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- PDB-5ymw: Crystal structure of 8-mer peptide from Rous sarcoma virus in com... -

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Basic information

Entry
Database: PDB / ID: 5ymw
TitleCrystal structure of 8-mer peptide from Rous sarcoma virus in complex with BF2*1201
Components
  • Beta-2-microglobulin
  • Class I histocompatibility antigen, F10 alpha chain
  • LEU-PRO-ALA-CYS-VAL-LEU-GLU-VAL
KeywordsIMMUNE SYSTEM / MHC / chicken / Rous sarcoma virus
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 / osteoclast development / extrinsic component of cytoplasmic side of plasma membrane / antigen processing and presentation of peptide antigen via MHC class I / negative regulation of intrinsic apoptotic signaling pathway / bone resorption ...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 / osteoclast development / extrinsic component of cytoplasmic side of plasma membrane / antigen processing and presentation of peptide antigen via MHC class I / negative regulation of intrinsic apoptotic signaling pathway / bone resorption / progesterone receptor signaling pathway / Neutrophil degranulation / cellular response to iron ion / negative regulation of extrinsic apoptotic signaling pathway / non-membrane spanning protein tyrosine kinase activity / non-specific protein-tyrosine kinase / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / 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 / antigen processing and presentation of exogenous peptide antigen via MHC class II / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / positive regulation of T cell activation / cellular response to nicotine / epidermal growth factor receptor signaling pathway / positive regulation of cellular senescence / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / late endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / cell adhesion / immune response / external side of plasma membrane / signaling receptor binding / lysosomal membrane / innate immune response / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular region / ATP binding / cytosol
Similarity search - Function
: / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / SH3 domain / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / SH2 domain / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like ...: / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / SH3 domain / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / SH2 domain / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Src homology 3 domains / MHC classes I/II-like antigen recognition protein / : / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Immunoglobulins / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Tyrosine-protein kinase transforming protein Src / Class I histocompatibility antigen, F10 alpha chain / Beta-2-microglobulin
Similarity search - Component
Biological speciesGallus gallus (chicken)
Rous sarcoma virus - Prague C
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.997 Å
AuthorsXiao, J. / Xiang, W. / Qi, J. / Chai, Y. / Liu, W.J. / Gao, G.F.
CitationJournal: J Immunol. / Year: 2018
Title: An Invariant Arginine in Common with MHC Class II Allows Extension at the C-Terminal End of Peptides Bound to Chicken MHC Class I.
Authors: Xiao, J. / Xiang, W. / Zhang, Y. / Peng, W. / Zhao, M. / Niu, L. / Chai, Y. / Qi, J. / Wang, F. / Qi, P. / Pan, C. / Han, L. / Wang, M. / Kaufman, J. / Gao, G.F. / Liu, W.J.
History
DepositionOct 22, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Class I histocompatibility antigen, F10 alpha chain
B: Beta-2-microglobulin
C: LEU-PRO-ALA-CYS-VAL-LEU-GLU-VAL
D: Class I histocompatibility antigen, F10 alpha chain
E: Beta-2-microglobulin
F: LEU-PRO-ALA-CYS-VAL-LEU-GLU-VAL
G: Class I histocompatibility antigen, F10 alpha chain
H: Beta-2-microglobulin
I: LEU-PRO-ALA-CYS-VAL-LEU-GLU-VAL
J: Class I histocompatibility antigen, F10 alpha chain
K: Beta-2-microglobulin
L: LEU-PRO-ALA-CYS-VAL-LEU-GLU-VAL


Theoretical massNumber of molelcules
Total (without water)172,09212
Polymers172,09212
Non-polymers00
Water19,8891104
1
A: Class I histocompatibility antigen, F10 alpha chain
B: Beta-2-microglobulin
C: LEU-PRO-ALA-CYS-VAL-LEU-GLU-VAL


Theoretical massNumber of molelcules
Total (without water)43,0233
Polymers43,0233
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4720 Å2
ΔGint-20 kcal/mol
Surface area17660 Å2
MethodPISA
2
D: Class I histocompatibility antigen, F10 alpha chain
E: Beta-2-microglobulin
F: LEU-PRO-ALA-CYS-VAL-LEU-GLU-VAL


Theoretical massNumber of molelcules
Total (without water)43,0233
Polymers43,0233
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4740 Å2
ΔGint-22 kcal/mol
Surface area17640 Å2
MethodPISA
3
G: Class I histocompatibility antigen, F10 alpha chain
H: Beta-2-microglobulin
I: LEU-PRO-ALA-CYS-VAL-LEU-GLU-VAL


Theoretical massNumber of molelcules
Total (without water)43,0233
Polymers43,0233
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4770 Å2
ΔGint-21 kcal/mol
Surface area17520 Å2
MethodPISA
4
J: Class I histocompatibility antigen, F10 alpha chain
K: Beta-2-microglobulin
L: LEU-PRO-ALA-CYS-VAL-LEU-GLU-VAL


