[English] 日本語
Yorodumi
- PDB-5i81: aSMase with zinc -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5i81
TitleaSMase with zinc
ComponentsSphingomyelin phosphodiesterase
KeywordsHYDROLASE / acid sphingomyelinase
Function / homology
Function and homology information


acid sphingomyelin phosphodiesterase activity / sphingomyelin metabolic process / sphingomyelin catabolic process / sphingomyelin phosphodiesterase / lamellar body / sphingomyelin phosphodiesterase activity / phospholipase C / phosphatidylcholine phospholipase C activity / endolysosome / termination of signal transduction ...acid sphingomyelin phosphodiesterase activity / sphingomyelin metabolic process / sphingomyelin catabolic process / sphingomyelin phosphodiesterase / lamellar body / sphingomyelin phosphodiesterase activity / phospholipase C / phosphatidylcholine phospholipase C activity / endolysosome / termination of signal transduction / glycosphingolipid catabolic process / ceramide biosynthetic process / plasma membrane repair / Glycosphingolipid catabolism / response to type I interferon / hydrolase activity, acting on glycosyl bonds / 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 / lipid droplet / lysosomal lumen / 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 / extracellular exosome / zinc ion binding / 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
beta-D-mannopyranose / Sphingomyelin phosphodiesterase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / molecular replacement / Resolution: 2.25 Å
AuthorsZhou, Y.F. / Wei, R.R.
CitationJournal: Nat Commun / Year: 2016
Title: Human acid sphingomyelinase structures provide insight to molecular basis of Niemann-Pick disease.
Authors: Zhou, Y.F. / Metcalf, M.C. / Garman, S.C. / Edmunds, T. / Qiu, H. / Wei, R.R.
History
DepositionFeb 18, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2016Group: Database references
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_struct_oper_list / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / 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.occupancy / _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_struct_oper_list.symmetry_operation / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_comp_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_comp_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 24, 2021Group: Derived calculations / Source and taxonomy / Structure summary
Category: chem_comp / entity_src_gen / struct_conn
Item: _chem_comp.pdbx_synonyms / _entity_src_gen.pdbx_host_org_cell_line ..._chem_comp.pdbx_synonyms / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Sphingomyelin phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,16224
Polymers65,1141
Non-polymers4,04823
Water3,171176
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Sphingomyelin phosphodiesterase
hetero molecules

A: Sphingomyelin phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,32548
Polymers130,2292
Non-polymers8,09646
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_445-x-1,-y-1,z1
Buried area13500 Å2
ΔGint-341 kcal/mol
Surface area43810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.629, 132.629, 189.565
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-718-

SO4

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Sphingomyelin phosphodiesterase / / Acid sphingomyelinase / aSMase


Mass: 65114.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMPD1, ASM / Plasmid: pIRES2 / Cell line (production host): HEK293S Gnt1- / Production host: Homo sapiens (human)
References: UniProt: P17405, sphingomyelin phosphodiesterase

-
Sugars , 5 types, 10 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.: 1
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
#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: 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
#4: Polysaccharide beta-D-mannopyranose-(1-3)-alpha-D-mannopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-3DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a1122h-1a_1-5][a1122h-1b_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Manp]{[(3+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.: 6
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
#6: Sugar ChemComp-BMA / beta-D-mannopyranose / beta-D-mannose / D-mannose / mannose / Mannose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-mannopyranoseCOMMON NAMEGMML 1.0
b-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 3 types, 189 molecules

#7: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#8: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.7 Å3/Da / Density % sol: 66.72 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 1.5 M ammonium sulfate, 0.1 M sodium acetate pH 5.0-5.5, 12% glycerol
PH range: 5.0-5.5

-
Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.28304, 1.07213
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.283041
21.072131
ReflectionResolution: 2.25→50 Å / Num. obs: 88092 / % possible obs: 99.5 % / Redundancy: 10.3 % / Biso Wilson estimate: 46.96 Å2 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.029 / Rrim(I) all: 0.096 / Χ2: 1.039 / Net I/av σ(I): 22.861 / Net I/σ(I): 9.3 / Num. measured all: 909267
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.25-2.3350.732194.9
2.33-2.428.40.606199.9
2.42-2.5310.60.4771100
2.53-2.6711.30.3491100
2.67-2.8311.40.2591100
2.83-3.0511.40.1841100
3.05-3.3611.40.1221100
3.36-3.8511.30.0861100
3.85-4.8511.10.0681100
4.85-5011.10.053199.9

