[English] 日本語
Yorodumi
- PDB-4ra3: Crystal structure of dimeric S33C beta-2 microglobulin mutant in ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ra3
TitleCrystal structure of dimeric S33C beta-2 microglobulin mutant in complex with Thioflavin (ThT) at 2.8 Angstrom resolution
ComponentsBeta-2-microglobulin
KeywordsIMMUNE SYSTEM / amyloidosis / protein aggregation / thioflavin / covalent dimer / oligomerization / beta sandwich / inclusion bodies
Function / homology
Function and homology information


: / : / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC ...: / : / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / antigen processing and presentation of exogenous peptide antigen via MHC class II / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell activation / cellular response to nicotine / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / Interferon gamma signaling / MHC class II protein complex binding / positive regulation of protein binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / external side of plasma membrane / lysosomal membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
Beta-2-Microglobulin / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily ...Beta-2-Microglobulin / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-TFX / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsHalabelian, L. / Bolognesi, M. / Ricagno, S.
CitationJournal: Sci Rep / Year: 2015
Title: A covalent homodimer probing early oligomers along amyloid aggregation.
Authors: Halabelian, L. / Relini, A. / Barbiroli, A. / Penco, A. / Bolognesi, M. / Ricagno, S.
History
DepositionSep 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2015Group: Database references
Revision 1.2Nov 4, 2015Group: Database references
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beta-2-microglobulin
B: Beta-2-microglobulin
C: Beta-2-microglobulin
D: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9999
Polymers47,5824
Non-polymers1,4175
Water00
1
A: Beta-2-microglobulin
C: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6415
Polymers23,7912
Non-polymers8503
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-7 kcal/mol
Surface area12300 Å2
MethodPISA
2
B: Beta-2-microglobulin
D: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3584
Polymers23,7912
Non-polymers5672
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-9 kcal/mol
Surface area12150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.038, 80.038, 177.700
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPAA1 - 962 - 97
21ASPASPBB1 - 962 - 97
12ASPASPAA1 - 982 - 99
22ASPASPCC1 - 982 - 99
13ASPASPAA1 - 982 - 99
23ASPASPDD1 - 982 - 99
14ASPASPBB1 - 962 - 97
24ASPASPCC1 - 962 - 97
15ASPASPBB1 - 962 - 97
25ASPASPDD1 - 962 - 97
16METMETCC1 - 992 - 100
26METMETDD1 - 992 - 100

NCS ensembles :
ID
1
2
3
4
5
6

-
Components

#1: Protein
Beta-2-microglobulin


Mass: 11895.422 Da / Num. of mol.: 4 / Fragment: UNP residues 21-119 / Mutation: S33C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P, NM_004048 / Plasmid: pET21b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61769
#2: Chemical
ChemComp-TFX / 2-[4-(dimethylamino)phenyl]-3,6-dimethyl-1,3-benzothiazol-3-ium / Thioflavin T


Mass: 283.411 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C17H19N2S
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.45 Å3/Da / Density % sol: 64.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 25% v/v PEG4000, 0.1 M sodium chloride, 5 mM thioflavin, 0.1 M HEPES sodium, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97088 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 14, 2014
RadiationMonochromator: single crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97088 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.463
11-h,-k,l20.537
ReflectionResolution: 2.8→177.7 Å / Num. all: 16940 / Num. obs: 16940 / % possible obs: 100 % / Redundancy: 9.6 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 21.4
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 10 % / Rmerge(I) obs: 1.139 / Mean I/σ(I) obs: 2 / % possible all: 100

-
Processing

Software
NameVersionClassification
MxCuBEdata collection
BALBESphasing
REFMAC5.8.0069refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3S6C

3s6c


Resolution: 2.8→69.31 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.943 / SU B: 9.558 / SU ML: 0.188 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20649 862 5.1 %RANDOM
Rwork0.17075 ---
obs0.17252 16036 99.91 %-
all-16940 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 113.054 Å2
Baniso -1Baniso -2Baniso -3
1-26.34 Å20 Å20 Å2
2--26.34 Å20 Å2
3----52.68 Å2
Refinement stepCycle: LAST / Resolution: 2.8→69.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3307 0 100 0 3407
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193514
X-RAY DIFFRACTIONr_bond_other_d0.0010.023203
X-RAY DIFFRACTIONr_angle_refined_deg1.4531.9254773
X-RAY DIFFRACTIONr_angle_other_deg1.54837376
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.9265391
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.45423.966179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.40815591
X-RAY DIFFRACTIONr_dihedral_angle_4_deg28.3871520
X-RAY DIFFRACTIONr_chiral_restr0.0840.2479
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214410
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02858
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.82311.0821576
X-RAY DIFFRACTIONr_mcbond_other6.81911.0791575
X-RAY DIFFRACTIONr_mcangle_it9.8116.6061963
X-RAY DIFFRACTIONr_mcangle_other9.73416.2081964
X-RAY DIFFRACTIONr_scbond_it7.3311.4761938
X-RAY DIFFRACTIONr_scbond_other7.20411.2091939
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.51916.6062811
X-RAY DIFFRACTIONr_long_range_B_refined13.1352955
X-RAY DIFFRACTIONr_long_range_B_other13.1332956
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A50210.15
12B50210.15
21A52830.14
22C52830.14
31A51210.16
32D51210.16
41B49940.16
42C49940.16
51B49360.17
52D49360.17
61C53170.15
62D53170.15
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.798 68 -
Rwork0.525 1171 -
obs--99.84 %

+
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