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- PDB-3uez: Crystal structure of the human Colony-Stimulating Factor 1 (hCSF-... -

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Basic information

Entry
Database: PDB / ID: 3uez
TitleCrystal structure of the human Colony-Stimulating Factor 1 (hCSF-1) cytokine in complex with the viral receptor BARF1
Components
  • Macrophage colony-stimulating factor 1
  • Secreted protein BARF1
KeywordsCYTOKINE RECEPTOR/CYTOKINE / VIRAL RECEPTOR / RTKIII / EXTRACELLULAR / CYTOKINE RECEPTOR-CYTOKINE complex / CYTOKINE / FOUR-HELIX BUNDLE / GLYCOPROTEIN / IMMUNOGLOBULIN DOMAIN / ONCOGENE / RECEPTOR / CYTOKINE/SIGNALING / PROTEIN COMPLEX
Function / homology
Function and homology information


regulation of macrophage derived foam cell differentiation / mammary gland fat development / positive regulation of macrophage colony-stimulating factor signaling pathway / macrophage homeostasis / monocyte activation / macrophage colony-stimulating factor receptor binding / monocyte homeostasis / osteoclast proliferation / positive regulation of macrophage migration / developmental process involved in reproduction ...regulation of macrophage derived foam cell differentiation / mammary gland fat development / positive regulation of macrophage colony-stimulating factor signaling pathway / macrophage homeostasis / monocyte activation / macrophage colony-stimulating factor receptor binding / monocyte homeostasis / osteoclast proliferation / positive regulation of macrophage migration / developmental process involved in reproduction / positive regulation of odontogenesis of dentin-containing tooth / CSF1-CSF1R complex / macrophage colony-stimulating factor signaling pathway / positive regulation of microglial cell migration / mammary duct terminal end bud growth / microglial cell proliferation / positive regulation of macrophage differentiation / positive regulation of macrophage derived foam cell differentiation / positive regulation of mononuclear cell proliferation / myeloid leukocyte migration / neutrophil homeostasis / positive regulation of multicellular organism growth / positive regulation of monocyte differentiation / positive regulation of osteoclast differentiation / positive regulation of Ras protein signal transduction / branching involved in mammary gland duct morphogenesis / positive regulation of cell-matrix adhesion / Other interleukin signaling / positive regulation of macrophage chemotaxis / Interleukin-10 signaling / monocyte differentiation / macrophage differentiation / regulation of ossification / positive regulation of protein kinase activity / homeostasis of number of cells within a tissue / cell surface receptor protein tyrosine kinase signaling pathway / positive regulation of protein metabolic process / osteoclast differentiation / cytokine activity / response to ischemia / Post-translational protein phosphorylation / growth factor activity / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Signaling by CSF1 (M-CSF) in myeloid cells / Ras protein signal transduction / nuclear body / positive regulation of cell migration / inflammatory response / endoplasmic reticulum lumen / innate immune response / positive regulation of cell population proliferation / positive regulation of gene expression / perinuclear region of cytoplasm / protein homodimerization activity / extracellular space / extracellular region / identical protein binding / membrane / plasma membrane
Similarity search - Function
Macrophage colony stimulating factor-1 / Macrophage colony stimulating factor-1 (CSF-1) / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold ...Macrophage colony stimulating factor-1 / Macrophage colony stimulating factor-1 (CSF-1) / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Secreted protein BARF1 / Macrophage colony-stimulating factor 1
Similarity search - Component
Biological speciesHuman herpesvirus 4 (Epstein-Barr virus)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.414 Å
AuthorsElegheert, J. / Bracke, N. / Savvides, S.N.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: Allosteric competitive inactivation of hematopoietic CSF-1 signaling by the viral decoy receptor BARF1
Authors: Elegheert, J. / Bracke, N. / Pouliot, P. / Gutsche, I. / Shkumatov, A.V. / Tarbouriech, N. / Verstraete, K. / Bekaert, A. / Burmeister, W.P. / Svergun, D.I. / Lambrecht, B.N. / Vergauwen, B. / Savvides, S.N.
History
DepositionOct 31, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 22, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
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 / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_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
A: Secreted protein BARF1
B: Secreted protein BARF1
C: Secreted protein BARF1
D: Secreted protein BARF1
E: Macrophage colony-stimulating factor 1
F: Macrophage colony-stimulating factor 1
G: Macrophage colony-stimulating factor 1
H: Macrophage colony-stimulating factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,47012
Polymers165,1238
Non-polymers2,3464
Water00
1
A: Secreted protein BARF1
D: Secreted protein BARF1
E: Macrophage colony-stimulating factor 1
F: Macrophage colony-stimulating factor 1
hetero molecules

