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- PDB-4wc8: Heterogeneous dodecamer formed from macrocycles containing a sequ... -

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Basic information

Entry
Database: PDB / ID: 4wc8
TitleHeterogeneous dodecamer formed from macrocycles containing a sequence from beta-2-microglobulin(63-69).
Components
  • ORN-TYR-LEU-LEU-PHI-TYR-THR-GLU-ORN-LYS-VAL-ALA-MAA-ALA-VAL-LYS
  • ORN-TYR-LEU-LEU-PHI-TYR-THR-GLU-ORN-LYS-VAL-ALA-MLE-ALA-VAL-LYS
KeywordsIMMUNE SYSTEM / Heterogeneous dodecamer / hexamer / dimers
Function / homology
Function and homology information


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 ...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 / 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 / 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 / Immunoglobulin-like fold
Similarity search - Domain/homology
Beta-2-microglobulin
Similarity search - Component
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.908 Å
AuthorsSpencer, R.K. / Nowick, J.S.
CitationJournal: J.Am.Chem.Soc. / Year: 2015
Title: X-ray Crystallographic Structures of Oligomers of Peptides Derived from beta 2-Microglobulin.
Authors: Spencer, R.K. / Kreutzer, A.G. / Salveson, P.J. / Li, H. / Nowick, J.S.
History
DepositionSep 4, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1May 13, 2015Group: Database references
Revision 1.2Jun 3, 2015Group: Database references
Revision 2.0Dec 27, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / refine_hist / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.type_symbol / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ORN-TYR-LEU-LEU-PHI-TYR-THR-GLU-ORN-LYS-VAL-ALA-MAA-ALA-VAL-LYS
B: ORN-TYR-LEU-LEU-PHI-TYR-THR-GLU-ORN-LYS-VAL-ALA-MLE-ALA-VAL-LYS
C: ORN-TYR-LEU-LEU-PHI-TYR-THR-GLU-ORN-LYS-VAL-ALA-MLE-ALA-VAL-LYS
D: ORN-TYR-LEU-LEU-PHI-TYR-THR-GLU-ORN-LYS-VAL-ALA-MLE-ALA-VAL-LYS
E: ORN-TYR-LEU-LEU-PHI-TYR-THR-GLU-ORN-LYS-VAL-ALA-MAA-ALA-VAL-LYS
F: ORN-TYR-LEU-LEU-PHI-TYR-THR-GLU-ORN-LYS-VAL-ALA-MLE-ALA-VAL-LYS
G: ORN-TYR-LEU-LEU-PHI-TYR-THR-GLU-ORN-LYS-VAL-ALA-MLE-ALA-VAL-LYS
H: ORN-TYR-LEU-LEU-PHI-TYR-THR-GLU-ORN-LYS-VAL-ALA-MLE-ALA-VAL-LYS
I: ORN-TYR-LEU-LEU-PHI-TYR-THR-GLU-ORN-LYS-VAL-ALA-MAA-ALA-VAL-LYS
J: ORN-TYR-LEU-LEU-PHI-TYR-THR-GLU-ORN-LYS-VAL-ALA-MAA-ALA-VAL-LYS
K: ORN-TYR-LEU-LEU-PHI-TYR-THR-GLU-ORN-LYS-VAL-ALA-MAA-ALA-VAL-LYS
L: ORN-TYR-LEU-LEU-PHI-TYR-THR-GLU-ORN-LYS-VAL-ALA-MAA-ALA-VAL-LYS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,65434
Polymers24,08612
Non-polymers1,56822
Water97354
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.048, 58.048, 112.954
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11E-101-

SO4

21K-102-

CL

31D-101-

HOH

41L-103-

HOH

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Components

#1: Protein/peptide
ORN-TYR-LEU-LEU-PHI-TYR-THR-GLU-ORN-LYS-VAL-ALA-MAA-ALA-VAL-LYS


Mass: 1986.140 Da / Num. of mol.: 6 / Source method: obtained synthetically
Details: this sequence occurs naturally in humans beta-2-microglobulin.
Source: (synth.) synthetic construct (others) / References: UniProt: P61769*PLUS
#2: Protein/peptide
ORN-TYR-LEU-LEU-PHI-TYR-THR-GLU-ORN-LYS-VAL-ALA-MLE-ALA-VAL-LYS


Mass: 2028.219 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: UniProt: P61769*PLUS
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.98 Å3/Da / Density % sol: 37.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M Tris, pH 7.5, 0.2 M Li2SO4, 30% PEG 400 / Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 25, 2014
RadiationMonochromator: Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degs
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.908→31.59 Å / Num. all: 85498 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Biso Wilson estimate: 26.16 Å2 / Rmerge(I) obs: 0.08446 / Net I/σ(I): 12.15
Reflection shellResolution: 1.908→1.976 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.5385 / Mean I/σ(I) obs: 2.61 / % possible all: 96.93

