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- PDB-5uvg: Crystal structure of the human neutral sphingomyelinase 2 (nSMase... -

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Basic information

Entry
Database: PDB / ID: 5uvg
TitleCrystal structure of the human neutral sphingomyelinase 2 (nSMase2) catalytic domain with insertion deleted and calcium bound
ComponentsSphingomyelin phosphodiesterase 3,Sphingomyelin phosphodiesterase 3
KeywordsHYDROLASE / sphingomyelinase
Function / homology
Function and homology information


chondrocyte development involved in endochondral bone morphogenesis / neutral sphingomyelin phosphodiesterase activity / sphingolipid mediated signaling pathway / cellular response to redox state / mitotic nuclear division / Glycosphingolipid metabolism / sphingomyelin catabolic process / sphingomyelin metabolic process / sphingomyelin phosphodiesterase / sphingomyelin phosphodiesterase activity ...chondrocyte development involved in endochondral bone morphogenesis / neutral sphingomyelin phosphodiesterase activity / sphingolipid mediated signaling pathway / cellular response to redox state / mitotic nuclear division / Glycosphingolipid metabolism / sphingomyelin catabolic process / sphingomyelin metabolic process / sphingomyelin phosphodiesterase / sphingomyelin phosphodiesterase activity / peptide hormone secretion / regulation of leukocyte migration / dentinogenesis / Golgi cis cisterna / regulation of cartilage development / polysaccharide transport / bone growth / phospholipase activity / negative regulation of hyaluronan biosynthetic process / extracellular matrix assembly / ceramide metabolic process / cellular response to oxidised low-density lipoprotein particle stimulus / collagen metabolic process / cellular response to peptide / phosphatidic acid binding / endochondral ossification / positive regulation of exosomal secretion / cellular response to magnesium ion / TNFR1-mediated ceramide production / G1 to G0 transition / DNA biosynthetic process / lung alveolus development / BMP signaling pathway / bone mineralization / phosphatidylserine binding / platelet-derived growth factor receptor signaling pathway / hematopoietic progenitor cell differentiation / phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of mitotic nuclear division / positive regulation of smooth muscle cell proliferation / regulation of protein phosphorylation / multicellular organism growth / cellular response to hydrogen peroxide / cellular response to tumor necrosis factor / Golgi membrane / extracellular region / identical protein binding / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Sphingomyelinase C/phospholipase C / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily
Similarity search - Domain/homology
Sphingomyelin phosphodiesterase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.849 Å
AuthorsAirola, M.V. / Guja, K.E. / Garcia-Diaz, M. / Hannun, Y.A.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R37GM043825 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F32GM100679 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM100021 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)F30ES022930 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Structure of human nSMase2 reveals an interdomain allosteric activation mechanism for ceramide generation.
Authors: Airola, M.V. / Shanbhogue, P. / Shamseddine, A.A. / Guja, K.E. / Senkal, C.E. / Maini, R. / Bartke, N. / Wu, B.X. / Obeid, L.M. / Garcia-Diaz, M. / Hannun, Y.A.
History
DepositionFeb 20, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2May 9, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sphingomyelin phosphodiesterase 3,Sphingomyelin phosphodiesterase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3892
Polymers41,3481
Non-polymers401
Water3,819212
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-7 kcal/mol
Surface area17050 Å2
2
A: Sphingomyelin phosphodiesterase 3,Sphingomyelin phosphodiesterase 3
hetero molecules

A: Sphingomyelin phosphodiesterase 3,Sphingomyelin phosphodiesterase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,7774
Polymers82,6972
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_575-x,-y+2,z1
Buried area3350 Å2
ΔGint-39 kcal/mol
Surface area30900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.610, 91.050, 50.030
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Sphingomyelin phosphodiesterase 3,Sphingomyelin phosphodiesterase 3 / Neutral sphingomyelinase 2 / nSMase2 / Neutral sphingomyelinase II


Mass: 41348.461 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMPD3 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9NY59, sphingomyelin phosphodiesterase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 2.03 Å3/Da / Density % sol: 39.33 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEG 400, calcium chloride, glycerol, HEPES

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Data collection

DiffractionMean temperature: 193.15 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.849→43.85 Å / Num. obs: 29448 / % possible obs: 100 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.037 / Rrim(I) all: 0.095 / Net I/σ(I): 13.8
Reflection shellResolution: 1.849→1.855 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.882 / Mean I/σ(I) obs: 2.2 / Num. measured obs: 311 / Rpim(I) all: 0.365 / Rrim(I) all: 0.956 / % possible all: 100

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Processing

Software
NameVersionClassification
Aimlessdata scaling
BUSTERrefinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.849→43.85 Å / Cor.coef. Fo:Fc: 0.9456 / Cor.coef. Fo:Fc free: 0.9345 / SU R Cruickshank DPI: 0.243 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.138 / SU Rfree Blow DPI: 0.123 / SU Rfree Cruickshank DPI: 0.123
RfactorNum. reflection% reflectionSelection details
Rfree0.1969 1369 5.02 %RANDOM
Rwork0.1625 ---
obs0.1642 27267 86.85 %-
Displacement parametersBiso max: 128.39 Å2 / Biso mean: 24.93 Å2 / Biso min: 4.91 Å2
Baniso -1Baniso -2Baniso -3
1-0.3129 Å20 Å20 Å2
2---2.1587 Å20 Å2
3---1.8457 Å2
Refine analyzeLuzzati coordinate error obs: 0.177 Å
Refinement stepCycle: final / Resolution: 1.849→43.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2741 0 1 212 2954
Biso mean--30 34.87 -
Num. residues----348
LS refinement shellResolution: 1.849→1.88 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.1635 34 6.08 %
Rwork0.1538 525 -
all0.1544 559 -
obs--86.85 %
Refinement TLS params.Method: refined / Origin x: 15.1208 Å / Origin y: 105.234 Å / Origin z: 64.2526 Å
111213212223313233
T-0.0635 Å2-0.0138 Å2-0.0007 Å2--0.0737 Å2-0.0013 Å2---0.0199 Å2
L0.7408 °20.2085 °20.2382 °2-1.1712 °20.0025 °2--0.8063 °2
S-0.0375 Å °0.0243 Å °-0.0111 Å °-0.1444 Å °-0.0043 Å °-0.0225 Å °-0.032 Å °0.0607 Å °0.0418 Å °
Refinement TLS groupSelection details: { A|* }

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