Theoretical massNumber of molelcules
Total (without water)43,0233
Polymers43,0233
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4730 Å2
ΔGint-21 kcal/mol
Surface area17560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.817, 117.268, 92.507
Angle α, β, γ (deg.)90.00, 111.21, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Class I histocompatibility antigen, F10 alpha chain / B-F histocompatibility F10 antigen / B-F-beta-IV / B12


Mass: 31117.568 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Production host: Escherichia coli (E. coli) / References: UniProt: P15979
#2: Protein
Beta-2-microglobulin


Mass: 11062.404 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: B2M / Production host: Escherichia coli (E. coli) / References: UniProt: P21611
#3: Protein/peptide
LEU-PRO-ALA-CYS-VAL-LEU-GLU-VAL


Mass: 843.042 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Rous sarcoma virus - Prague C / References: UniProt: P00526*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1104 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.55 Å3/Da / Density % sol: 51.78 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1M BICINE pH 8.5, 20% W/V PEG 10000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.997→36.916 Å / Num. obs: 112857 / % possible obs: 96.46 % / Redundancy: 5.4 % / Net I/σ(I): 16

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXDphasing
RefinementResolution: 1.997→36.916 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.44
RfactorNum. reflection% reflection
Rfree0.2351 5652 5.01 %
Rwork0.1941 --
obs0.1961 112824 96.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.997→36.916 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12124 0 0 1104 13228
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00612500
X-RAY DIFFRACTIONf_angle_d1.03616984
X-RAY DIFFRACTIONf_dihedral_angle_d15.5494532
X-RAY DIFFRACTIONf_chiral_restr0.0421712
X-RAY DIFFRACTIONf_plane_restr0.0052232
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9966-2.01930.25941450.2192619X-RAY DIFFRACTION71
2.0193-2.0430.25841750.21593052X-RAY DIFFRACTION84
2.043-2.06790.25621870.21113546X-RAY DIFFRACTION95
2.0679-2.09410.28461870.2133576X-RAY DIFFRACTION98
2.0941-2.12170.28351850.20923586X-RAY DIFFRACTION96
2.1217-2.15070.25082020.21213536X-RAY DIFFRACTION97
2.1507-2.18140.29741930.20563563X-RAY DIFFRACTION97
2.1814-2.2140.25051790.2043595X-RAY DIFFRACTION97
2.214-2.24860.23641870.19863603X-RAY DIFFRACTION97
2.2486-2.28550.26641980.20793532X-RAY DIFFRACTION96
2.2855-2.32490.24132000.20583608X-RAY DIFFRACTION98
2.3249-2.36710.24211690.20913618X-RAY DIFFRACTION97
2.3671-2.41260.25091890.20513610X-RAY DIFFRACTION97
2.4126-2.46190.25241750.20473610X-RAY DIFFRACTION98
2.4619-2.51540.25771810.20093648X-RAY DIFFRACTION98
2.5154-2.57390.24861960.20163597X-RAY DIFFRACTION98
2.5739-2.63820.2351920.20773635X-RAY DIFFRACTION98
2.6382-2.70960.26681920.21493623X-RAY DIFFRACTION98
2.7096-2.78930.23541720.21823665X-RAY DIFFRACTION99
2.7893-2.87930.25351780.21483658X-RAY DIFFRACTION99
2.8793-2.98210.24451780.21263696X-RAY DIFFRACTION99
2.9821-3.10150.28182090.20673622X-RAY DIFFRACTION98
3.1015-3.24250.23431980.20493651X-RAY DIFFRACTION99
3.2425-3.41340.22322000.20023655X-RAY DIFFRACTION99
3.4134-3.62710.23422060.19353662X-RAY DIFFRACTION99
3.6271-3.90680.23381720.18293701X-RAY DIFFRACTION99
3.9068-4.29950.20281960.17473682X-RAY DIFFRACTION99
4.2995-4.92040.1951850.15753681X-RAY DIFFRACTION99
4.9204-6.19440.20462280.16953653X-RAY DIFFRACTION98
6.1944-36.92250.20371980.17143689X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 74.8807 Å / Origin y: -11.4182 Å / Origin z: 265.1987 Å
111213212223313233
T0.1377 Å2-0 Å2-0.0015 Å2-0.1322 Å2-0.0021 Å2--0.1433 Å2
L0.024 °20.021 °20.0182 °2-0.0198 °20.0009 °2--0.0756 °2
S0.01 Å °0.0163 Å °-0.0093 Å °-0.0032 Å °0.0085 Å °-0.0058 Å °-0.0077 Å °0.0041 Å °0 Å °
Refinement TLS groupSelection details: all

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