[English] 日本語
Yorodumi
- PDB-1n69: Crystal structure of human saposin B -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1n69
TitleCrystal structure of human saposin B
ComponentsSAPOSIN B
KeywordsLIPID BINDING PROTEIN / GLYCOSPHINGOLIPID ACTIVATOR PROTEIN
Function / homology
Function and homology information


positive regulation of beta-galactosidase activity / ganglioside GM1 transport to membrane / ganglioside GM2 binding / ganglioside GM3 binding / ganglioside GP1c binding / ganglioside GM1 binding / ganglioside GT1b binding / sphingolipid metabolic process / prostate gland growth / epithelial cell differentiation involved in prostate gland development ...positive regulation of beta-galactosidase activity / ganglioside GM1 transport to membrane / ganglioside GM2 binding / ganglioside GM3 binding / ganglioside GP1c binding / ganglioside GM1 binding / ganglioside GT1b binding / sphingolipid metabolic process / prostate gland growth / epithelial cell differentiation involved in prostate gland development / Glycosphingolipid catabolism / azurophil granule membrane / lysosomal transport / regulation of lipid metabolic process / lysosomal lumen / enzyme activator activity / Peptide ligand-binding receptors / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / phospholipid binding / late endosome / Platelet degranulation / protease binding / scaffold protein binding / : / G alpha (i) signalling events / lysosome / regulation of autophagy / lysosomal membrane / intracellular membrane-bounded organelle / Neutrophil degranulation / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Saposin, chordata / Saposin-like / NK-Lysin / Saposin A-type domain / Saposin / : / Saposin A-type domain / Saposin A-type domain profile. / Saposin/surfactant protein-B A-type DOMAIN / Saposin-like type B, region 1 ...Saposin, chordata / Saposin-like / NK-Lysin / Saposin A-type domain / Saposin / : / Saposin A-type domain / Saposin A-type domain profile. / Saposin/surfactant protein-B A-type DOMAIN / Saposin-like type B, region 1 / Saposin-like type B, region 1 / Saposin B type, region 2 / Saposin-like type B, region 2 / Saposin (B) Domains / Saposin B type domain / Saposin-like / Saposin B type domain profile. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
1,2-Distearoyl-sn-glycerophosphoethanolamine / Prosaposin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsAhn, V.E. / Faull, K.F. / Whitelegge, J.P. / Fluharty, A.L. / Prive, G.G.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Crystal Structure of saposin B reveals a dimeric shell for lipid binding
Authors: Ahn, V.E. / Faull, K.F. / Whitelegge, J.P. / Fluharty, A.L. / Prive, G.G.
#1: Journal: Protein Expr.Purif. / Year: 2003
Title: Expression, purification, crystallization and preliminary X-ray analysis of recombinant human saposin B
Authors: Ahn, V.E. / Faull, K.F. / Whitelegge, J.P. / Higginson, J. / Fluharty, A.L. / Prive, G.G.
History
DepositionNov 8, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 7, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 2.0Jun 30, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif / struct_site
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_comp_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_unobs_or_zero_occ_atoms.auth_comp_id / _pdbx_unobs_or_zero_occ_atoms.label_comp_id / _struct_ref_seq_dif.details / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 9BIOLOGICAL_UNIT: HOMODIMER
Remark 10OTHER DETAILS: METHIONINES SUBSTITUTED WITH SELENOMETHIONINE
Remark 600HETEROGEN The PEH ligand is disordered and is probably a mixture of phosphatidylethanolamines with ...HETEROGEN The PEH ligand is disordered and is probably a mixture of phosphatidylethanolamines with different acyl chain lengths. This ensemble has been modelled as a single phospholipid. As a result, the PEH atoms C2I, C3F, C3G, C3H and C3I are not present in this model.
Remark 5WARNING 1N69: THE PEH LIGAND IS DISORDERED
Remark 300 BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 ... BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 CHAINS (A,B AND C). CHAINS A AND B FORM AN ASYMMETRIC HOMODIMER. CHAIN C FORMS A HOMODIMER WITH A CRYSTALLOGRAPHICALLY RELATED SYMMETRY MATE. SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S).

