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- PDB-3bes: Structure of a Poxvirus ifngbp/ifng Complex -

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Basic information

Entry
Database: PDB / ID: 3bes
TitleStructure of a Poxvirus ifngbp/ifng Complex
Components
  • Interferon gamma
  • Interferon-gamma binding protein C4R
KeywordsIMMUNE SYSTEM / ectromelia virus / orthopoxvirus / interferon / protein complex / Antiviral defense / Cytokine / Glycoprotein / Receptor
Function / homology
Function and homology information


positive regulation of fructose 1,6-bisphosphate 1-phosphatase activity / positive regulation of iron ion import across plasma membrane / positive regulation of fructose 1,6-bisphosphate metabolic process / positive regulation of tumor necrosis factor (ligand) superfamily member 11 production / type II interferon receptor binding / negative regulation of tau-protein kinase activity / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation involved in immune response / positive regulation of NMDA glutamate receptor activity / : / positive regulation of vitamin D biosynthetic process ...positive regulation of fructose 1,6-bisphosphate 1-phosphatase activity / positive regulation of iron ion import across plasma membrane / positive regulation of fructose 1,6-bisphosphate metabolic process / positive regulation of tumor necrosis factor (ligand) superfamily member 11 production / type II interferon receptor binding / negative regulation of tau-protein kinase activity / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation involved in immune response / positive regulation of NMDA glutamate receptor activity / : / positive regulation of vitamin D biosynthetic process / positive regulation of interleukin-23 production / positive regulation of peptidyl-serine phosphorylation of STAT protein / negative regulation of amyloid-beta clearance / positive regulation of cellular respiration / positive regulation of calcidiol 1-monooxygenase activity / positive regulation of protein deacetylation / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / type III interferon-mediated signaling pathway / positive regulation of smooth muscle cell apoptotic process / positive regulation of core promoter binding / neuroinflammatory response / positive regulation of exosomal secretion / macrophage activation involved in immune response / positive regulation of killing of cells of another organism / negative regulation of interleukin-17 production / positive regulation of membrane protein ectodomain proteolysis / positive regulation of osteoclast differentiation / positive regulation of MHC class II biosynthetic process / positive regulation of signaling receptor activity / positive regulation of neurogenesis / negative regulation of epithelial cell differentiation / IFNG signaling activates MAPKs / positive regulation of amyloid-beta formation / positive regulation of epithelial cell migration / cytokine binding / positive regulation of nitric-oxide synthase biosynthetic process / cell surface receptor signaling pathway via JAK-STAT / regulation of insulin secretion / humoral immune response / macrophage differentiation / positive regulation of phagocytosis / positive regulation of autophagy / type II interferon-mediated signaling pathway / Regulation of IFNG signaling / extrinsic apoptotic signaling pathway / positive regulation of chemokine production / positive regulation of tyrosine phosphorylation of STAT protein / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / positive regulation of interleukin-12 production / positive regulation of glycolytic process / positive regulation of interleukin-1 beta production / cytokine activity / negative regulation of smooth muscle cell proliferation / astrocyte activation / positive regulation of cytokine production / positive regulation of protein-containing complex assembly / positive regulation of protein localization to plasma membrane / microglial cell activation / response to virus / positive regulation of protein serine/threonine kinase activity / cellular response to virus / positive regulation of inflammatory response / positive regulation of interleukin-6 production / positive regulation of protein import into nucleus / positive regulation of nitric oxide biosynthetic process / Interferon gamma signaling / positive regulation of tumor necrosis factor production / defense response to virus / adaptive immune response / cell surface receptor signaling pathway / negative regulation of gene expression / negative regulation of DNA-templated transcription / apoptotic process / positive regulation of cell population proliferation / positive regulation of gene expression / negative regulation of transcription by RNA polymerase II / extracellular space / extracellular region / membrane / identical protein binding
Similarity search - Function
Helix Hairpins - #1480 / Interferon gamma receptor, D2 domain, poxvirus/mammal / Interferon gamma receptor (IFNGR1), D2 domain / Interferon gamma / Interferon gamma / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Helix Hairpins / Helix non-globular ...Helix Hairpins - #1480 / Interferon gamma receptor, D2 domain, poxvirus/mammal / Interferon gamma receptor (IFNGR1), D2 domain / Interferon gamma / Interferon gamma / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Helix Hairpins / Helix non-globular / Fibronectin type III superfamily / Special / Immunoglobulins / Immunoglobulin-like fold / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / Interferon gamma / IFN-gamma receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Ectromelia virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsNuara, A.A. / Walter, M.R.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Structure and mechanism of IFN-gamma antagonism by an orthopoxvirus IFN-gamma-binding protein.
Authors: Nuara, A.A. / Walter, L.J. / Logsdon, N.J. / Yoon, S.I. / Jones, B.C. / Schriewer, J.M. / Buller, R.M. / Walter, M.R.
History
DepositionNov 20, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
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_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Interferon gamma
R: Interferon-gamma binding protein C4R
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1517
Polymers45,0582
Non-polymers1,0935
Water4,270237
1
L: Interferon gamma
R: Interferon-gamma binding protein C4R
hetero molecules

L: Interferon gamma
R: Interferon-gamma binding protein C4R
hetero molecules

L: Interferon gamma
R: Interferon-gamma binding protein C4R
hetero molecules

L: Interferon gamma
R: Interferon-gamma binding protein C4R
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,60328
Polymers180,2338
Non-polymers4,37120
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area45680 Å2
MethodPISA
2
L: Interferon gamma
R: Interferon-gamma binding protein C4R
hetero molecules

L: Interferon gamma
R: Interferon-gamma binding protein C4R
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,30214
Polymers90,1164
Non-polymers2,18510
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area16970 Å2
MethodPISA
3
L: Interferon gamma
hetero molecules

L: Interferon gamma
hetero molecules

R: Interferon-gamma binding protein C4R
hetero molecules

R: Interferon-gamma binding protein C4R
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,30214
Polymers90,1164
Non-polymers2,18510
Water724
TypeNameSymmetry operationNumber
crystal symmetry operation7_545-x+1/2,y-1/2,-z+1/21
crystal symmetry operation8_455x-1/2,-y+1/2,-z+1/21
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area11080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.63, 119.13, 184.74
Angle α, β, γ (deg.)90, 90, 90
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11R-1-

PO4

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Components

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Protein , 2 types, 2 molecules LR

#1: Protein Interferon gamma / / IFN-gamma / Immune interferon


Mass: 16336.715 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IFNG / Production host: Escherichia coli (E. coli) / References: UniProt: P01579
#2: Protein Interferon-gamma binding protein C4R / Interferon-gamma receptor


Mass: 28721.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ectromelia virus / Genus: Orthopoxvirus / Gene: C4R, IFNGR / Cell line (production host): S2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q66793

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Sugars , 2 types, 2 molecules

#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 240 molecules

#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 237 / 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

Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.8M NaH2PO4/0.8M KH2PO4 solutions, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 5, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 28006 / Num. obs: 27031 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Rmerge(I) obs: 0.049 / Rsym value: 0.049

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Processing

Software
NameVersionClassification
SERGUIID22data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→20 Å / Isotropic thermal model: isotropic / Cross valid method: R-Free / σ(F): 0 / σ(I): -3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.245 1367 -random
Rwork0.219 ---
all0.219 28006 --
obs0.219 27031 99.6 %-
Displacement parametersBiso mean: 44.4 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3114 0 68 237 3419
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3

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