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- PDB-1hmc: THREE-DIMENSIONAL STRUCTURE OF DIMERIC HUMAN RECOMBINANT MACROPHA... -

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Basic information

Entry
Database: PDB / ID: 1hmc
TitleTHREE-DIMENSIONAL STRUCTURE OF DIMERIC HUMAN RECOMBINANT MACROPHAGE COLONY STIMULATING FACTOR
ComponentsHUMAN MACROPHAGE COLONY STIMULATING FACTOR
KeywordsMACROPHAGE COLONY STIMULATING FACTOR
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 / branching involved in mammary gland duct morphogenesis / positive regulation of macrophage derived foam cell differentiation / 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 / macrophage differentiation / monocyte 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
Macrophage colony stimulating factor-1 / Macrophage colony stimulating factor-1 (CSF-1) / Four-helical cytokine-like, core
Similarity search - Domain/homology
Macrophage colony-stimulating factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsBohm, A. / Pandit, J. / Jancarik, J. / Halenbeck, R. / Koths, K. / Kim, S.-H.
CitationJournal: Science / Year: 1992
Title: Three-dimensional structure of dimeric human recombinant macrophage colony-stimulating factor.
Authors: Pandit, J. / Bohm, A. / Jancarik, J. / Halenbeck, R. / Koths, K. / Kim, S.H.
History
DepositionDec 22, 1993Processing site: BNL
Revision 1.0Apr 30, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HUMAN MACROPHAGE COLONY STIMULATING FACTOR
B: HUMAN MACROPHAGE COLONY STIMULATING FACTOR


Theoretical massNumber of molelcules
Total (without water)34,5852
Polymers34,5852
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.370, 64.750, 157.870
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.925055, -0.377203, -0.043564), (-0.378219, 0.905231, 0.193665), (-0.033617, 0.195637, -0.9801)
Vector: 140.3392, -8.14815, 355.75006)
DetailsTHE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN A WHEN APPLIED TO CHAIN B.

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Components

#1: Protein HUMAN MACROPHAGE COLONY STIMULATING FACTOR / Coordinate model: Cα atoms only


Mass: 17292.590 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P09603
Sequence detailsSEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: : ...SEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: :CSF1_HUMAN SWISS-PROT RESIDUE PDB ATOM RECORDS NAME NUMBER NAME CHAIN SEQ/INSERT CODE ASP 183 GLY A 150 VAL 184 HIS A 151

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.11 %
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.2 M1reservoirMgCl2
2100 mMTris-HCl1reservoir
323 %PEG40001reservoir
410 mg/mlprotein1drop

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2 Å / Num. obs: 18842 / Num. measured all: 65871 / Rmerge(I) obs: 0.0701

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.5→8 Å / Rfactor Rwork: 0.197 / Rfactor obs: 0.197 / σ(F): 2
Details: THE SEQUENCE THAT WAS CRYSTALLIZED RAN FROM RESIDUE 4 THROUGH RESIDUE 158. NEITHER OF THE TWO TERMINI COULD BE LOCATED IN THE ELECTRON DENSITY MAPS. THE TWO CRYSTALLOGRAPHICALLY UNIQUE ...Details: THE SEQUENCE THAT WAS CRYSTALLIZED RAN FROM RESIDUE 4 THROUGH RESIDUE 158. NEITHER OF THE TWO TERMINI COULD BE LOCATED IN THE ELECTRON DENSITY MAPS. THE TWO CRYSTALLOGRAPHICALLY UNIQUE MONOMERS HAVE BEEN ASSIGNED CHAIN INDICATORS *A* AND *B*.
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms291 0 0 0 291
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.019
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 8 Å / σ(F): 2 / Rfactor obs: 0.197
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3.7

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