[English] 日本語
Yorodumi
- PDB-5tcd: Human alkaline sphingomyelinase (ENPP7) in complex with phosphocholine -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5tcd
TitleHuman alkaline sphingomyelinase (ENPP7) in complex with phosphocholine
ComponentsEctonucleotide pyrophosphatase/phosphodiesterase family member 7
KeywordsHYDROLASE / sphingomyelinase / sphingomyelin / phosphocholine / glycosylphosphatidylinositol
Function / homology
Function and homology information


regulation of intestinal lipid absorption / positive regulation of intestinal cholesterol absorption / sphingomyelin metabolic process / Glycosphingolipid metabolism / positive regulation of sphingomyelin catabolic process / lipid digestion / sphingomyelin phosphodiesterase / sphingomyelin phosphodiesterase activity / positive regulation of ceramide biosynthetic process / glycosphingolipid metabolic process ...regulation of intestinal lipid absorption / positive regulation of intestinal cholesterol absorption / sphingomyelin metabolic process / Glycosphingolipid metabolism / positive regulation of sphingomyelin catabolic process / lipid digestion / sphingomyelin phosphodiesterase / sphingomyelin phosphodiesterase activity / positive regulation of ceramide biosynthetic process / glycosphingolipid metabolic process / phosphoric diester hydrolase activity / negative regulation of DNA replication / microvillus / fatty acid homeostasis / negative regulation of cell population proliferation / Golgi apparatus / zinc ion binding / membrane / plasma membrane
Similarity search - Function
Type I phosphodiesterase/nucleotide pyrophosphatase/phosphate transferase / Type I phosphodiesterase / nucleotide pyrophosphatase / Alkaline Phosphatase, subunit A / Alkaline Phosphatase, subunit A / Alkaline-phosphatase-like, core domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
IODIDE ION / PHOSPHOCHOLINE / Ectonucleotide pyrophosphatase/phosphodiesterase family member 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsGorelik, A. / Liu, F. / Illes, K. / Nagar, B.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-133535 Canada
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Crystal structure of the human alkaline sphingomyelinase provides insights into substrate recognition.
Authors: Gorelik, A. / Liu, F. / Illes, K. / Nagar, B.
History
DepositionSep 14, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1May 10, 2017Group: Database references
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Data collection / Category: chem_comp / pdbx_audit_support
Item: _chem_comp.type / _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / 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 / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ectonucleotide pyrophosphatase/phosphodiesterase family member 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,64047
Polymers48,3801
Non-polymers7,26146
Water3,693205
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)104.223, 104.223, 113.893
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Ectonucleotide pyrophosphatase/phosphodiesterase family member 7 / NPP-7 / Alkaline sphingomyelin phosphodiesterase / Intestinal alkaline sphingomyelinase / Alk-SMase


Mass: 48379.531 Da / Num. of mol.: 1 / Fragment: UNP residues 22-433
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ENPP7, UNQ3077/PRO9912 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q6UWV6, sphingomyelin phosphodiesterase

-
Sugars , 4 types, 5 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: 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 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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

-
Non-polymers , 5 types, 246 molecules

#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Chemical...
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 37 / Source method: obtained synthetically / Formula: I
#9: Chemical ChemComp-PC / PHOSPHOCHOLINE / Phosphocholine


Mass: 184.151 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H15NO4P
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 3.69 Å3/Da / Density % sol: 66.67 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: sodium iodide, PEG 3350

-
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: May 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.18→50 Å / Num. obs: 65605 / % possible obs: 93.6 % / Redundancy: 5.2 % / Net I/σ(I): 17.5

