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- PDB-3bew: 10mer Crystal Structure of chicken MHC class I haplotype B21 -

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Basic information

Entry
Database: PDB / ID: 3bew
Title10mer Crystal Structure of chicken MHC class I haplotype B21
Components
  • 10-mer from Tubulin beta-6 chain
  • Beta-2-microglobulin
  • Major histocompatibility complex class I glycoprotein haplotype B21
KeywordsIMMUNE SYSTEM / MHC class I / chicken / 10mer / bulge / water cushion / Immune response / Immunoglobulin domain / MHC I / Polymorphism / Secreted / GTP-binding / Microtubule / Nucleotide-binding
Function / homology
Function and homology information


Intraflagellar transport / Kinesins / Aggrephagy / Post-translational modification: synthesis of GPI-anchored proteins / Transferrin endocytosis and recycling / COPI-dependent Golgi-to-ER retrograde traffic / Resolution of Sister Chromatid Cohesion / EML4 and NUDC in mitotic spindle formation / Separation of Sister Chromatids / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand ...Intraflagellar transport / Kinesins / Aggrephagy / Post-translational modification: synthesis of GPI-anchored proteins / Transferrin endocytosis and recycling / COPI-dependent Golgi-to-ER retrograde traffic / Resolution of Sister Chromatid Cohesion / EML4 and NUDC in mitotic spindle formation / Separation of Sister Chromatids / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / ER-Phagosome pathway / Endosomal/Vacuolar pathway / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / DAP12 signaling / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / COPI-mediated anterograde transport / microtubule-based process / spindle assembly / Neutrophil degranulation / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / lumenal side of endoplasmic reticulum membrane / cellular response to iron ion / negative regulation of forebrain neuron differentiation / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / structural constituent of cytoskeleton / 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 / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / microtubule cytoskeleton organization / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation / MHC class II protein complex binding / late endosome membrane / mitotic cell cycle / protein homotetramerization / microtubule / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / immune response / lysosomal membrane / external side of plasma membrane / signaling receptor binding / GTPase activity / GTP binding / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular region / cytoplasm / cytosol
Similarity search - Function
: / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain ...: / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / 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 / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Tubulin beta-6 chain / Beta-2-microglobulin / MHC class I alpha chain 2
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsKoch, M. / Camp, S. / Collen, T. / Avila, D. / Salomonsen, J. / Wallny, H.J. / van Hateren, A. / Hunt, L. / Jacob, J.P. / Johnston, F. ...Koch, M. / Camp, S. / Collen, T. / Avila, D. / Salomonsen, J. / Wallny, H.J. / van Hateren, A. / Hunt, L. / Jacob, J.P. / Johnston, F. / Marston, D.A. / Shaw, I. / Dunbar, P.R. / Cerundolo, V. / Jones, E.Y. / Kaufman, J.
CitationJournal: Immunity / Year: 2007
Title: Structures of an MHC class I molecule from b21 chickens illustrate promiscuous Peptide binding
Authors: Koch, M. / Camp, S. / Collen, T. / Avila, D. / Salomonsen, J. / Wallny, H.-J. / van Hateren, A. / Hunt, L. / Jacob, J.P. / Johnston, F. / Marston, D.A. / Shaw, I. / Dunbar, P.R. / Cerundolo, ...Authors: Koch, M. / Camp, S. / Collen, T. / Avila, D. / Salomonsen, J. / Wallny, H.-J. / van Hateren, A. / Hunt, L. / Jacob, J.P. / Johnston, F. / Marston, D.A. / Shaw, I. / Dunbar, P.R. / Cerundolo, V. / Jones, E.Y. / Kaufman, J.
History
DepositionNov 20, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: 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 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Major histocompatibility complex class I glycoprotein haplotype B21
B: Beta-2-microglobulin
C: 10-mer from Tubulin beta-6 chain
D: Major histocompatibility complex class I glycoprotein haplotype B21
E: Beta-2-microglobulin
F: 10-mer from Tubulin beta-6 chain


Theoretical massNumber of molelcules
Total (without water)86,6256
Polymers86,6256
Non-polymers00
Water2,306128
1
A: Major histocompatibility complex class I glycoprotein haplotype B21
B: Beta-2-microglobulin
C: 10-mer from Tubulin beta-6 chain


Theoretical massNumber of molelcules
Total (without water)43,3123
Polymers43,3123
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5060 Å2
MethodPISA
2
D: Major histocompatibility complex class I glycoprotein haplotype B21
E: Beta-2-microglobulin
F: 10-mer from Tubulin beta-6 chain


Theoretical massNumber of molelcules
Total (without water)43,3123
Polymers43,3123
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.393, 88.711, 100.230
Angle α, β, γ (deg.)90.00, 80.01, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
31A
41D
12A
22D
32A
42D
52A
62D
13B
23E

