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- PDB-4fa8: Multi-pronged modulation of cytokine signaling -

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Basic information

Entry
Database: PDB / ID: 4fa8
TitleMulti-pronged modulation of cytokine signaling
Components
  • Macrophage colony-stimulating factor 1
  • Secreted protein BARF1
KeywordsViral Protein/Cytokine / immunoglobulin-like domains / 4-helix bundle fold / Viral Protein-Cytokine 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 / monocyte homeostasis / macrophage homeostasis / macrophage colony-stimulating factor receptor binding / positive regulation of macrophage migration / osteoclast proliferation / positive regulation of odontogenesis of dentin-containing tooth / 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 / monocyte homeostasis / macrophage homeostasis / macrophage colony-stimulating factor receptor binding / positive regulation of macrophage migration / osteoclast proliferation / positive regulation of odontogenesis of dentin-containing tooth / developmental process involved in reproduction / CSF1-CSF1R complex / monocyte activation / macrophage colony-stimulating factor signaling pathway / positive regulation of microglial cell migration / mammary duct terminal end bud growth / microglial cell proliferation / positive regulation of mononuclear cell proliferation / positive regulation of macrophage differentiation / myeloid leukocyte migration / neutrophil homeostasis / positive regulation of monocyte differentiation / positive regulation of multicellular organism growth / 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 / Other interleukin signaling / positive regulation of cell-matrix adhesion / positive regulation of macrophage chemotaxis / Interleukin-10 signaling / positive regulation of protein metabolic process / monocyte differentiation / macrophage differentiation / regulation of ossification / Transcriptional and post-translational regulation of MITF-M expression and activity / homeostasis of number of cells within a tissue / cell surface receptor protein tyrosine kinase signaling pathway / osteoclast differentiation / response to ischemia / cytokine activity / 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 / endoplasmic reticulum lumen / 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 / membrane / plasma membrane
Similarity search - Function
: / BARF1 second Ig-like domain / 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 ...: / BARF1 second Ig-like domain / 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 / Immunoglobulin-like fold / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Macrophage colony-stimulating factor 1 / Secreted protein BARF1
Similarity search - Component
Biological speciesHuman herpesvirus 4 (Epstein-Barr virus)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsHe, X. / Shim, A.H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Multipronged attenuation of macrophage-colony stimulating factor signaling by Epstein-Barr virus BARF1.
Authors: Shim, A.H. / Chang, R.A. / Chen, X. / Longnecker, R. / He, X.
History
DepositionMay 21, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_PDB_caveat / 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.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 / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 20, 2024Group: 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_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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


Theoretical massNumber of molelcules
Total (without water)121,97112
Polymers119,5486
Non-polymers2,4236
Water7,963442
1
A: Secreted protein BARF1
B: 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
hetero molecules

A: Secreted protein BARF1
B: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)243,94224
Polymers239,09612
Non-polymers4,84712
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area34380 Å2
ΔGint-43 kcal/mol
Surface area94120 Å2
MethodPISA
2
A: Secreted protein BARF1
B: Secreted protein BARF1
D: Secreted protein BARF1
hetero molecules

A: Secreted protein BARF1
B: Secreted protein BARF1
D: Secreted protein BARF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,52612
Polymers136,0076
Non-polymers3,5196
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area19830 Å2
ΔGint-19 kcal/mol
Surface area55070 Å2
MethodPISA
3
E: Macrophage colony-stimulating factor 1
hetero molecules

E: Macrophage colony-stimulating factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8054
Polymers34,3632
Non-polymers4422
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area2060 Å2
ΔGint-3 kcal/mol
Surface area15890 Å2
MethodPISA
4
F: Macrophage colony-stimulating factor 1
G: Macrophage colony-stimulating factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8054
Polymers34,3632
Non-polymers4422
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-2 kcal/mol
Surface area15660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)199.554, 162.701, 57.337
Angle α, β, γ (deg.)90.00, 95.87, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-447-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31D
12E
22F
32G

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALLEULEUAA21 - 2193 - 201
21VALVALLEULEUBB21 - 2193 - 201
31VALVALLEULEUDC21 - 2193 - 201
12ASPASPCYSCYSED2 - 1461 - 145
22ASPASPCYSCYSFE2 - 1461 - 145
32ASPASPCYSCYSGF2 - 1461 - 145

NCS ensembles :
ID
1
2
Detailsthe biological assembly of BARF1 is a hexamer / the biological unit of M-CSF is a dimer