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→38.444 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2081 3186 8.12 %
Rwork0.1727 --
obs0.1755 39213 72.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→38.444 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3145 0 198 205 3548
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033409
X-RAY DIFFRACTIONf_angle_d0.614649
X-RAY DIFFRACTIONf_dihedral_angle_d12.9611983
X-RAY DIFFRACTIONf_chiral_restr0.041519
X-RAY DIFFRACTIONf_plane_restr0.003590
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.43580.3279440.2426415X-RAY DIFFRACTION20
2.4358-2.47390.2744470.2241502X-RAY DIFFRACTION24
2.4739-2.51440.2272470.2561560X-RAY DIFFRACTION26
2.5144-2.55780.258530.2182649X-RAY DIFFRACTION30
2.5578-2.60430.2311690.2226721X-RAY DIFFRACTION33
2.6043-2.65440.2778750.2373840X-RAY DIFFRACTION39
2.6544-2.70850.31071020.2271014X-RAY DIFFRACTION47
2.7085-2.76740.26741100.23411214X-RAY DIFFRACTION57
2.7674-2.83180.28361340.22921457X-RAY DIFFRACTION68
2.8318-2.90260.29721340.21731602X-RAY DIFFRACTION72
2.9026-2.9810.23171520.21861648X-RAY DIFFRACTION77
2.981-3.06870.23631500.21551796X-RAY DIFFRACTION83
3.0687-3.16770.24521760.19922029X-RAY DIFFRACTION92
3.1677-3.28090.24771830.19052150X-RAY DIFFRACTION99
3.2809-3.41210.2271860.18012138X-RAY DIFFRACTION100
3.4121-3.56730.221900.16712148X-RAY DIFFRACTION100
3.5673-3.75530.17921940.1442174X-RAY DIFFRACTION100
3.7553-3.99030.16051960.14582149X-RAY DIFFRACTION100
3.9903-4.2980.19521960.13442168X-RAY DIFFRACTION100
4.298-4.72990.14981840.12712176X-RAY DIFFRACTION100
4.7299-5.41270.15741920.13062152X-RAY DIFFRACTION100
5.4127-6.81320.17821870.17682152X-RAY DIFFRACTION100
6.8132-38.44920.23711850.1992173X-RAY DIFFRACTION99
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)
12.88980.52830.27571.14651.73913.7870.18530.2044-0.0949-0.3289-0.14480.15850.40790.2035-0.05880.33360.003-0.02910.1893-0.01350.127741.849230.335744.21
21.75820.1771-0.29092.0293-0.28752.53240.18410.13330.2316-0.2019-0.0050.28480.1227-0.2547-0.15650.2071-0.013-0.00490.25270.02220.168237.351343.037739.7568
33.18080.3061.94632.56694.33338.26410.0075-0.2877-0.3217-0.0612-0.07750.42860.731-0.69310.02330.4635-0.1696-0.06860.29790.02450.256933.320726.046546.5864
41.9624-0.0393-0.83572.5923-0.17240.83590.1467-0.20680.09470.20820.02050.08740.2708-0.1584-0.17270.2391-0.00270.00120.3090.0090.146343.071238.799350.4829
51.89280.78041.67085.799-0.50093.1498-0.026-0.36160.87950.0083-0.069-0.205-0.87230.29360.06130.4233-0.10670.1080.4098-0.19120.584748.744464.226757.8166
61.5594-0.0261-0.24521.90130.26642.42330.1006-0.27290.3790.0510.1142-0.351-0.08180.6123-0.18530.2043-0.02010.04870.3676-0.07490.271752.432947.761451.1991
73.2750.45450.03482.105-1.1151.95720.14540.11170.0759-0.2527-0.03130.27920.332-0.0448-0.15780.46370.07090.05690.35490.0150.079850.78535.969428.0017
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 30 through 51 )
2X-RAY DIFFRACTION2chain 'A' and (resid 52 through 209 )
3X-RAY DIFFRACTION3chain 'A' and (resid 210 through 232 )
4X-RAY DIFFRACTION4chain 'A' and (resid 233 through 264 )
5X-RAY DIFFRACTION5chain 'A' and (resid 265 through 292 )
6X-RAY DIFFRACTION6chain 'A' and (resid 293 through 383 )
7X-RAY DIFFRACTION7chain 'A' and (resid 384 through 417 )

+
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