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- PDB-5jg8: Crystal structure of human acid sphingomyelinase -

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Basic information

Entry
Database: PDB / ID: 5jg8
TitleCrystal structure of human acid sphingomyelinase
ComponentsSphingomyelin phosphodiesterase
KeywordsHYDROLASE / Lysosomal hydrolase / Neimann-Pick disease / Sphingolipid / Saposin
Function / homology
Function and homology information


acid sphingomyelin phosphodiesterase activity / sphingomyelin catabolic process / sphingomyelin metabolic process / sphingomyelin phosphodiesterase / sphingomyelin phosphodiesterase activity / lamellar body / phospholipase C / phosphatidylcholine phospholipase C activity / endolysosome / termination of signal transduction ...acid sphingomyelin phosphodiesterase activity / sphingomyelin catabolic process / sphingomyelin metabolic process / sphingomyelin phosphodiesterase / sphingomyelin phosphodiesterase activity / lamellar body / phospholipase C / phosphatidylcholine phospholipase C activity / endolysosome / termination of signal transduction / glycosphingolipid catabolic process / ceramide biosynthetic process / plasma membrane repair / Glycosphingolipid catabolism / hydrolase activity, acting on glycosyl bonds / response to type I interferon / response to ionizing radiation / positive regulation of endocytosis / response to tumor necrosis factor / positive regulation of protein dephosphorylation / cellular response to calcium ion / cholesterol metabolic process / response to interleukin-1 / lysosomal lumen / lipid droplet / negative regulation of MAP kinase activity / response to cocaine / wound healing / response to virus / cellular response to UV / nervous system development / positive regulation of viral entry into host cell / lysosome / endosome / response to xenobiotic stimulus / symbiont entry into host cell / positive regulation of apoptotic process / signal transduction / extracellular space / zinc ion binding / extracellular exosome / plasma membrane
Similarity search - Function
Sphingomyelin phosphodiesterase / Acid sphingomyelinase/endopolyphosphatase, metallophosphatase domain / Sphingomyelin phosphodiesterase, C-terminal domain / Acid sphingomyelin phosphodiesterase C-terminal region / Saposin (B) Domains / Saposin B type domain / Saposin-like / Saposin B type domain profile. / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like
Similarity search - Domain/homology
ACETATE ION / Sphingomyelin phosphodiesterase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsXiong, Z.J. / Prive, G.G.
CitationJournal: J.Mol.Biol. / Year: 2016
Title: Structure of Human Acid Sphingomyelinase Reveals the Role of the Saposin Domain in Activating Substrate Hydrolysis.
Authors: Xiong, Z.J. / Huang, J. / Poda, G. / Pomes, R. / Prive, G.G.
History
DepositionApr 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2016Group: Database references
Revision 1.2Aug 17, 2016Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / citation / 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_struct_oper_list / pdbx_validate_close_contact / 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 / _citation.journal_id_CSD / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_oper_list.symmetry_operation / _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
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 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sphingomyelin phosphodiesterase
B: Sphingomyelin phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,42820
Polymers130,6472
Non-polymers4,78118
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9310 Å2
ΔGint-127 kcal/mol
Surface area43430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.531, 143.658, 193.620
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 83:95 or (resid 96 and (name...
21(chain B and (resseq 83:95 or (resid 96 and (name...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYLEULEU(chain A and (resseq 83:95 or (resid 96 and (name...AA83 - 9540 - 52
12PHEPHEPHEPHE(chain A and (resseq 83:95 or (resid 96 and (name...AA9653
13GLYGLYMETMET(chain A and (resseq 83:95 or (resid 96 and (name...AA83 - 61140 - 568
14GLYGLYMETMET(chain A and (resseq 83:95 or (resid 96 and (name...AA83 - 61140 - 568
15GLYGLYMETMET(chain A and (resseq 83:95 or (resid 96 and (name...AA83 - 61140 - 568
16GLYGLYMETMET(chain A and (resseq 83:95 or (resid 96 and (name...AA83 - 61140 - 568
17GLYGLYMETMET(chain A and (resseq 83:95 or (resid 96 and (name...AA83 - 61140 - 568
18GLYGLYMETMET(chain A and (resseq 83:95 or (resid 96 and (name...AA83 - 61140 - 568
19GLYGLYMETMET(chain A and (resseq 83:95 or (resid 96 and (name...AA83 - 61140 - 568
110GLYGLYMETMET(chain A and (resseq 83:95 or (resid 96 and (name...AA83 - 61140 - 568
21GLYGLYLEULEU(chain B and (resseq 83:95 or (resid 96 and (name...BB83 - 9540 - 52
22PHEPHEPHEPHE(chain B and (resseq 83:95 or (resid 96 and (name...BB9653
23PHEPHEMETMET(chain B and (resseq 83:95 or (resid 96 and (name...BB82 - 61139 - 568
24PHEPHEMETMET(chain B and (resseq 83:95 or (resid 96 and (name...BB82 - 61139 - 568
25PHEPHEMETMET(chain B and (resseq 83:95 or (resid 96 and (name...BB82 - 61139 - 568
26PHEPHEMETMET(chain B and (resseq 83:95 or (resid 96 and (name...BB82 - 61139 - 568
27PHEPHEMETMET(chain B and (resseq 83:95 or (resid 96 and (name...BB82 - 61139 - 568
28PHEPHEMETMET(chain B and (resseq 83:95 or (resid 96 and (name...BB82 - 61139 - 568
29PHEPHEMETMET(chain B and (resseq 83:95 or (resid 96 and (name...BB82 - 61139 - 568
210PHEPHEMETMET(chain B and (resseq 83:95 or (resid 96 and (name...BB82 - 61139 - 568

