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- PDB-4cvx: COMPLEX OF A B2 CHICKEN MHC CLASS I MOLECULE AND A 9MER CHICKEN P... -

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Basic information

Entry
Database: PDB / ID: 4cvx
TitleCOMPLEX OF A B2 CHICKEN MHC CLASS I MOLECULE AND A 9MER CHICKEN PEPTIDE
Components
  • BETA-2-MICROGLOBULINBeta-2 microglobulin
  • MHC CLASS I ALPHA CHAIN 2
  • SELF-PEPTIDE
KeywordsIMMUNE SYSTEM
Function / homology
Function and homology information


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 / vesicle docking involved in exocytosis / Neutrophil degranulation / negative regulation of forebrain neuron differentiation / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport ...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 / vesicle docking involved in exocytosis / Neutrophil degranulation / 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 / 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 / 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 / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / negative regulation of epithelial cell proliferation / positive regulation of T cell activation / protein transport / MHC class II protein complex binding / late endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / immune response / lysosomal membrane / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular region / membrane / cytosol
Similarity search - Function
Sec1-like, domain 2 / Sec1-like, domain 3a / Sec1-like protein / Sec1-like superfamily / Sec1 family / 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 ...Sec1-like, domain 2 / Sec1-like, domain 3a / Sec1-like protein / Sec1-like superfamily / Sec1 family / 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
MHC class I alpha chain 2 / Beta-2-microglobulin / Uncharacterized protein
Similarity search - Component
Biological speciesGALLUS GALLUS (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsChappell, P.E. / Roversi, P. / Harrison, M.C. / Mears, L.E. / Kaufman, J.F. / Lea, S.M.
CitationJournal: Elife / Year: 2015
Title: Expression levels of MHC class I molecules are inversely correlated with promiscuity of peptide binding.
Authors: Chappell, P. / Meziane, e.l..K. / Harrison, M. / Magiera, L. / Hermann, C. / Mears, L. / Wrobel, A.G. / Durant, C. / Nielsen, L.L. / Buus, S. / Ternette, N. / Mwangi, W. / Butter, C. / Nair, ...Authors: Chappell, P. / Meziane, e.l..K. / Harrison, M. / Magiera, L. / Hermann, C. / Mears, L. / Wrobel, A.G. / Durant, C. / Nielsen, L.L. / Buus, S. / Ternette, N. / Mwangi, W. / Butter, C. / Nair, V. / Ahyee, T. / Duggleby, R. / Madrigal, A. / Roversi, P. / Lea, S.M. / Kaufman, J.
History
DepositionMar 31, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2019Group: Data collection / Database references / Other
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc / pdbx_database_status
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _pdbx_database_status.recvd_author_approval
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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MHC CLASS I ALPHA CHAIN 2
B: BETA-2-MICROGLOBULIN
C: SELF-PEPTIDE
D: MHC CLASS I ALPHA CHAIN 2
E: BETA-2-MICROGLOBULIN
F: SELF-PEPTIDE


Theoretical massNumber of molelcules
Total (without water)94,8976
Polymers94,8976
Non-polymers00
Water1448
1
D: MHC CLASS I ALPHA CHAIN 2
E: BETA-2-MICROGLOBULIN
F: SELF-PEPTIDE


Theoretical massNumber of molelcules
Total (without water)47,4493
Polymers47,4493
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4610 Å2
ΔGint-25.9 kcal/mol
Surface area18420 Å2
MethodPISA
2
A: MHC CLASS I ALPHA CHAIN 2
B: BETA-2-MICROGLOBULIN
C: SELF-PEPTIDE


Theoretical massNumber of molelcules
Total (without water)47,4493
Polymers47,4493
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4600 Å2
ΔGint-25.1 kcal/mol
Surface area18640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.850, 173.850, 87.510
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12B
22E

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUPROPROAA1 - 2721 - 272
21GLUGLUPROPRODD1 - 2721 - 272
12LEULEUGLUGLUBB2 - 972 - 97
22LEULEUGLUGLUEE2 - 972 - 97

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(0.60889, -0.79323, 0.00685), (-0.79324, -0.60891, -0.00084), (0.00484, -0.00492, -0.99998)-0.279, -0.63289, 33.15112
2given(0.60869, -0.79333, 0.01137), (-0.79339, -0.60871, 0.00208), (0.00528, -0.01029, -0.99993)-0.40067, -0.78775, 32.8933

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Components

#1: Protein MHC CLASS I ALPHA CHAIN 2 / MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I GLYCOPROTEIN HAPLO TYPE B2


Mass: 35349.094 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAINS, RESIDUES 22-293
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GALLUS GALLUS (chicken) / Description: B2 HAPLOTYPE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS ROSETTA CELLS / References: UniProt: O46789
#2: Protein BETA-2-MICROGLOBULIN / Beta-2 microglobulin


Mass: 11062.404 Da / Num. of mol.: 2 / Fragment: RESIDUES 22-319
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GALLUS GALLUS (chicken) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS ROSETTA CELLS / References: UniProt: P21611
#3: Protein/peptide SELF-PEPTIDE


Mass: 1037.166 Da / Num. of mol.: 2 / Fragment: RESIDUES 314-322 / Source method: obtained synthetically / Details: 9-MER PEPTIDE / Source: (synth.) GALLUS GALLUS (chicken) / References: UniProt: Q5ZJG4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 4.03 Å3/Da / Density % sol: 69.51 % / Description: NONE
Crystal growpH: 7 / Details: 0.1M MMT BUFFER, PH 7.0, 25% W/V PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.979
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 10, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.615
11K, H, -L20.385
ReflectionResolution: 3.3→75.66 Å / Num. obs: 22882 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 7.3 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 11.1
Reflection shellResolution: 3.3→3.56 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 3.8 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSTHROUGH XIA2data reduction
AimlessTHROUGH XIA2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YF6

2yf6
PDB Unreleased entry


Resolution: 3.3→75.66 Å / Cor.coef. Fo:Fc: 0.863 / Cor.coef. Fo:Fc free: 0.879 / SU B: 24.155 / SU ML: 0.389 / Cross valid method: THROUGHOUT / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.26168 1150 5 %RANDOM
Rwork0.23681 ---
obs0.23804 21707 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 76.988 Å2
Baniso -1Baniso -2Baniso -3
1-30.13 Å20 Å20 Å2
2--30.13 Å20 Å2
3----60.26 Å2
Refinement stepCycle: LAST / Resolution: 3.3→75.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6052 0 0 8 6060
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0196242
X-RAY DIFFRACTIONr_bond_other_d0.0010.025616
X-RAY DIFFRACTIONr_angle_refined_deg0.7591.9388498
X-RAY DIFFRACTIONr_angle_other_deg0.6993.00212916
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.7595748
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.96223.418316
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.70215954
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3381546
X-RAY DIFFRACTIONr_chiral_restr0.0470.2852
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0217166
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021528
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2177.7983010
X-RAY DIFFRACTIONr_mcbond_other0.2177.7983009
X-RAY DIFFRACTIONr_mcangle_it0.41611.6973752
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.0697.7723232
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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 / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A148570.08
12D148570.08
21B51860.06
22E51860.06
LS refinement shellResolution: 3.3→3.386 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.45 92 -
Rwork0.44 1582 -
obs--99.64 %

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