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- PDB-2x89: Structure of the Beta2_microglobulin involved in amyloidogenesis -

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Basic information

Entry
Database: PDB / ID: 2x89
TitleStructure of the Beta2_microglobulin involved in amyloidogenesis
Components
  • ANTIBODY
  • BETA-2-MICROGLOBULIN
KeywordsIMMUNE SYSTEM
Function / homology
Function and homology information


immunoglobulin complex / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / 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 ...immunoglobulin complex / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / 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 / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / adaptive immune response / intracellular iron ion homeostasis / learning or memory / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / lysosomal membrane / external side of plasma 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 / metal ion binding / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
: / Immunoglobulin V-Type / Beta-2-Microglobulin / Immunoglobulin V-set domain / Immunoglobulin V-set domain / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin ...: / Immunoglobulin V-Type / Beta-2-Microglobulin / Immunoglobulin V-set domain / Immunoglobulin V-set domain / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / 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
R2 protein / Beta-2-microglobulin
Similarity search - Component
Biological speciesCAMELUS DROMEDARIUS (Arabian camel)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.16 Å
AuthorsDomanska, K. / Srinivasan, V. / Vanderhaegen, S. / Pardon, E. / Marquez, J.A. / Bellotti, V. / Wyns, L. / Steyaert, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Atomic Structure of a Nanobody-Trapped Domain-Swapped Dimer of an Amyloidogenic {Beta}2-Microglobulin Variant.
Authors: Domanska, K. / Vanderhaegen, S. / Srinivasan, V. / Pardon, E. / Dupeux, F. / Marquez, J.A. / Giorgetti, S. / Stoppini, M. / Wyns, L. / Bellotti, V. / Steyaert, J.
History
DepositionMar 7, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2013Group: Derived calculations / Other ...Derived calculations / Other / Refinement description / Source and taxonomy / Version format compliance
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.3Oct 16, 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: ANTIBODY
B: ANTIBODY
C: ANTIBODY
D: BETA-2-MICROGLOBULIN
E: BETA-2-MICROGLOBULIN
F: BETA-2-MICROGLOBULIN
G: BETA-2-MICROGLOBULIN


Theoretical massNumber of molelcules
Total (without water)87,1027
Polymers87,1027
Non-polymers00
Water5,314295
1
F: BETA-2-MICROGLOBULIN
G: BETA-2-MICROGLOBULIN


Theoretical massNumber of molelcules
Total (without water)22,3072
Polymers22,3072
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-11.6 kcal/mol
Surface area11370 Å2
MethodPISA
2
D: BETA-2-MICROGLOBULIN
E: BETA-2-MICROGLOBULIN


Theoretical massNumber of molelcules
Total (without water)22,3072
Polymers22,3072
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2760 Å2
ΔGint-10.6 kcal/mol
Surface area11630 Å2
MethodPISA
3
C: ANTIBODY


Theoretical massNumber of molelcules
Total (without water)14,1631
Polymers14,1631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
B: ANTIBODY


Theoretical massNumber of molelcules
Total (without water)14,1631
Polymers14,1631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
A: ANTIBODY


Theoretical massNumber of molelcules
Total (without water)14,1631
Polymers14,1631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.490, 100.864, 83.743
Angle α, β, γ (deg.)90.00, 106.43, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
12D
22E
32F
42G

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A95 - 220
2114B95 - 220
3114C95 - 220
1124D1 - 92
2124E1 - 92
3124F1 - 92
4124G1 - 92

NCS ensembles :
ID
1
2

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Components

#1: Antibody ANTIBODY


Mass: 14162.595 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CAMELUS DROMEDARIUS (Arabian camel) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: A2KD59*PLUS
#2: Protein
BETA-2-MICROGLOBULIN / BETA-2-MICROGLOBULIN FORM PI 5.3


Mass: 11153.478 Da / Num. of mol.: 4 / Fragment: RESIDUES 27-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P61769
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / 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

