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- PDB-4adq: CRYSTAL STRUCTURE OF THE MOUSE COLONY-STIMULATING FACTOR 1 (MCSF-... -

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Basic information

Entry
Database: PDB / ID: 4adq
TitleCRYSTAL STRUCTURE OF THE MOUSE COLONY-STIMULATING FACTOR 1 (MCSF-1) CYTOKINE IN COMPLEX WITH THE VIRAL RECEPTOR BARF1
Components
  • MACROPHAGE COLONY-STIMULATING FACTOR 1
  • SECRETED PROTEIN BARF1
KeywordsIMMUNE SYSTEM/RECEPTOR / IMMUNE SYSTEM-RECEPTOR COMPLEX / RTKIII / EXTRACELLULAR / CYTOKINE RECEPTOR-CYTOKINE COMPLEX / FOUR-HELIX BUNDLE / GLYCOPROTEIN / IMMUNOGLOBULIN DOMAIN / ONCOGENE / CYTOKINE/SIGNALING
Function / homology
Function and homology information


Other interleukin signaling / mammary gland fat development / positive regulation of macrophage colony-stimulating factor signaling pathway / monocyte homeostasis / macrophage homeostasis / macrophage colony-stimulating factor receptor binding / osteoclast proliferation / positive regulation of odontogenesis of dentin-containing tooth / developmental process involved in reproduction / CSF1-CSF1R complex ...Other interleukin signaling / mammary gland fat development / positive regulation of macrophage colony-stimulating factor signaling pathway / monocyte homeostasis / macrophage homeostasis / macrophage colony-stimulating factor receptor binding / osteoclast proliferation / positive regulation of odontogenesis of dentin-containing tooth / developmental process involved in reproduction / CSF1-CSF1R complex / macrophage colony-stimulating factor signaling pathway / positive regulation of microglial cell migration / Transcriptional and post-translational regulation of MITF-M expression and activity / mammary duct terminal end bud growth / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / microglial cell proliferation / positive regulation of macrophage 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 macrophage derived foam cell differentiation / branching involved in mammary gland duct morphogenesis / positive regulation of Ras protein signal transduction / positive regulation of leukocyte migration / positive regulation of cell-matrix adhesion / positive regulation of macrophage chemotaxis / monocyte differentiation / positive regulation of protein metabolic process / macrophage differentiation / regulation of ossification / homeostasis of number of cells within a tissue / osteoclast differentiation / cell surface receptor protein tyrosine kinase signaling pathway / response to ischemia / cytokine activity / growth factor activity / Ras protein signal transduction / nuclear body / inflammatory response / 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 / plasma membrane
Similarity search - Function
: / BARF1 second Ig-like domain / Macrophage colony stimulating factor-1 / Macrophage colony stimulating factor-1 (CSF-1) / Four-helical cytokine-like, core / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Secreted protein BARF1 / Macrophage colony-stimulating factor 1 / Secreted protein BARF1
Similarity search - Component
Biological speciesHuman gammaherpesvirus 4 (Epstein-Barr virus)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.5 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
DepositionJan 2, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 22, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2012Group: Database references
Revision 1.2Feb 28, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.gene_src_common_name / _entity_src_gen.host_org_common_name ..._entity_src_gen.gene_src_common_name / _entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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_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_database_status.status_code_sf / _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_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)167,64712
Polymers165,1398
Non-polymers2,5084
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)251,22818
Polymers247,70912
Non-polymers3,5196
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation2_555-y,x-y,z1
Buried area30930 Å2
ΔGint-186.5 kcal/mol
Surface area112620 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)251,71418
Polymers247,70912
Non-polymers4,0066
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation2_555-y,x-y,z1
Buried area31140 Å2
ΔGint-190.8 kcal/mol
Surface area112930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)234.750, 234.750, 96.040
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.6637, -0.748, 0.0052), (-0.7479, -0.6637, -0.0042), (0.0066, -0.0011, -1)0.3084, -0.102, -40.1119
2given(0.6625, -0.749, 0.0015), (-0.749, -0.6625, 0.007), (-0.0042, -0.0058, -1)0.0741, 0.0738, -40.4821
3given(0.6981, -0.7129, 0.0658), (-0.7063, -0.7009, -0.0996), (0.1172, 0.0231, -0.9928)1.7183, -6.3739, -83.1758
4given(0.6351, -0.7724, 0.0085), (-0.7724, -0.6349, 0.0175), (-0.0081, -0.0176, -0.9998)-0.5144, -1.523, -40.3845
5given(0.9922, -0.0871, -0.0888), (0.0911, 0.9949, 0.0429), (0.0846, -0.0507, 0.9951)-0.2093, -1.0458, -43.0755

