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- PDB-3mzt: Protein-induced photophysical changes to the amyloid indicator dy... -

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Basic information

Entry
Database: PDB / ID: 3mzt
TitleProtein-induced photophysical changes to the amyloid indicator dye, thioflavin T
ComponentsBeta-2-microglobulin
KeywordsIMMUNE SYSTEM / Thioflavin T / amyloid / Parkinson's / Alzheimer's
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 / 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 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 / 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 / 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 / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / 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 / MHC class I protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / multicellular organismal-level iron ion homeostasis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / 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 / positive regulation of immune response / Interferon gamma signaling / positive regulation of T cell activation / Modulation by Mtb of host immune system / sensory perception of smell / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / iron ion transport / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / 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 / Golgi apparatus / endoplasmic reticulum / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / Chem-TFX / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsWolfe, L.S. / Calabrese, M.F. / Nath, A. / Blaho, D.V. / Miranker, A.D. / Xiong, Y.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Protein-induced photophysical changes to the amyloid indicator dye thioflavin T.
Authors: Wolfe, L.S. / Calabrese, M.F. / Nath, A. / Blaho, D.V. / Miranker, A.D. / Xiong, Y.
History
DepositionMay 13, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 9, 2012Group: Other
Revision 1.3Mar 14, 2018Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.4Sep 6, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_label_asym_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

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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
C: Beta-2-microglobulin
D: Beta-2-microglobulin
E: Beta-2-microglobulin
F: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,56215
Polymers71,3306
Non-polymers1,2329
Water91951
1
A: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9522
Polymers11,8881
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2353
Polymers11,8881
Non-polymers3472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9522
Polymers11,8881
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2353
Polymers11,8881
Non-polymers3472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9522
Polymers11,8881
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2353
Polymers11,8881
Non-polymers3472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.891, 116.592, 66.317
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
12B
22D
32F
/ NCS ensembles :
ID
1
2

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Components

#1: Protein
Beta-2-microglobulin / Beta-2-microglobulin form pI 5.3


Mass: 11888.383 Da / Num. of mol.: 6 / Mutation: H13F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#2: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-TFX / 2-[4-(dimethylamino)phenyl]-3,6-dimethyl-1,3-benzothiazol-3-ium / Thioflavin T


Mass: 283.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C17H19N2S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.52 Å3/Da / Density % sol: 51.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 5mM ThT, 50mM diammonium tartrate, 22.5% PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 14, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 23314 / Num. obs: 22778 / % possible obs: 97.7 % / Observed criterion σ(I): 11.8 / Redundancy: 6.5 % / Rmerge(I) obs: 0.127 / Rsym value: 0.127
Reflection shellResolution: 2.7→2.769 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.922 / Mean I/σ(I) obs: 1.68 / Rsym value: 0.922 / % possible all: 87.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0088refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 3CIQ

3ciq


Resolution: 2.7→20 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.926 / SU B: 41.08 / SU ML: 0.36 / Cross valid method: THROUGHOUT / ESU R Free: 0.369 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25637 1035 5.1 %RANDOM
Rwork0.23896 ---
obs0.23985 19092 98.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 92.602 Å2
Baniso -1Baniso -2Baniso -3
1-10.52 Å2-0 Å2-0 Å2
2---6.34 Å20 Å2
3----4.18 Å2
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5028 0 66 51 5145
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0225304
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2951.9747194
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7025594
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.19624270
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.22615906
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.7681530
X-RAY DIFFRACTIONr_chiral_restr0.0810.2726
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214122
X-RAY DIFFRACTIONr_gen_planes_other
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_it7.1481.53012
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it11.06924920
X-RAY DIFFRACTIONr_scbond_it14.14232292
X-RAY DIFFRACTIONr_scangle_it17.9054.52274
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

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A839tight positional0.040.05
11B839tight positional0.050.05
11C839tight positional0.040.05
11D839tight positional0.060.05
11E839tight positional0.060.05
11F839tight positional0.050.05
22B40tight positional0.030.05
22D40tight positional0.020.05
22F40tight positional0.010.05
11A839tight thermal1.270.5
11B839tight thermal1.340.5
11C839tight thermal0.90.5
11D839tight thermal0.930.5
11E839tight thermal1.060.5
11F839tight thermal0.830.5
22B40tight thermal0.070.5
22D40tight thermal0.070.5
22F40tight thermal0.10.5
LS refinement shellResolution: 2.7→2.769 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 96 -
Rwork0.326 1323 -
obs--96.93 %
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)
10.6163-1.28220.38612.0858-0.67580.9247-0.05280.00530.01291.1236-0.04280.1085-0.3826-0.01660.09551.43080.119-0.06550.5463-0.03540.5436-25.790522.4893-4.1565
20.705-1.20950.23671.80530.62491.217-0.17150.1127-0.14351.37210.07620.2737-0.02030.28160.09531.33550.19030.01290.5555-0.02910.5255-18.842-7.1734-4.182
30.51820.4637-0.44041.7378-0.79820.81590.2314-0.27420.18150.1510.1050.66620.16320.0461-0.33640.56370.0367-0.01410.56840.00350.9984-34.0746-11.2478-15.9643
41.7539-0.7135-0.69242.41310.1771-1.55360.0442-0.10680.1419-0.7352-0.01280.16770.08710.0082-0.03140.42790.0015-0.19470.6579-0.02120.7157-18.5027-0.9447-40.1207
52.6016-0.23371.30753.5008-0.782-1.85120.1669-0.0751-0.3283-0.1363-0.08160.2552-0.1779-0.0193-0.08530.38990.0138-0.08710.6884-0.060.6137-28.878115.8403-39.8684
62.0129-0.41230.50530.8091-1.18421.3207-0.1506-0.2677-0.05630.5514-0.0997-0.1863-0.39720.02480.25020.82230.0582-0.25230.5601-0.01010.6442-11.746626.4181-17.0085
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 99
2X-RAY DIFFRACTION1A201
3X-RAY DIFFRACTION1F100
4X-RAY DIFFRACTION2B0 - 99
5X-RAY DIFFRACTION2B201
6X-RAY DIFFRACTION3C0 - 99
7X-RAY DIFFRACTION3C201
8X-RAY DIFFRACTION3B100
9X-RAY DIFFRACTION4D0 - 99
10X-RAY DIFFRACTION4D201
11X-RAY DIFFRACTION5E0 - 99
12X-RAY DIFFRACTION5E201
13X-RAY DIFFRACTION5D100
14X-RAY DIFFRACTION6F0 - 99
15X-RAY DIFFRACTION6F201

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