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- PDB-5ckg: Human beta-2 microglobulin mutant V85E -

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Basic information

Entry
Database: PDB / ID: 5ckg
TitleHuman beta-2 microglobulin mutant V85E
ComponentsBeta-2-microglobulin
KeywordsIMMUNE SYSTEM / Aggregation propensity / Amyloid / beta-sandwitch / fold stability
Function / homology
Function and homology information


early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / T cell mediated cytotoxicity / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / regulation of iron ion transport / cellular response to iron(III) ion / negative regulation of iron ion transport ...early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / T cell mediated cytotoxicity / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / regulation of iron ion transport / cellular response to iron(III) ion / negative regulation of iron ion transport / negative regulation of forebrain neuron differentiation / response to molecule of bacterial origin / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / HFE-transferrin receptor complex / MHC class I peptide loading complex / transferrin transport / negative regulation of receptor-mediated endocytosis / cellular response to iron ion / positive regulation of T cell cytokine production / multicellular organismal-level iron ion homeostasis / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / negative regulation of epithelial cell proliferation / cellular response to nicotine / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / specific granule lumen / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / peptide antigen binding / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of T cell activation / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / T cell differentiation in thymus / sensory perception of smell / Modulation by Mtb of host immune system / tertiary granule lumen / positive regulation of cellular senescence / MHC class II protein complex binding / DAP12 signaling / negative regulation of neuron projection development / late endosome membrane / protein refolding / ER-Phagosome pathway / early endosome membrane / amyloid fibril formation / protein homotetramerization / intracellular iron ion homeostasis / learning or memory / endoplasmic reticulum lumen / Amyloid fiber formation / external side of plasma membrane / Golgi membrane / lysosomal membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / Golgi apparatus / structural molecule activity / endoplasmic reticulum / protein homodimerization activity / : / 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 ...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
ACETATE ION / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsSala, B.M. / De Rosa, M. / Bolognesi, M. / Ricagno, S.
Funding support Italy, 1items
OrganizationGrant numberCountry
Italian Ministry of University and ResearchFIRB RBFR109EOS Italy
CitationJournal: Sci Rep / Year: 2016
Title: Rational design of mutations that change the aggregation rate of a protein while maintaining its native structure and stability.
Authors: Camilloni, C. / Sala, B.M. / Sormanni, P. / Porcari, R. / Corazza, A. / De Rosa, M. / Zanini, S. / Barbiroli, A. / Esposito, G. / Bolognesi, M. / Bellotti, V. / Vendruscolo, M. / Ricagno, S.
History
DepositionJul 15, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 20, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0295
Polymers23,8192
Non-polymers2103
Water2,162120
1
A: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9682
Polymers11,9091
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0603
Polymers11,9091
Non-polymers1512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.578, 28.860, 87.719
Angle α, β, γ (deg.)90.00, 110.11, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-269-

HOH

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Components

#1: Protein Beta-2-microglobulin


Mass: 11909.339 Da / Num. of mol.: 2 / Fragment: RESIDUES 21-119 / Mutation: V85E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pET29B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61769
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.21 Å3/Da / Density % sol: 44.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M sodium acetate, 30% w/v PEG 4000, 15% glycerol, 0.2 M ammonium acetate

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.99 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 1.75→27.71 Å / Num. obs: 20777 / % possible obs: 97 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 9.3
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.9 / % possible all: 96.9