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement
RefinementMethod to determine structure: SAD / Resolution: 1.908→31.588 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2186 2782 9.84 %phenix.refine generated
Rwork0.1687 ---
obs0.1736 28278 98.49 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.908→31.588 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1602 0 74 54 1730
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081700
X-RAY DIFFRACTIONf_angle_d1.1782283
X-RAY DIFFRACTIONf_dihedral_angle_d29.606775
X-RAY DIFFRACTIONf_chiral_restr0.05253
X-RAY DIFFRACTIONf_plane_restr0.005249
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9079-1.94080.3061140.23341133X-RAY DIFFRACTION86
1.9408-1.97610.25011450.22881278X-RAY DIFFRACTION100
1.9761-2.01410.26821450.21461298X-RAY DIFFRACTION100
2.0141-2.05520.26591410.2111289X-RAY DIFFRACTION100
2.0552-2.09990.28031400.20031271X-RAY DIFFRACTION100
2.0999-2.14880.22641410.19781300X-RAY DIFFRACTION99
2.1488-2.20250.2781370.18941254X-RAY DIFFRACTION98
2.2025-2.2620.27741410.19291286X-RAY DIFFRACTION100
2.262-2.32850.24491460.18791316X-RAY DIFFRACTION100
2.3285-2.40370.19651350.18291293X-RAY DIFFRACTION100
2.4037-2.48960.26881440.17971286X-RAY DIFFRACTION100
2.4896-2.58920.23871420.17171274X-RAY DIFFRACTION100
2.5892-2.7070.22281430.16771265X-RAY DIFFRACTION99
2.707-2.84960.20681410.1651256X-RAY DIFFRACTION97
2.8496-3.0280.20191390.15291296X-RAY DIFFRACTION100
3.028-3.26160.17341420.14731298X-RAY DIFFRACTION100
3.2616-3.58940.22411380.15351293X-RAY DIFFRACTION100
3.5894-4.10780.18651370.13921261X-RAY DIFFRACTION97
4.1078-5.17180.17091340.13861282X-RAY DIFFRACTION99
5.1718-31.59270.25151370.19331267X-RAY DIFFRACTION97
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)
17.8171-5.2991-4.7869.71435.55683.8885-0.365-0.00250.18890.14440.16960.31170.16510.2660.18890.27930.0047-0.06350.29590.01010.24211.15548.25575.1373
28.4545-3.58575.4126.8728-4.88226.76180.4034-0.0004-0.79510.06280.13510.31250.261-0.1667-0.54640.1948-0.0631-0.02330.21920.03420.20237.804111.231319.7399
38.32023.30414.78296.05961.56035.5545-0.39480.03190.1701-0.48770.09750.2983-0.5165-0.37560.28790.21310.0103-0.03810.19470.04150.15378.72620.912611.4353
43.85555.3536-5.47269.3359-5.91299.81590.2397-0.14380.51510.0491-0.1821-0.1422-0.20690.63210.01130.17030.0084-0.05080.23940.00980.251117.77620.033620.7471
58.3614-6.4787-6.12637.23265.06199.26540.51260.53320.6085-0.4572-0.2788-0.7967-0.1521-0.2336-0.15920.2716-0.0586-0.01170.17070.02960.25843.76381.262312.0597
64.3235-1.39671.47723.6859-4.67016.12290.15260.28240.0957-0.4726-0.13930.380.2959-0.05390.00750.2692-0.0599-0.0060.25560.02750.192714.032310.02443.8259
74.82745.5077-1.4416.3059-1.45585.6346-0.0917-0.4353-0.534-0.1235-0.2374-0.35180.1016-0.08950.30610.2204-0.007-0.03110.21340.02350.27918.89114.129414.1894
85.7593-0.94815.78327.7295-1.469.3414-0.13690.32160.1198-0.18240.0936-0.2897-0.45120.5950.00730.2029-0.01610.01560.28390.02340.177424.366314.86979.8585
97.5073-5.9178-5.74099.60255.70974.7081-0.33120.8257-0.41180.1003-0.20910.02820.3304-0.60420.49230.2495-0.0386-0.01510.31710.01530.321227.48312.064224.5605
107.1084-3.6221-3.7262.86962.64969.25740.2352-0.321-0.1318-0.22020.25630.2028-0.0114-0.4789-0.54820.2714-0.07360.01320.25540.06220.272120.49745.162727.0864
119.0623-6.682-6.53185.06734.92554.7711-0.1251-0.54360.0860.41270.4087-0.2360.53830.2773-0.28950.2686-0.01160.00680.3255-0.00840.230816.078925.36091.6809
127.2886-1.4622-1.99522.21762.02718.5761-0.0409-0.64060.57290.2326-0.270.1537-0.50830.06190.1690.3495-0.0381-0.05830.3452-0.0520.417522.36527.717410.105
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 16 )
2X-RAY DIFFRACTION2chain 'B' and (resid 1 through 16 )
3X-RAY DIFFRACTION3chain 'C' and (resid 1 through 16 )
4X-RAY DIFFRACTION4chain 'D' and (resid 1 through 16 )
5X-RAY DIFFRACTION5chain 'E' and (resid 1 through 16 )
6X-RAY DIFFRACTION6chain 'F' and (resid 1 through 16 )
7X-RAY DIFFRACTION7chain 'G' and (resid 1 through 16 )
8X-RAY DIFFRACTION8chain 'H' and (resid 1 through 16 )
9X-RAY DIFFRACTION9chain 'I' and (resid 1 through 16 )
10X-RAY DIFFRACTION10chain 'J' and (resid 1 through 16 )
11X-RAY DIFFRACTION11chain 'K' and (resid 1 through 16 )
12X-RAY DIFFRACTION12chain 'L' and resid ' 6 ' and name ' I ' and altloc ' '

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