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Components

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


Mass: 22667.824 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 4 (Epstein-Barr virus)
Gene: BARF1 / Organ (production host): Human Embryonic Kidney cells / Production host: Homo sapiens (human) / References: UniProt: P0CW72
#2: Protein Macrophage colony-stimulating factor 1 / CSF-1 / M-CSF / MCSF / Lanimostim / Processed macrophage colony-stimulating factor 1


Mass: 17181.467 Da / Num. of mol.: 3 / Fragment: UNP residues 36-180
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSF1 / Organ (production host): Human Embryonic Kidney cells / Production host: Homo sapiens (human) / 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.: 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: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 442 / 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: 3.87 Å3/Da / Density % sol: 68.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 8% PEG8000, 0.1M imidazole pH8.0, 0.22M calcium acetate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 1, 2010
RadiationMonochromator: NA / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.2→125.83 Å / Num. all: 89831 / Num. obs: 89831 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.2→2.3 Å / % possible all: 90.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.92 / SU B: 15.528 / SU ML: 0.179 / Cross valid method: THROUGHOUT / ESU R: 0.207 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26002 4499 5 %RANDOM
Rwork0.22163 ---
obs0.22353 85332 97.6 %-
all-89831 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.47 Å2
Baniso -1Baniso -2Baniso -3
1--3.47 Å20 Å2-2.85 Å2
2---2.13 Å20 Å2
3---5.77 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8075 0 159 442 8676
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.028453
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3741.96711475
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3685994
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.14824.427393
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.179151437
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0491539
X-RAY DIFFRACTIONr_chiral_restr0.0930.21302
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216304
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5671.55006
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.08128146
X-RAY DIFFRACTIONr_scbond_it1.86133448
X-RAY DIFFRACTIONr_scangle_it2.8984.53332
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1492medium positional0.340.5
11B1492medium positional0.460.5
11D1492medium positional0.380.5
22E1187medium positional0.510.5
22F1187medium positional0.510.5
22G1187medium positional0.660.5
11A1492medium thermal0.542
11B1492medium thermal0.52
11D1492medium thermal0.552
22E1187medium thermal0.562
22F1187medium thermal0.672
22G1187medium thermal0.582
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 325 -
Rwork0.382 5820 -
obs--92.09 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.42842.83621.08092.92420.77070.58430.2225-0.3629-0.00170.3008-0.2427-0.05730.0126-0.1420.02020.1239-0.00660.02130.1412-0.00580.0214.026-16.736-14.068
20.72131.52040.11565.7108-0.04610.0557-0.07290.1343-0.0582-0.37530.0636-0.21950.00510.06840.00930.1273-0.02920.03160.16960.03270.026136.33412.242-25.044
34.0947-1.04621.95540.5548-0.48610.961-0.1878-0.42560.21160.13460.06940.132-0.1403-0.23640.11840.1788-0.00110.01830.2365-0.030.138214.78739.9-13.691
42.8666-1.01961.68861.7143-1.8794.52180.2683-0.5603-0.38530.0706-0.00020.26261.0672-0.028-0.26810.60440.0248-0.0530.32210.02380.194410.63-56.005-10.526
54.6945-1.2277-0.83921.63620.08350.9273-0.03240.235-0.2598-0.3358-0.01370.11540.1108-0.03680.0460.2004-0.04760.02940.1723-0.01140.032368.32632.807-18.599
61.03920.08190.41582.83851.71542.0364-0.061-0.17390.10980.0275-0.02590.2455-0.0665-0.26020.0870.1166-0.00560.04370.2031-0.00640.116547.13855.9964.754
763.185-13.50930.488259.3154-42.71437.93141.53861.17440.1484-1.3649-0.2842.07181.38140.576-1.25460.42890.1954-0.15110.2505-0.15240.22610.563-10.009-21.049
8101.8406-31.425233.73953.9555-32.610322.35780.72011.0941.00180.171-0.1151.6803-0.00520.2702-0.60510.34630.1595-0.17990.6157-0.18640.356623.14622.169-28.665
90.5567-0.08652.748128.998114.275621.34720.2177-0.04590.002-0.1205-0.3865-0.00530.9818-0.47880.16880.1619-0.0639-0.05610.2718-0.01730.419716.95523.345-14.764
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A20 - 219
2X-RAY DIFFRACTION2B20 - 219
3X-RAY DIFFRACTION3D20 - 219
4X-RAY DIFFRACTION4E2 - 146
5X-RAY DIFFRACTION5F2 - 146
6X-RAY DIFFRACTION6G2 - 146
7X-RAY DIFFRACTION7A301 - 303
8X-RAY DIFFRACTION8B301 - 303
9X-RAY DIFFRACTION9D301 - 303

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