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Z9T

2z9t


Resolution: 1.75→27.71 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.232 1995 9.63 %
Rwork0.183 --
obs0.188 20722 96.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→27.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1651 0 14 120 1785
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0181825
X-RAY DIFFRACTIONf_angle_d1.7892495
X-RAY DIFFRACTIONf_dihedral_angle_d14.321697
X-RAY DIFFRACTIONf_chiral_restr0.095264
X-RAY DIFFRACTIONf_plane_restr0.009328
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.79370.32261420.27921341X-RAY DIFFRACTION96
1.7937-1.84220.25541380.24681314X-RAY DIFFRACTION97
1.8422-1.89640.28191370.2151285X-RAY DIFFRACTION94
1.8964-1.95760.24141390.19561301X-RAY DIFFRACTION95
1.9576-2.02760.23511450.19441346X-RAY DIFFRACTION97
2.0276-2.10870.22441430.19621336X-RAY DIFFRACTION97
2.1087-2.20470.27871420.19111341X-RAY DIFFRACTION97
2.2047-2.32080.27971370.19781286X-RAY DIFFRACTION94
2.3208-2.46620.26671450.19891357X-RAY DIFFRACTION98
2.4662-2.65640.23041430.20571337X-RAY DIFFRACTION97
2.6564-2.92350.23551450.19851361X-RAY DIFFRACTION97
2.9235-3.34590.23541420.18091341X-RAY DIFFRACTION97
3.3459-4.21310.21981470.15381370X-RAY DIFFRACTION96
4.2131-27.71270.19791500.16431411X-RAY DIFFRACTION96
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)
16.08144.0012-5.09954.8299-3.66584.95780.1650.4150.1519-0.13530.16360.0046-0.3783-0.5392-0.39440.3370.03810.04280.25320.02950.217414.82617.27520.2253
27.307-1.1469-3.84921.761-2.25942.02230.523-0.72190.46310.51250.83091.94551.5183-1.83810.47520.2820.08660.27340.90040.43440.8162-6.8371-2.512513.5967
36.52012.4432-6.1044.6644-4.37038.3999-0.22110.7602-0.0289-0.13210.45240.10720.2244-1.0477-0.22050.2413-0.03010.00990.207-0.00690.140810.66510.0413.8551
48.23391.7999-5.37125.9545-1.4794.6333-0.2069-0.7004-0.9536-0.068-0.3003-0.17221.23840.68190.36520.40830.0048-0.00990.33590.05910.311411.9042-5.142815.3734
54.18282.9061-4.22536.8465-5.05685.4869-0.62481.1455-0.5086-0.7810.5674-0.00120.9857-1.50960.1250.3906-0.0572-0.02510.45530.01360.305610.3379-2.46630.0144
67.55931.4216-5.11743.7284-0.74867.2542-0.2138-1.1234-0.09740.42070.10720.3544-0.312-0.3395-0.05990.36220.11130.06530.46760.0520.27036.81961.248217.8662
78.6944.5217-2.29283.6699-2.99942.97860.2118-0.8019-0.10070.8078-0.46470.2163-0.35630.2507-0.090.4557-0.06870.07620.2209-0.02330.254522.37048.24748.4635
84.53474.2833-4.14985.9403-3.01014.40920.04610.57672.52450.57180.91251.4065-1.2551-1.4709-0.43160.50880.11770.10780.4128-0.02670.48984.15037.062314.4056
94.15984.4203-2.97613.2323-2.55326.14430.3745-0.15620.30160.1-0.15940.0683-0.2856-0.0491-0.12450.19870.0445-0.03760.1215-0.01180.217929.522319.3515-40.1714
104.1488-1.1527-2.10848.8091-2.01536.76610.0968-0.84810.24120.6161-0.06330.7257-0.0087-0.8123-0.05920.2213-0.01250.01210.6615-0.04810.31887.565911.1292-29.6757
119.68381.4858-2.81291.8911-0.40162.2436-0.0417-0.1936-0.24920.1035-0.0018-0.1560.0453-0.31980.07020.1756-0.0164-0.0490.2106-0.02190.169925.423312.3459-38.1375
125.972.8984-3.92223.0086-2.91523.110.1337-0.96790.00280.0575-0.078-0.01270.17890.0096-0.01070.2658-0.0076-0.09350.38030.03440.228728.16199.5737-28.6991
132.063-0.9624-0.30838.46014.69563.3012-0.2447-1.0754-2.3197-0.0051-0.31640.33551.6695-0.11020.51720.7528-0.01660.06290.5640.07070.550824.64154.0858-26.0297
148.88534.7383-4.42799.8595-3.40333.1392-0.40630.4568-0.1064-0.85070.03010.12230.2945-0.02080.37320.2634-0.0254-0.04980.2836-0.01770.187529.139911.125-48.0717
157.18873.0919-5.1093.7163-2.55094.1464-0.23670.3407-0.19390.0780.13430.22680.1769-0.72950.11960.1854-0.0464-0.02820.26020.00880.183821.85028.7582-37.2922
164.2088-1.4438-4.99825.4649-1.83288.5243-0.0094-1.46291.46570.6761-0.05210.0394-0.7692-0.4637-0.07270.53430.0614-0.01770.7802-0.01470.397713.637712.2889-19.3094
175.19881.9272-2.03141.0771-0.98945.8270.3172-0.7160.13860.2955-0.2803-0.2047-0.69570.56550.01780.2396-0.0507-0.08270.2557-0.0090.242532.682816.6382-30.8694
182.80444.5612-1.76867.5454-1.56658.35630.3727-0.75592.43370.5885-0.16861.027-1.1201-0.9227-0.00780.35750.0865-0.0090.3924-0.15420.390919.279118.9832-27.5458
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 0 THROUGH 11 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 12 THROUGH 19 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 20 THROUGH 35 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 36 THROUGH 50 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 51 THROUGH 71 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 72 THROUGH 83 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 84 THROUGH 90 )
8X-RAY DIFFRACTION8CHAIN 'A' AND (RESID 91 THROUGH 99 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 0 THROUGH 11 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 12 THROUGH 19 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 20 THROUGH 35 )
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESID 36 THROUGH 41 )
13X-RAY DIFFRACTION13CHAIN 'B' AND (RESID 42 THROUGH 50 )
14X-RAY DIFFRACTION14CHAIN 'B' AND (RESID 51 THROUGH 60 )
15X-RAY DIFFRACTION15CHAIN 'B' AND (RESID 61 THROUGH 71 )
16X-RAY DIFFRACTION16CHAIN 'B' AND (RESID 72 THROUGH 77 )
17X-RAY DIFFRACTION17CHAIN 'B' AND (RESID 78 THROUGH 90 )
18X-RAY DIFFRACTION18CHAIN 'B' AND (RESID 91 THROUGH 99 )

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