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Sample preparation

CrystalDensity Matthews: 2.91 Å3/Da / Density % sol: 57.7 % / Description: NONE
Crystal growDetails: 6%PEG4000, 0.2M AMMONIUM SULPHATE, 0.1M NA-ACETEATE PH4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97812
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97812 Å / Relative weight: 1
ReflectionResolution: 2.16→20 Å / Num. obs: 66127 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.6
Reflection shellResolution: 2.16→2.24 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3.1 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKLdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD
Starting model: PDB ENTRY 1BMG

1bmg


Resolution: 2.16→19.85 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.921 / SU B: 9.727 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R: 0.215 / ESU R Free: 0.186
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ONE MOLECULE IN THE ASYMMETRIC UNIT IS DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.26691 3356 5.1 %RANDOM
Rwork0.23813 ---
obs0.23962 62741 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.626 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å2-0.03 Å2
2--0.04 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.16→19.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5930 0 0 295 6225
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0226078
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.4391.9338226
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.845735
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.27123.625309
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.96515985
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.781544
X-RAY DIFFRACTIONr_chiral_restr0.1870.2853
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024722
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2820.22794
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3180.23956
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2230.2414
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.290.287
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.170.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4821.53792
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.26925899
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.67832702
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.5964.52327
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
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
11A974medium positional0.430.5
12B974medium positional0.610.5
13C974medium positional0.410.5
21D672medium positional1.320.5
22E672medium positional1.510.5
23F672medium positional1.190.5
24G672medium positional1.370.5
11A974medium thermal2.232
12B974medium thermal2.092
13C974medium thermal2.272
21D672medium thermal1.972
22E672medium thermal2.082
23F672medium thermal2.212
24G672medium thermal2.232
LS refinement shellResolution: 2.16→2.215 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 216 -
Rwork0.269 4562 -
obs--98.88 %
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)
14.02791.0529-1.29642.5568-0.81821.97270.13510.12230.3975-0.1184-0.04010.1939-0.1895-0.2109-0.095-0.2350.00910.0082-0.2469-0.0029-0.2336-67.824718.30466.6027
23.11110.6746-1.40723.3466-2.22653.75380.02670.2415-0.06-0.04130.04770.08630.2038-0.2467-0.0743-0.31280.0094-0.0055-0.3256-0.0193-0.3015-33.1805-5.265419.2975
32.5541-0.11961.06261.59140.22785.97060.0276-0.0349-0.3027-0.03590.0610.03540.5604-0.0167-0.0886-0.24860.02530.0349-0.32750.0131-0.2599-32.33672.5009-44.2155
41.2732-0.319-0.68441.2346-1.95595.93680.0951-0.21610.049-0.0216-0.0187-0.2374-0.0650.4987-0.0763-0.2763-0.03-0.0036-0.15740.0347-0.1379-40.70713.4972-4.8917
50.3420.0119-0.60621.565-1.19473.77960.1249-0.14880.16880.05040.06810.0521-0.11920.0901-0.193-0.19640.00780.0093-0.2662-0.044-0.2359-39.93420.8889-22.2631
62.31971.4266-0.03091.63470.3724.2338-0.02530.31870.1339-0.32540.2494-0.1578-0.16170.3897-0.2241-0.2208-0.00910.016-0.22010.0333-0.2161-11.38385.49252.3181
71.0058-0.0829-0.09070.06150.74469.94050.12050.30620.2385-0.02850.1114-0.0256-0.6295-0.0463-0.2319-0.10110.0149-0.0122-0.12610.0518-0.0751-14.00423.2311-16.8882
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 128
2X-RAY DIFFRACTION2B1 - 128
3X-RAY DIFFRACTION3C1 - 128
4X-RAY DIFFRACTION4D6 - 97
5X-RAY DIFFRACTION5E6 - 96
6X-RAY DIFFRACTION6F6 - 96
7X-RAY DIFFRACTION7G6 - 97

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