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- PDB-4d0d: COMPLEX OF A B2 CHICKEN MHC CLASS I MOLECULE AND A 8MER CHICKEN P... -

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Basic information

Entry
Database: PDB / ID: 4d0d
TitleCOMPLEX OF A B2 CHICKEN MHC CLASS I MOLECULE AND A 8MER CHICKEN PEPTIDE
Components
  • BETA-2-MICROGLOBULIN
  • MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I GLYCOPROTEIN HAPLOTYPE B2
  • SLP-76 ADAPTOR PROTEIN
KeywordsIMMUNE SYSTEM
Function / homology
Function and homology information


MHC class I protein binding, via antigen binding groove / 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 / 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 ...MHC class I protein binding, via antigen binding groove / 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 / 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 / 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 / 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 / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / immune response / lysosomal membrane / external side of plasma membrane / signaling receptor binding / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular region / cytosol
Similarity search - Function
SAM domain (Sterile alpha motif) / Sterile alpha motif domain / Sterile alpha motif/pointed 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 ...SAM domain (Sterile alpha motif) / Sterile alpha motif domain / Sterile alpha motif/pointed 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 / SH2 domain / Src homology 2 (SH2) domain profile. / MHC classes I/II-like antigen recognition protein / Src homology 2 domains / SH2 domain / SH2 domain superfamily / 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 / SLP-76 adaptor protein
Similarity search - Component
Biological speciesGALLUS GALLUS (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.13 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.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. ...Authors: Chappell, P. / Meziane, E.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
DepositionApr 25, 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 1.2Mar 27, 2019Group: Data collection / Database references / Category: citation_author / pdbx_database_proc / Item: _citation_author.name
Revision 1.3Dec 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I GLYCOPROTEIN HAPLOTYPE B2
B: BETA-2-MICROGLOBULIN
C: SLP-76 ADAPTOR PROTEIN
D: MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I GLYCOPROTEIN HAPLOTYPE B2
E: BETA-2-MICROGLOBULIN
F: SLP-76 ADAPTOR PROTEIN
G: MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I GLYCOPROTEIN HAPLOTYPE B2
H: BETA-2-MICROGLOBULIN
I: SLP-76 ADAPTOR PROTEIN
J: MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I GLYCOPROTEIN HAPLOTYPE B2
K: BETA-2-MICROGLOBULIN
L: SLP-76 ADAPTOR PROTEIN


Theoretical massNumber of molelcules
Total (without water)189,14612
Polymers189,14612
Non-polymers00
Water1629
1
A: MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I GLYCOPROTEIN HAPLOTYPE B2
B: BETA-2-MICROGLOBULIN
C: SLP-76 ADAPTOR PROTEIN


Theoretical massNumber of molelcules
Total (without water)47,2873
Polymers47,2873
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5380 Å2
ΔGint-31 kcal/mol
Surface area22610 Å2
MethodPQS
2
D: MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I GLYCOPROTEIN HAPLOTYPE B2
E: BETA-2-MICROGLOBULIN
F: SLP-76 ADAPTOR PROTEIN


Theoretical massNumber of molelcules
Total (without water)47,2873
Polymers47,2873
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5640 Å2
ΔGint-30.5 kcal/mol
Surface area22220 Å2
MethodPQS
3
G: MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I GLYCOPROTEIN HAPLOTYPE B2
H: BETA-2-MICROGLOBULIN
I: SLP-76 ADAPTOR PROTEIN


Theoretical massNumber of molelcules
Total (without water)47,2873
Polymers47,2873
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5370 Å2
ΔGint-34 kcal/mol
Surface area22170 Å2
MethodPQS
4
J: MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I GLYCOPROTEIN HAPLOTYPE B2
K: BETA-2-MICROGLOBULIN
L: SLP-76 ADAPTOR PROTEIN


