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- PDB-4e0l: FYLLYYT segment from human Beta 2 Microglobulin (62-68) displayed... -

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Basic information

Entry
Database: PDB / ID: 4e0l
TitleFYLLYYT segment from human Beta 2 Microglobulin (62-68) displayed on 54-membered macrocycle scaffold
ComponentsCyclic pseudo-peptide FYLLYYT(ORN)KN(HAO)SA(ORN)
KeywordsPROTEIN FIBRIL / amyloid / out-of-register / fiber-forming / macrocycle
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 / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent ...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 / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / 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 / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / 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 / positive regulation of immune response / Interferon gamma signaling / Modulation by Mtb of host immune system / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / tertiary granule lumen / DAP12 signaling / positive regulation of protein binding / MHC class II protein complex binding / T cell differentiation in thymus / late endosome membrane / ER-Phagosome pathway / iron ion transport / protein refolding / early endosome membrane / 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
Beta-2-microglobulin
Similarity search - Component
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsZhao, M. / Liu, C. / Michael, S.R. / Eisenberg, D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Out-of-register beta-sheets suggest a pathway to toxic amyloid aggregates.
Authors: Liu, C. / Zhao, M. / Jiang, L. / Cheng, P.N. / Park, J. / Sawaya, M.R. / Pensalfini, A. / Gou, D. / Berk, A.J. / Glabe, C.G. / Nowick, J. / Eisenberg, D.
History
DepositionMar 4, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Sep 20, 2017Group: Advisory / Category: pdbx_validate_polymer_linkage
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_main_chain_plane / pdbx_validate_rmsd_angle / struct_conn / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cyclic pseudo-peptide FYLLYYT(ORN)KN(HAO)SA(ORN)
B: Cyclic pseudo-peptide FYLLYYT(ORN)KN(HAO)SA(ORN)
C: Cyclic pseudo-peptide FYLLYYT(ORN)KN(HAO)SA(ORN)
D: Cyclic pseudo-peptide FYLLYYT(ORN)KN(HAO)SA(ORN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,6256
Polymers7,3884
Non-polymers2362
Water28816
1
A: Cyclic pseudo-peptide FYLLYYT(ORN)KN(HAO)SA(ORN)
B: Cyclic pseudo-peptide FYLLYYT(ORN)KN(HAO)SA(ORN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,8123
Polymers3,6942
Non-polymers1181
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area880 Å2
ΔGint-11 kcal/mol
Surface area2930 Å2
MethodPISA
2
C: Cyclic pseudo-peptide FYLLYYT(ORN)KN(HAO)SA(ORN)
D: Cyclic pseudo-peptide FYLLYYT(ORN)KN(HAO)SA(ORN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,8123
Polymers3,6942
Non-polymers1181
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area880 Å2
ΔGint-11 kcal/mol
Surface area2890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.990, 40.780, 23.990
Angle α, β, γ (deg.)90.00, 98.76, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein/peptide
Cyclic pseudo-peptide FYLLYYT(ORN)KN(HAO)SA(ORN)


Mass: 1847.055 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: Synthetic molecule / References: UniProt: P61769*PLUS
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O

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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: 2.19 Å3/Da / Density % sol: 43.88 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 0.1M Na/K phosphate buffer pH 6.2, 35% (v/v) 2-methyl-2,4-pentanediol, vapor diffusion, hanging drop, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97949 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 25, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionNumber: 16557 / Rmerge(I) obs: 0.154 / D res high: 2.31 Å / Num. obs: 5394 / % possible obs: 93.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
7.3110.3412410010.129
5.977.3114210010.107
5.175.9719510010.118
4.625.1720110010.12
4.224.6223299.610.134
3.914.2222899.610.112
3.653.9125999.210.137
3.453.6526399.610.164
3.273.4531899.710.139
3.123.273129910.183
2.983.1230899.410.212
2.872.9834910010.211
2.762.8735310010.291
2.672.7636099.410.338
2.582.6738797.510.421
2.512.5834993.810.332
2.442.5136591.510.336
2.372.4434185.210.332
2.312.3724954.410.299
ReflectionResolution: 1.7→19.41 Å / Num. obs: 6471 / % possible obs: 91.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 14.51 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 10.04
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.7-1.750.532.38164.5
1.75-1.80.4293.14175.6
1.8-1.850.4123.54193.8
1.85-1.910.2595.39195.5
1.91-1.970.3225.36196.3
1.97-2.040.2416.69193.8
2.04-2.110.2497.17196.5
2.11-2.20.2357.67194.5
2.2-2.30.1659.24198.5
2.3-2.410.1479.74193.7
2.41-2.540.14610.54199.4
2.54-2.690.10412.43194.6
2.69-2.880.08813.02197.5
2.88-3.110.07916.2194.8
3.11-3.410.06618.09196.5
3.41-3.810.05420.35192.2
3.81-4.40.05122.44190.4
4.4-5.390.04424.54193.4
5.39-7.620.04323.46194.7
7.620.03623.42185.2

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→19.41 Å / Cor.coef. Fo:Fc: 0.9173 / Cor.coef. Fo:Fc free: 0.893 / Occupancy max: 1 / Occupancy min: 0.6 / SU B: 6.917 / SU ML: 0.098 / SU R Cruickshank DPI: 0.1455 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.146 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2575 648 10.01 %RANDOM
Rwork0.2282 ---
obs0.2311 6471 91.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.69 Å2
Baniso -1Baniso -2Baniso -3
1-0.1524 Å20 Å20.0563 Å2
2---0.4799 Å20 Å2
3---0.3274 Å2
Refine analyzeLuzzati coordinate error obs: 0.256 Å
Refinement stepCycle: LAST / Resolution: 1.7→19.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms524 0 16 16 556
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.008558HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.96684HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d152SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes4HARMONIC2
X-RAY DIFFRACTIONt_gen_planes60HARMONIC5
X-RAY DIFFRACTIONt_it558HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion
X-RAY DIFFRACTIONt_other_torsion
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact
LS refinement shellResolution: 1.7→1.9 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2188 141 8.89 %
Rwork0.1937 1445 -
all0.1959 1586 -
obs--91.09 %
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)
10.09-0.8402-0.32550.59450.46780.43260.0041-0.0004-0.01010.04010.00510.0728-0.0117-0.0539-0.00920.14330.03240.0062-0.05960.0498-0.069212.29570.491810.0964
20.6084-0.2729-0.37611.7169-0.38910.19390.0048-0.0080.0139-0.02720.0061-0.0071-0.01820.067-0.01090.10860.01420.0073-0.04990.007-0.053119.75560.16344.7258
3-0.1134-0.66390.36780.0138-0.54120.76680.0032-0.0252-0.0070.01550.0132-0.0523-0.00380.0068-0.01640.08640.01860.0292-0.063-0.0418-0.017619.6394-7.8136-0.9761
40.5734-0.00710.56021.28420.44140.1590.00850.012-0.0032-0.0101-0.00380.02750.0226-0.0555-0.00470.09750.02030.0261-0.04620.0158-0.04114.1546-7.5871-8.2623
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 13
2X-RAY DIFFRACTION2B0 - 13
3X-RAY DIFFRACTION3C0 - 13
4X-RAY DIFFRACTION4D0 - 13

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