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Components

#1: Protein
SECRETED PROTEIN BARF1 / BARF1 / 33 KDA EARLY PROTEIN / P33


Mass: 23412.654 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human gammaherpesvirus 4 (Epstein-Barr virus)
Strain: B95-8 / Plasmid: PHLSEC / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: P0CW72, UniProt: P03228*PLUS
#2: Protein
MACROPHAGE COLONY-STIMULATING FACTOR 1 / CSF-1 / M-CSF / MCSF / PROCESSED MACROPHAGE COLONY-STIMULATING FACTOR 1


Mass: 17872.107 Da / Num. of mol.: 4 / Fragment: RESIDUES 21-221
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus / Plasmid: PET15B / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): CODONPLUS RIL / References: UniProt: P07141
#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.: 3
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
#4: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
Compound detailsENGINEERED RESIDUE IN CHAIN A, THR 169 TO SER ENGINEERED RESIDUE IN CHAIN B, THR 169 TO SER ...ENGINEERED RESIDUE IN CHAIN A, THR 169 TO SER ENGINEERED RESIDUE IN CHAIN B, THR 169 TO SER ENGINEERED RESIDUE IN CHAIN C, THR 169 TO SER ENGINEERED RESIDUE IN CHAIN D, THR 169 TO SER
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: 3.38 Å3/Da / Density % sol: 61.4 % / Description: NONE
Crystal growpH: 8 / Details: pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97887
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 8, 2011 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97887 Å / Relative weight: 1
ReflectionResolution: 4.5→40 Å / Num. obs: 11082 / % possible obs: 94.5 % / Observed criterion σ(I): 2 / Redundancy: 1.7 % / Biso Wilson estimate: 138.7 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 5.7
Reflection shellResolution: 4.5→4.62 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 1.6 / % possible all: 93.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2CH8 AND 3UF5

2ch8

3uf5


Resolution: 4.5→117.375 Å / SU ML: 0.58 / σ(F): 1.96 / Phase error: 27.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2622 1112 10.04 %
Rwork0.2226 --
obs0.2265 11078 94.46 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 164.595 Å2 / ksol: 0.346 e/Å3
Displacement parametersBiso mean: 187.44 Å2
Baniso -1Baniso -2Baniso -3
1--22.3592 Å20 Å20 Å2
2---22.3592 Å20 Å2
3---44.7184 Å2
Refinement stepCycle: LAST / Resolution: 4.5→117.375 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10591 0 167 0 10758
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311044
X-RAY DIFFRACTIONf_angle_d0.71314959
X-RAY DIFFRACTIONf_dihedral_angle_d16.9244057
X-RAY DIFFRACTIONf_chiral_restr0.0411694
X-RAY DIFFRACTIONf_plane_restr0.0031900
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.5001-4.70490.3491410.3271252X-RAY DIFFRACTION94
4.7049-4.9530.3341360.28061245X-RAY DIFFRACTION94
4.953-5.26330.30691380.26571237X-RAY DIFFRACTION95
5.2633-5.66970.3411300.24611186X-RAY DIFFRACTION90
5.6697-6.24020.25861450.2231266X-RAY DIFFRACTION96
6.2402-7.14310.30481440.22711267X-RAY DIFFRACTION96
7.1431-8.9990.21271430.17511252X-RAY DIFFRACTION96
8.999-117.41490.18861350.17991261X-RAY DIFFRACTION95

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