[English] 日本語
Yorodumi
- PDB-1h8u: Crystal Structure of the Eosinophil Major Basic Protein at 1.8A: ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1h8u
TitleCrystal Structure of the Eosinophil Major Basic Protein at 1.8A: An Atypical Lectin with a Paradigm Shift in Specificity
ComponentsEOSINOPHIL GRANULE MAJOR BASIC PROTEIN 1
KeywordsLECTIN / EOSINOPHIL GRANULE PROTEIN / EMBP
Function / homology
Function and homology information


extracellular matrix structural constituent conferring compression resistance / defense response to nematode / negative regulation of macrophage cytokine production / negative regulation of interleukin-10 production / positive regulation of interleukin-4 production / transport vesicle / heparin binding / carbohydrate binding / collagen-containing extracellular matrix / ficolin-1-rich granule lumen ...extracellular matrix structural constituent conferring compression resistance / defense response to nematode / negative regulation of macrophage cytokine production / negative regulation of interleukin-10 production / positive regulation of interleukin-4 production / transport vesicle / heparin binding / carbohydrate binding / collagen-containing extracellular matrix / ficolin-1-rich granule lumen / defense response to bacterium / immune response / Neutrophil degranulation / extracellular exosome / extracellular region
Similarity search - Function
Eosinophil major basic protein / Eosinophil major basic protein, C-type lectin-like domain / C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) ...Eosinophil major basic protein / Eosinophil major basic protein, C-type lectin-like domain / C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold / Roll / Alpha Beta
Similarity search - Domain/homology
Bone marrow proteoglycan
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSwaminathan, G.J. / Weaver, A.J. / Loegering, D.A. / Checkel, J.L. / Leonidas, D.D. / Gleich, G.J. / Acharya, K.R.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: Crystal Structure of the Eosinophil Major Basic Protein at 1.8A. An Atypical Lectin with a Paradigm Shift in Specificity
Authors: Swaminathan, G.J. / Weaver, A.J. / Loegering, D.A. / Checkel, J.L. / Leonidas, D.D. / Gleich, G.J. / Acharya, K.R.
History
DepositionFeb 15, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 2001Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: EOSINOPHIL GRANULE MAJOR BASIC PROTEIN 1
B: EOSINOPHIL GRANULE MAJOR BASIC PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,59412
Polymers27,6422
Non-polymers95310
Water2,846158
1
A: EOSINOPHIL GRANULE MAJOR BASIC PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4858
Polymers13,8211
Non-polymers6657
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: EOSINOPHIL GRANULE MAJOR BASIC PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1094
Polymers13,8211
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)74.328, 57.487, 60.961
Angle α, β, γ (deg.)90.00, 113.20, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.717976, -0.022182, 0.695715), (-0.024788, -0.999673, -0.006293), (0.695627, -0.012728, -0.718291)
Vector: -29.556, 18.169, 71.51)

-
Components

#1: Protein EOSINOPHIL GRANULE MAJOR BASIC PROTEIN 1 / MBP


Mass: 13820.900 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell: EOSINOPHIL / Cellular location: SECRETORY GRANULES / Organelle: PRIMARY GRANULE / Tissue: BLOOD / References: UniProt: P13727
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O
Compound detailsINVOLVED IN ANTIPARASITIC DEFENSE MECHANISMS AND IMMUNE HYPERSENSITIVITY REACTIONS. INDUCES ...INVOLVED IN ANTIPARASITIC DEFENSE MECHANISMS AND IMMUNE HYPERSENSITIVITY REACTIONS. INDUCES NONCYTOLYTIC HISTAMINE RELEASE FROM HUMAN BASOPHILS.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 45 %
Crystal growpH: 6
Details: 100MM MALONIC ACID PH6, 140MM POTTASIUM DIHYDROGEN PHOSPHATE., pH 6.00
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
116 mg/mlprotein1drop
2100 mMmalonic acid1reservoir
3160 mMpotassium phosphate1reservoir
45 mML-DTT1reservoir
5160 mMsodium acetate1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.244
DetectorType: ADSC CCD / Detector: CCD / Date: May 15, 2000 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.244 Å / Relative weight: 1
ReflectionResolution: 1.8→40 Å / Num. obs: 21127 / % possible obs: 96 % / Redundancy: 10.27 % / Biso Wilson estimate: 24 Å2 / Rsym value: 0.07 / Net I/σ(I): 16.2
Reflection shellResolution: 1.8→1.86 Å / Mean I/σ(I) obs: 5.18 / Rsym value: 0.229 / % possible all: 91.8
Reflection
*PLUS
Lowest resolution: 40 Å / Num. measured all: 217030 / Rmerge(I) obs: 0.07
Reflection shell
*PLUS
% possible obs: 91.8 % / Rmerge(I) obs: 0.229

-
Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LIT

1lit


Resolution: 1.8→36.18 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 905624.99 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: N-TERMINAL RESIDUES THR A1 AND CYS A2 WERE NOT SEEN IN ELECTRON DENSITY MAPS N-TERMINAL RESIDUE THR B1 WERE NOT SEEN IN ELECTRON DENSITY MAPS. NO SIDE CHAIN DENSITY SEEN FOR RESIDUES ARG B3 ...Details: N-TERMINAL RESIDUES THR A1 AND CYS A2 WERE NOT SEEN IN ELECTRON DENSITY MAPS N-TERMINAL RESIDUE THR B1 WERE NOT SEEN IN ELECTRON DENSITY MAPS. NO SIDE CHAIN DENSITY SEEN FOR RESIDUES ARG B3 AND ARG B98 WHICH WERE MODELED AS ALANINES IN THE FINAL STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.264 1001 4.7 %RANDOM
Rwork0.234 ---
obs0.234 21127 95.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.0733 Å2 / ksol: 0.386404 e/Å3
Displacement parametersBiso mean: 27.1 Å2
Baniso -1Baniso -2Baniso -3
1-17.08 Å20 Å210.16 Å2
2---9.14 Å20 Å2
3----7.95 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 1.8→36.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1914 0 52 158 2124
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.91.5
X-RAY DIFFRACTIONc_mcangle_it1.552
X-RAY DIFFRACTIONc_scbond_it1.062
X-RAY DIFFRACTIONc_scangle_it1.632.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.387 153 4.5 %
Rwork0.36 3224 -
obs--92.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4GLYCEROL.PARGLYCEROL.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.78
LS refinement shell
*PLUS
Rfactor Rwork: 0.36

+
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