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- PDB-7afv: Crystal structure of tetrameric beta-2-microglobulin deltaN6 S52C... -

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Basic information

Entry
Database: PDB / ID: 7afv
TitleCrystal structure of tetrameric beta-2-microglobulin deltaN6 S52C stabilized by a covalent ligand
ComponentsBeta-2-microglobulinBeta-2 microglobulin
KeywordsIMMUNE SYSTEM / beta-2-microglobulin / tetramer / covalent inhibitor
Function / homology
Function and homology information


positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to iron(III) ion ...positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / recycling endosome membrane / specific granule lumen / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / ER-Phagosome pathway / iron ion transport / early endosome membrane / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / Amyloid fiber formation / lysosomal membrane / external side of plasma membrane / endoplasmic reticulum lumen / Golgi membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / membrane / identical protein binding / 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 / Immunoglobulin-like fold
Similarity search - Domain/homology
Chem-SJK / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsGuthertz, N. / Cawood, E. / Karamanos, T.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust109154/Z/15/A United Kingdom
Wellcome Trust109984 United Kingdom
CitationJournal: J.Am.Chem.Soc. / Year: 2020
Title: Modulation of Amyloidogenic Protein Self-Assembly Using Tethered Small Molecules.
Authors: Cawood, E.E. / Guthertz, N. / Ebo, J.S. / Karamanos, T.K. / Radford, S.E. / Wilson, A.J.
History
DepositionSep 20, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: 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 / struct_ncs_dom_lim
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)22,1695
Polymers21,5322
Non-polymers6373
Water59433
1
A: Beta-2-microglobulin
B: Beta-2-microglobulin
hetero molecules

A: Beta-2-microglobulin
B: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,33810
Polymers43,0644
Non-polymers1,2746
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Methodsedimentation velocity analytical ultracentrifugation
Unit cell
Length a, b, c (Å)87.572, 87.572, 56.458
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETHISHISAA6 - 511 - 46
21METMETHISHISBB6 - 511 - 46
12ASPASPASPASPAA53 - 9648 - 91
22ASPASPASPASPBB53 - 9648 - 91

NCS ensembles :
ID
1
2

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Components

#1: Protein Beta-2-microglobulin / Beta-2 microglobulin


Mass: 10766.065 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61769
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical ChemComp-SJK / 5-oxidanylidene-~{N}-(2-sulfanylethyl)-2,3-dihydro-[1,3]thiazolo[3,2-a]pyrimidine-6-carboxamide


Mass: 257.333 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H11N3O2S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density meas: 0.98 Mg/m3 / Density % sol: 50.16 % / Description: 2 molecules in the asymmetric unit
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Drop protein volume 0.2 uL Drop well volume 0.1 uL 0.04 M Porpheus Alcohol Mix (Complex ingredient) 0.1 M Morpheus Buffer System 3 pH 8.5 (Buffer) 31 %w/v Morpheus Precipitant Mix 4 ...Details: Drop protein volume 0.2 uL Drop well volume 0.1 uL 0.04 M Porpheus Alcohol Mix (Complex ingredient) 0.1 M Morpheus Buffer System 3 pH 8.5 (Buffer) 31 %w/v Morpheus Precipitant Mix 4 (Precipitant) Stock Solutions: Porpheus Alcohol Mix 0.2 M 1,6-hexanediol, 0.2 M 1-butanol, 0.2 M (RS)-1,2-propanediol, 0.2 M 2-propanol, 0.2 M 1,4-butanediol, 0.2 M 1,3-propanediol (for a final concentration of 6.7 mM of 1,6-hexanediol, 1-butanol, (RS)-1,2-propanediol, 2-propanol, 1,4-butanediol, 1,3-propanediol) Morpheus Buffer System 3 pH 8.5 1M Tris and 1M BICINE (for a final concentration of 39.1 mM Bicine pH = 5.03 and 60.9 M Tris pH = 10.83) Morpheus Precipitant Mix 25% w/v PEG 3350, 25% w/v PEG 1000, 25% v/v MPD (for a final concentration of 7.75% w/v PEG 1000, 7.75% w/v PEG 3350 and 7.75% v/v MPD)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.4→61.92 Å / Num. obs: 8519 / % possible obs: 100 % / Redundancy: 23 % / CC1/2: 0.999 / Net I/σ(I): 9.8
Reflection shellResolution: 2.4→2.53 Å / Rmerge(I) obs: 1.913 / Num. measured obs: 208526 / Num. unique obs: 8519 / CC1/2: 0.789 / Rsym value: 0.399

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
xia2data processing
DIALSdata processing
XSCALEdata reduction
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YXF

2yxf


Resolution: 2.4→61.92 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.925 / SU B: 14.782 / SU ML: 0.322 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.473 / ESU R Free: 0.302 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2884 452 5 %RANDOM
Rwork0.2333 ---
obs0.2361 8519 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 160.46 Å2 / Biso mean: 74.502 Å2 / Biso min: 39.45 Å2
Baniso -1Baniso -2Baniso -3
1--1.7 Å20 Å20 Å2
2---1.7 Å20 Å2
3---3.39 Å2
Refinement stepCycle: final / Resolution: 2.4→61.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1520 0 784 33 2337
Biso mean--81.7 69.1 -
Num. residues----92
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0131576
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171366
X-RAY DIFFRACTIONr_angle_refined_deg1.5531.6842123
X-RAY DIFFRACTIONr_angle_other_deg1.1441.6173189
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8435171
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.39923.40988
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.00615257
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.823156
X-RAY DIFFRACTIONr_chiral_restr0.0510.2187
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021689
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02335
X-RAY DIFFRACTIONr_mcbond_it5.6217.677700
X-RAY DIFFRACTIONr_mcbond_other5.6237.677699
X-RAY DIFFRACTIONr_mcangle_it8.65211.508865
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A10290.19
12B10290.19
21A9800.16
22B9800.16
LS refinement shellResolution: 2.404→2.467 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.468 34 -
Rwork0.37 626 -
all-660 -
obs--99.55 %

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