NCS domain segments:

Refine code: 3

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLUGLUILEILEAA1 - 1011 - 101
211GLUGLUILEILEDD1 - 1011 - 101
321ILEILEGLUGLUAA107 - 180107 - 180
421ILEILEGLUGLUDD107 - 180107 - 180
112ARGARGGLUGLUAA181 - 190181 - 190
212ARGARGGLUGLUDD181 - 190181 - 190
322LEULEULYSLYSAA195 - 215195 - 215
422LEULEULYSLYSDD195 - 215195 - 215
532GLNGLNTRPTRPAA225 - 270225 - 270
632GLNGLNTRPTRPDD225 - 270225 - 270
113LEULEUHOHHOHBB - H2 - 993
213LEULEUHOHHOHEE - J2 - 993

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Major histocompatibility complex class I glycoprotein haplotype B21 / MHC class I molecule precursor / MHC class I alpha chain 2 / MHC class I antigen / MHC class I glycoprotein


Mass: 30930.408 Da / Num. of mol.: 2 / Fragment: UNP residues 1-270
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Strain: B21 / Gene: BFIV21, B-FIV, BF2 / Plasmid: pET22b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q95601
#2: Protein Beta-2-microglobulin


Mass: 11193.601 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Strain: B21 / Gene: B2M / Plasmid: pET22b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P21611
#3: Protein/peptide 10-mer from Tubulin beta-6 chain / 10mer peptide from B2 / Beta-tubulin class-VI


Mass: 1188.308 Da / Num. of mol.: 2 / Fragment: UNP residues 324-333 / Source method: obtained synthetically
Details: This sequence occurs naturally in B21 chickens. The peptide was synthesized by solid-phase synthesis.
References: UniProt: P09207
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.9 Å3/Da / Density % sol: 57.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 27% PEG 3350, 0.1M HEPES pH 7.0, 0.1M MgCl2, vapor diffusion, sitting drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9765 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 29, 2005
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 39205 / Rmerge(I) obs: 0.097 / Rsym value: 0.097 / Net I/σ(I): 13.2
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.323 / Mean I/σ(I) obs: 2.8 / Num. unique all: 1560 / Rsym value: 0.323

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.004data extraction
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3BEV

3bev


Resolution: 2.6→29.15 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.854 / SU B: 12.883 / SU ML: 0.282 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.8 / ESU R Free: 0.366 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.295 1514 5 %RANDOM
Rwork0.234 ---
obs0.237 30179 97.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.337 Å2
Baniso -1Baniso -2Baniso -3
1-3.59 Å20 Å21.67 Å2
2---1.88 Å20 Å2
3----2.29 Å2
Refinement stepCycle: LAST / Resolution: 2.6→29.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6104 0 0 128 6232
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0226261
X-RAY DIFFRACTIONr_bond_other_d0.0020.024299
X-RAY DIFFRACTIONr_angle_refined_deg1.3361.9378504
X-RAY DIFFRACTIONr_angle_other_deg0.9743.00210337
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4245751
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.04423.354322
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.9415994
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3921554
X-RAY DIFFRACTIONr_chiral_restr0.1150.2871
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027069
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021355
X-RAY DIFFRACTIONr_nbd_refined0.2130.21202
X-RAY DIFFRACTIONr_nbd_other0.2020.24189
X-RAY DIFFRACTIONr_nbtor_refined0.1840.22802
X-RAY DIFFRACTIONr_nbtor_other0.0840.23526
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.2190
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.10.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2090.256
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1660.23
X-RAY DIFFRACTIONr_mcbond_it3.6842.54834
X-RAY DIFFRACTIONr_mcbond_other1.4612.51537
X-RAY DIFFRACTIONr_mcangle_it4.7523.56060
X-RAY DIFFRACTIONr_scbond_it5.3323.53020
X-RAY DIFFRACTIONr_scangle_it6.7694.92444
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1027TIGHT POSITIONAL0.040.05
1A1427LOOSE POSITIONAL0.555
1A1027TIGHT THERMAL0.130.5
1A1427LOOSE THERMAL3.9610
2A446TIGHT POSITIONAL0.040.05
2A608LOOSE POSITIONAL0.565
2A446TIGHT THERMAL0.170.5
2A608LOOSE THERMAL4.6710
3B565TIGHT POSITIONAL0.040.05
3B740LOOSE POSITIONAL0.395
3B565TIGHT THERMAL0.110.5
3B740LOOSE THERMAL3.2310
LS refinement shellResolution: 2.6→2.657 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 88 -
Rwork0.304 1828 -
all-1916 -
obs--84.33 %

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