-
Phasing

Phasing
Method
SAD
molecular replacement

-
Processing

Software
NameVersionClassification
PHENIX(dev_2229: ???)refinement
HKL-2000data collection
HKL-2000data scaling
SOLVEphasing
RESOLVEphasing
PHASER2.5.7phasing
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 2.25→43.809 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.94 / Phase error: 20.52 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2047 4369 4.96 %
Rwork0.1837 --
obs0.1847 88030 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.25→43.809 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4161 0 241 177 4579
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134585
X-RAY DIFFRACTIONf_angle_d1.1716270
X-RAY DIFFRACTIONf_dihedral_angle_d15.1922649
X-RAY DIFFRACTIONf_chiral_restr0.069686
X-RAY DIFFRACTIONf_plane_restr0.008782
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2501-2.27570.31371370.28342509X-RAY DIFFRACTION90
2.2757-2.30250.29481310.25162639X-RAY DIFFRACTION96
2.3025-2.33060.26731730.2462814X-RAY DIFFRACTION99
2.3306-2.36010.27091710.24282790X-RAY DIFFRACTION100
2.3601-2.39110.2621400.23362752X-RAY DIFFRACTION100
2.3911-2.42390.24431260.22272820X-RAY DIFFRACTION100
2.4239-2.45850.2361510.20852828X-RAY DIFFRACTION100
2.4585-2.49520.26671190.21692818X-RAY DIFFRACTION100
2.4952-2.53420.22881550.1992785X-RAY DIFFRACTION100
2.5342-2.57570.24751850.20712774X-RAY DIFFRACTION100
2.5757-2.62010.27371310.20152806X-RAY DIFFRACTION100
2.6201-2.66780.25231640.20362799X-RAY DIFFRACTION100
2.6678-2.71910.21111320.20692826X-RAY DIFFRACTION100
2.7191-2.77460.24061520.2112780X-RAY DIFFRACTION100
2.7746-2.83490.23041240.20422837X-RAY DIFFRACTION100
2.8349-2.90080.24671580.21742782X-RAY DIFFRACTION100
2.9008-2.97330.25541430.21982819X-RAY DIFFRACTION100
2.9733-3.05370.24341340.22052791X-RAY DIFFRACTION100
3.0537-3.14360.24891550.21322811X-RAY DIFFRACTION100
3.1436-3.2450.25311680.21912803X-RAY DIFFRACTION100
3.245-3.36090.221210.1952806X-RAY DIFFRACTION100
3.3609-3.49540.23731530.19942833X-RAY DIFFRACTION100
3.4954-3.65440.23311390.18382783X-RAY DIFFRACTION100
3.6544-3.8470.17211440.17612791X-RAY DIFFRACTION100
3.847-4.08790.15421210.15652840X-RAY DIFFRACTION100
4.0879-4.40320.15711440.14472820X-RAY DIFFRACTION100
4.4032-4.84580.15561610.13322769X-RAY DIFFRACTION100
4.8458-5.54580.15971370.14552832X-RAY DIFFRACTION100
5.5458-6.98260.19111720.17852787X-RAY DIFFRACTION100
6.9826-43.8170.16481280.17352817X-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)
11.07971.29420.19963.6801-0.69021.2152-0.36210.5330.203-0.40270.41010.3683-0.00880.0686-0.03830.5662-0.3006-0.0460.91030.02920.538-28.402-49.0409-43.958
23.23790.86172.08090.30570.6921.55680.350.0782-0.8466-0.00240.2146-0.15360.4988-0.1568-0.56610.56-0.1907-0.07120.6229-0.00040.5785-21.0121-62.0982-27.7504
31.58560.18370.71671.09190.10761.3559-0.24160.70740.0865-0.27030.23050.0159-0.06460.37410.01520.3177-0.1931-0.01880.64730.02620.3847-2.5386-38.8394-28.1774
41.7209-0.51920.85151.7502-0.98682.3363-0.35250.16930.43930.0460.21880.1237-0.3730.01220.10230.3195-0.0802-0.10410.37550.0370.4031-8.2575-27.3396-13.348
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 87 through 147 )
2X-RAY DIFFRACTION2chain 'A' and (resid 148 through 181 )
3X-RAY DIFFRACTION3chain 'A' and (resid 182 through 510 )
4X-RAY DIFFRACTION4chain 'A' and (resid 511 through 611 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more