Theoretical massNumber of molelcules
Total (without water)47,2873
Polymers47,2873
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5820 Å2
ΔGint-37.6 kcal/mol
Surface area22590 Å2
MethodPQS
Unit cell
Length a, b, c (Å)88.080, 92.540, 223.630
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.90928, 0.07617, -0.40915), (0.0775, -0.9969, -0.01335), (-0.4089, -0.01957, -0.91237)23.06852, -40.77456, 99.01662
2given(-0.04658, -0.89999, 0.43342), (0.99884, -0.03655, 0.03145), (-0.01246, 0.43438, 0.90064)-65.5183, 21.24869, 76.87175
3given(-0.06587, 0.99775, 0.01249), (-0.99777, -0.066, 0.01022), (0.01102, -0.01179, 0.99987)-22.34212, -23.1485, 55.84542
4given(0.90966, 0.05919, -0.41111), (0.05435, -0.99825, -0.02347), (-0.41177, -0.00099, -0.91129)22.51104, -40.63344, 99.81913
5given(-0.0177, -0.89392, 0.44787), (0.9988, 0.00465, 0.04874), (-0.04566, 0.4482, 0.89277)-64.55205, 23.08082, 76.72356
6given(-0.06455, 0.99728, 0.03547), (-0.99739, -0.06563, 0.03019), (0.03244, -0.03343, 0.99891)-22.60219, -23.50065, 56.16111

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Components

#1: Protein
MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I GLYCOPROTEIN HAPLOTYPE B2


Mass: 35349.094 Da / Num. of mol.: 4 / Fragment: EXTRACELLULAR DOMAINS, RESIDUES 22-293
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GALLUS GALLUS (chicken) / Description: B2 HAPLOTYPE / Plasmid: PET22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS ROSETTA / References: UniProt: O46789
#2: Protein
BETA-2-MICROGLOBULIN


Mass: 11062.404 Da / Num. of mol.: 4 / Fragment: RESIDUES 22-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GALLUS GALLUS (chicken) / Plasmid: PET22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS ROSETTA / References: UniProt: P21611
#3: Protein/peptide
SLP-76 ADAPTOR PROTEIN


Mass: 875.086 Da / Num. of mol.: 4 / Fragment: RESIDUES 159-166 / Source method: obtained synthetically / Source: (synth.) GALLUS GALLUS (chicken) / References: UniProt: Q9DG07
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.46 Å3/Da / Density % sol: 50.01 % / 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
DetectorDate: Dec 10, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.13→88.08 Å / Num. obs: 32916 / % possible obs: 99.6 % / Observed criterion σ(I): 1 / Redundancy: 4.6 % / Biso Wilson estimate: 73.64 Å2 / Rmerge(I) obs: 0.18 / Net I/σ(I): 8.8
Reflection shellResolution: 3.13→3.21 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2.1 / % possible all: 98.8

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Processing

Software
NameVersionClassification
BUSTER2.11.4refinement
XDSTHROUGH XIA2data reduction
AimlessTHROUGH XIA2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YF6

2yf6
PDB Unreleased entry


Resolution: 3.13→81.95 Å / Cor.coef. Fo:Fc: 0.8066 / Cor.coef. Fo:Fc free: 0.8083 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.556
RfactorNum. reflection% reflectionSelection details
Rfree0.2986 1665 5.08 %RANDOM
Rwork0.2925 ---
obs0.2928 32760 99.11 %-
Displacement parametersBiso mean: 46.99 Å2
Baniso -1Baniso -2Baniso -3
1-7.6305 Å20 Å20 Å2
2---4.9839 Å20 Å2
3----2.6467 Å2
Refine analyzeLuzzati coordinate error obs: 0.882 Å
Refinement stepCycle: LAST / Resolution: 3.13→81.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12102 0 0 9 12111
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00712475HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.8216969HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4146SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes309HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1821HARMONIC5
X-RAY DIFFRACTIONt_it12475HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion1.55
X-RAY DIFFRACTIONt_other_torsion19.33
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1515SEMIHARMONIC5
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_contact12614SEMIHARMONIC4
LS refinement shellResolution: 3.13→3.23 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.3613 151 5.26 %
Rwork0.3608 2720 -
all0.3608 2871 -
obs--99.11 %

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