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SAPOSIN B
B: SAPOSIN B
C: SAPOSIN B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1344
Polymers27,3863
Non-polymers7481
Water1,62190
1
A: SAPOSIN B
B: SAPOSIN B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0053
Polymers18,2572
Non-polymers7481
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-50 kcal/mol
Surface area8840 Å2
MethodPISA
2
C: SAPOSIN B

C: SAPOSIN B


Theoretical massNumber of molelcules
Total (without water)18,2572
Polymers18,2572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Unit cell
Length a, b, c (Å)72.140, 72.140, 94.366
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein SAPOSIN B / Proactivator polypeptide / Sap-B / Sphingolipid activator protein 1 / SAP-1 / Cerebroside sulfate ...Proactivator polypeptide / Sap-B / Sphingolipid activator protein 1 / SAP-1 / Cerebroside sulfate activator / CSAct / CS-Act / Sulfatide/GM1 activator / GALACTOSYLCERBROSIDE ACTIVATOR


Mass: 9128.529 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Prosaposin, PSAP / Plasmid: PET-16(B) / Production host: Escherichia coli (E. coli) / Strain (production host): AD494(DE3) / References: UniProt: P07602
#2: Chemical ChemComp-3PE / 1,2-Distearoyl-sn-glycerophosphoethanolamine / 3-SN-PHOSPHATIDYLETHANOLAMINE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE


Mass: 748.065 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: POLYETHYLENE GLYCOL 3350, MAGNESIUM ACETATE, SODIUM CACODYLATE, PH 5.8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K. THE CRYSTAL WAS TREATED WITH A MOTHER LIQUOR SOLUTION CONTAINING 0.1% ...Details: POLYETHYLENE GLYCOL 3350, MAGNESIUM ACETATE, SODIUM CACODYLATE, PH 5.8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K. THE CRYSTAL WAS TREATED WITH A MOTHER LIQUOR SOLUTION CONTAINING 0.1% HYDROGEN PEROXIDE PRIOR TO FREEZING.
Crystal grow
*PLUS
Details: Ahn, V.E., (2003) Protein Expression Purif., 27, 186.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
130 mg/mlprotein1drop
216 %PEG33501reservoir
30.2 Mmagnesium acetate1reservoir
40.1 Msodium cacodylate1reservoirpH5.8

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.9789, 0.9793
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 21, 2000
RadiationProtocol: MAD, SE-MET / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97891
20.97931
ReflectionResolution: 2.2→37 Å / Num. all: 14644 / Num. obs: 14644 / % possible obs: 98.3 % / Redundancy: 10.5 % / Biso Wilson estimate: 22.7 Å2 / Rsym value: 0.059 / Net I/σ(I): 9
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 14644 / Rsym value: 0.289 / % possible all: 98.3
Reflection
*PLUS
Lowest resolution: 37 Å / Rmerge(I) obs: 0.059
Reflection shell
*PLUS
% possible obs: 98.3 % / Rmerge(I) obs: 0.289

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SnBphasing
SHARPphasing
DMmodel building
CNS1.1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.2→19.74 Å / Rfactor Rfree error: 0.01 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.262 729 5 %RANDOM
Rwork0.222 ---
obs0.222 14613 98.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.3682 Å2 / ksol: 0.321762 e/Å3
Displacement parametersBiso mean: 45.8 Å2
Baniso -1Baniso -2Baniso -3
1--3.05 Å21.75 Å20 Å2
2---3.05 Å20 Å2
3---6.11 Å2
Refine analyzeLuzzati coordinate error free: 0.31 Å / Luzzati sigma a free: 0.22 Å
Refinement stepCycle: LAST / Resolution: 2.2→19.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1819 0 46 90 1955
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d18.3
X-RAY DIFFRACTIONc_improper_angle_d0.82
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.291 110 5 %
Rwork0.235 2096 -
obs--90.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3PEH.PARAMPEH.TOP
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0077
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.82

+
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