162.703-0.18091.06410.04370.0693-0.3163-0.17460.0347-0.02890.21570.044-0.05740.21070.0096-0.02870.1996-0.03760.25637.178510.1623150.6724
151.06510.29780.26091.18890.5010.2695-0.0685-0.1023-0.08130.05130.055-0.11630.20150.0183-0.05680.20410.0081-0.01360.17240.01010.198913.564612.4957150.8899
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 100 through 192 )
2X-RAY DIFFRACTION2chain 'A' and (resid 193 through 237 )
3X-RAY DIFFRACTION3chain 'A' and (resid 238 through 392 )
4X-RAY DIFFRACTION4chain 'A' and (resid 393 through 634 )
5X-RAY DIFFRACTION5chain 'A' and (resid 635 through 684 )
6X-RAY DIFFRACTION6chain 'A' and (resid 685 through 723 )
7X-RAY DIFFRACTION7chain 'A' and (resid 724 through 780 )
8X-RAY DIFFRACTION8chain 'B' and (resid 99 through 192 )
9X-RAY DIFFRACTION9chain 'B' and (resid 193 through 237 )
10X-RAY DIFFRACTION10chain 'B' and (resid 238 through 413 )
11X-RAY DIFFRACTION11chain 'B' and (resid 414 through 477 )
12X-RAY DIFFRACTION12chain 'B' and (resid 478 through 634 )
13X-RAY DIFFRACTION13chain 'B' and (resid 635 through 684 )
14X-RAY DIFFRACTION14chain 'B' and (resid 685 through 723 )
15X-RAY DIFFRACTION15chain 'B' and (resid 724 through 779 )

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