A: Secreted protein BARF1
D: Secreted protein BARF1
E: Macrophage colony-stimulating factor 1
F: Macrophage colony-stimulating factor 1
hetero molecules

A: Secreted protein BARF1
D: Secreted protein BARF1
E: Macrophage colony-stimulating factor 1
F: Macrophage colony-stimulating factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)251,20418
Polymers247,68512
Non-polymers3,5196
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area32770 Å2
ΔGint-59 kcal/mol
Surface area89330 Å2
MethodPISA
2
B: Secreted protein BARF1
C: Secreted protein BARF1
G: Macrophage colony-stimulating factor 1
H: Macrophage colony-stimulating factor 1
hetero molecules

B: Secreted protein BARF1
C: Secreted protein BARF1
G: Macrophage colony-stimulating factor 1
H: Macrophage colony-stimulating factor 1
hetero molecules

B: Secreted protein BARF1
C: Secreted protein BARF1
G: Macrophage colony-stimulating factor 1
H: Macrophage colony-stimulating factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)251,20418
Polymers247,68512
Non-polymers3,5196
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area32630 Å2
ΔGint-66 kcal/mol
Surface area88770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)235.240, 235.240, 95.710
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein
Secreted protein BARF1 / 33 kDa early protein / p33


Mass: 23412.654 Da / Num. of mol.: 4 / Mutation: T169S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 4 (Epstein-Barr virus)
Strain: B95-8 / Gene: BARF1 / Plasmid: pHLSec / Cell (production host): HEK293 / Production host: Homo Sapiens (human) / References: UniProt: P03228
#2: Protein
Macrophage colony-stimulating factor 1 / CSF-1 / M-CSF / MCSF / Lanimostim / Processed macrophage colony-stimulating factor 1


Mass: 17868.219 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 33-181
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSF1 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) CodonPlus RIL / References: UniProt: P09603
#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.: 4
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

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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: 3.09 Å3/Da / Density % sol: 60.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris HCl, 1.0M ammonium sulphate, pH 8.50, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9714 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 11, 2009
RadiationMonochromator: Bartels monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9714 Å / Relative weight: 1
ReflectionResolution: 3.4→58.81 Å / Num. all: 25862 / Num. obs: 25862 / % possible obs: 96.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 3.41→3.5 Å / % possible all: 90.6

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: dev_874) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.414→40 Å / SU ML: 1 / σ(F): 1.96 / Phase error: 27.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2735 1296 5.01 %RANDOM
Rwork0.2314 ---
all0.2336 25859 --
obs0.2336 25859 96.41 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 26.999 Å2 / ksol: 0.296 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.9074 Å20 Å20 Å2
2---5.9074 Å20 Å2
3---11.8149 Å2
Refinement stepCycle: LAST / Resolution: 3.414→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10531 0 156 0 10687
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00210971
X-RAY DIFFRACTIONf_angle_d0.64314855
X-RAY DIFFRACTIONf_dihedral_angle_d17.3624041
X-RAY DIFFRACTIONf_chiral_restr0.0381696
X-RAY DIFFRACTIONf_plane_restr0.0021869
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.414-3.55070.3151430.2846257492
3.5507-3.71220.3411430.2759273797
3.7122-3.90790.32221450.2461279898
3.9079-4.15270.2711440.2171277397
4.1527-4.47320.24411450.203272298
4.4732-4.92320.25771450.2043277497
4.9232-5.63510.28181440.2223274997
5.6351-7.09770.26871420.2339272797
7.0977-58.81870.24231450.2348270995

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