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Sphingomyelin phosphodiesterase / Acid sphingomyelinase / aSMase


Mass: 65323.453 Da / Num. of mol.: 2 / Fragment: UNP residues 47-629
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMPD1, ASM / Production host: Homo sapiens (human)
References: UniProt: P17405, sphingomyelin phosphodiesterase

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Sugars , 4 types, 12 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.: 4 / 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 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-3DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a3-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-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
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#7: 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


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, 6 molecules

#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2

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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: 3.7 Å3/Da / Density % sol: 70 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG8000, sodium potassium tartrate, sodium acetate, sodium cacodylate, MES, pH 6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.63 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.63 Å / Relative weight: 1
ReflectionResolution: 2.8→29.44 Å / Num. obs: 45859 / % possible obs: 94.1 % / Redundancy: 3.9 % / Biso Wilson estimate: 59.86 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.207 / Rpim(I) all: 0.111 / Rrim(I) all: 0.236 / Net I/σ(I): 5 / Num. measured all: 177605 / Scaling rejects: 71
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.8-2.92.72.209957834890.2561.3432.6040.673.3
10.84-29.443.60.04429708300.9950.0260.05218.386.6

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data reduction
Aimless0.5.23data scaling
PHENIXphasing
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EBE

5ebe


Resolution: 2.8→26.761 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.16 / Stereochemistry target values: ML
Details: THE X-RAY DIFFRACTION DATA EXHIBITED STRONG ANISOTROPY, WITH CC1/2 VALUES FALLING TO 50% AT RESOLUTIONS OF 1/3.4, 1/3.0 AND 1/2.8 A IN A*, B* AND C*, RESPECTIVELY. DATA REDUCTION STATISTICS ...Details: THE X-RAY DIFFRACTION DATA EXHIBITED STRONG ANISOTROPY, WITH CC1/2 VALUES FALLING TO 50% AT RESOLUTIONS OF 1/3.4, 1/3.0 AND 1/2.8 A IN A*, B* AND C*, RESPECTIVELY. DATA REDUCTION STATISTICS FOR AN ELLIPTICALLY TRUNCATED DATASET ARE INCLUDED IN TABLE 1 OF XIONG ET AL., JMB (2016). AN ELLIPTICALLY TRUNCATED DATASET WAS NOT USED IN REFINEMENT, HOWEVER, AS RECOMMENDED BY THE AUTHORS OF PHENIX.
RfactorNum. reflection% reflection
Rfree0.2793 1975 4.34 %
Rwork0.2296 43581 -
obs0.2318 45556 93.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 194.45 Å2 / Biso mean: 61.9809 Å2 / Biso min: 18.54 Å2
Refinement stepCycle: final / Resolution: 2.8→26.761 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8343 0 335 0 8678
Biso mean--104.37 --
Num. residues----1059
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048967
X-RAY DIFFRACTIONf_angle_d0.92912330
X-RAY DIFFRACTIONf_chiral_restr0.0511366
X-RAY DIFFRACTIONf_plane_restr0.0161567
X-RAY DIFFRACTIONf_dihedral_angle_d12.6673275
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5017X-RAY DIFFRACTION6.88TORSIONAL
12B5017X-RAY DIFFRACTION6.88TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8-2.870.41021040.37182309241370
2.87-2.94750.39651260.37142785291185
2.9475-3.03410.41611380.34873032317093
3.0341-3.13190.33411450.33033210335597
3.1319-3.24360.37931440.29483162330698
3.2436-3.37330.32811450.28063217336298
3.3733-3.52650.33971480.27213249339798
3.5265-3.71190.29781470.24133236338398
3.7119-3.94380.28731440.23523191333597
3.9438-4.24720.30681450.21173202334796
4.2472-4.67260.21921450.18643220336596
4.6726-5.34410.21231480.16983222337096
5.3441-6.71530.23891470.20533242338996
6.7153-26.76190.22441490.17813304345393

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