[English] 日本語
Yorodumi
- PDB-5lxf: Crystal structure of the human Macrophage Colony Stimulating Fact... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5lxf
TitleCrystal structure of the human Macrophage Colony Stimulating Factor M- CSF_C31S variant
ComponentsMacrophage colony-stimulating factor 1
KeywordsSIGNALING PROTEIN / Drug design / rational protein engineering / receptor tyrosine kinase / osteoporosis
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; / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Macrophage colony-stimulating factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsShahar, A. / Papo, N. / Zarivach, R. / Kosloff, M. / Bakhman, A. / Rosenfeld, L. / Zur, Y. / Levaot, N.
CitationJournal: Biochem. J. / Year: 2017
Title: Engineering a monomeric variant of macrophage colony-stimulating factor (M-CSF) that antagonizes the c-FMS receptor.
Authors: Zur, Y. / Rosenfeld, L. / Bakhman, A. / Ilic, S. / Hayun, H. / Shahar, A. / Akabayov, B. / Kosloff, M. / Levaot, N. / Papo, N.
History
DepositionSep 21, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 31, 2018Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.3Oct 16, 2019Group: Data collection / Category: reflns / reflns_shell / Item: _reflns.pdbx_CC_half / _reflns_shell.pdbx_CC_half
Revision 1.4Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Macrophage colony-stimulating factor 1
B: Macrophage colony-stimulating factor 1


Theoretical massNumber of molelcules
Total (without water)42,7092
Polymers42,7092
Non-polymers00
Water4,702261
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-9 kcal/mol
Surface area15000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.271, 65.471, 158.632
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Macrophage colony-stimulating factor 1 / MCSF / Lanimostim


Mass: 21354.736 Da / Num. of mol.: 2 / Mutation: C31S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSF1 / Production host: Komagataella phaffii GS115 (fungus) / References: UniProt: P09603
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 1.88 Å3/Da / Density % sol: 34.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: 0.03M Bis-Tris pH 6.5; 0.17M Mg Formate; 16.67% PEG 3350; 0.07M Bis-Tris pH 5.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→39.66 Å / Num. obs: 20774 / % possible obs: 95.1 % / Redundancy: 8.7 % / Rpim(I) all: 0.025 / Net I/σ(I): 26.5
Reflection shellResolution: 2→2.03 Å / Redundancy: 8.2 % / Mean I/σ(I) obs: 1 / CC1/2: 0.727 / % possible all: 85.7

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UF2

3uf2


Resolution: 2→39.66 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2531 1027 4.94 %Random selection
Rwork0.1885 ---
obs0.1917 20774 85.32 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→39.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2407 0 0 261 2668
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092491
X-RAY DIFFRACTIONf_angle_d1.1763367
X-RAY DIFFRACTIONf_dihedral_angle_d7.0732147
X-RAY DIFFRACTIONf_chiral_restr0.062375
X-RAY DIFFRACTIONf_plane_restr0.006437
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.10540.331810.23051417X-RAY DIFFRACTION44
2.1054-2.23730.26251190.24362256X-RAY DIFFRACTION70
2.2373-2.41010.36911510.23612863X-RAY DIFFRACTION89
2.4101-2.65260.3011500.21363158X-RAY DIFFRACTION96
2.6526-3.03630.27991800.20143265X-RAY DIFFRACTION99
3.0363-3.8250.2541700.17543307X-RAY DIFFRACTION99
3.825-41.14510.19441760.15953481X-RAY DIFFRACTION99
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)
11.04050.1210.42022.32293.42475.07590.17440.0185-0.26390.44290.1031-0.15080.8822-0.1941-0.11980.111-0.04120.02240.1488-0.02360.2088-5.4147-16.626811.9395
20.4681-0.49310.17540.5141-0.18740.0644-0.3831-0.05890.17160.22770.0391-0.1091-0.77920.1686-0.16090.6325-0.0153-0.08490.1349-0.0190.269-4.32381.320125.5752
32.6573-1.6681.32164.52993.15845.27160.3013-0.61490.42481.3899-0.39820.9586-0.6026-0.73870.17020.6650.05890.03530.6894-0.30560.5359-17.46723.680510.5941
43.9821-1.27141.86292.0193-0.02915.1636-0.45610.19450.07950.14280.3269-0.2063-0.92810.71630.17670.2946-0.09950.02570.2341-0.05960.2272-0.9362-3.988713.6565
50.84820.2338-0.28160.10560.12961.02780.06390.114-0.02010.01430.1864-0.0382-0.04210.39080.13170.026-0.05660.03250.3281-0.14920.2491.9602-12.159111.2943
64.12650.0572-0.92540.22790.43311.077-0.20060.83571.2021-0.8986-0.0064-0.9837-1.69630.10360.01530.8664-0.1206-0.0680.4110.1140.5167-6.77113.63430.0327
70.48940.28270.51291.90110.91444.2973-0.11690.04910.22020.0033-0.19220.2522-1.0163-0.38930.09770.25220.0382-0.0330.2184-0.04290.2593-11.3795-3.961410.5809
82.56170.35210.67331.5734-2.64186.56140.19830.0024-0.48590.5571-0.0031-0.33160.69350.70750.01050.59250.1519-0.11240.263-0.04780.366410.3604-16.331646.9336
97.2825-2.11310.08952.46633.7919.2043-0.4160.57010.7987-0.42630.3654-0.3587-1.65490.69560.00540.4733-0.1581-0.03170.4757-0.02180.18433.9015-1.675428.2453
101.767-0.69930.69611.7544-0.22883.6801-0.1074-0.08860.3450.0245-0.0841-0.2918-0.07040.20640.03770.29440.0786-0.02580.0943-0.03580.28918.93935.624846.9958
113.85-0.07762.96411.09141.1674.51190.198-0.2758-0.04220.5636-0.0328-0.21430.4998-0.1249-0.120.39990.0557-0.02780.1286-0.02650.28175.7948-3.557751.2563
125.26281.9443-0.97471.26060.47033.2614-0.0784-0.14910.2930.0732-0.0780.281-0.0475-0.47860.2170.26830.0508-0.00330.1597-0.02710.2018-5.3914-10.830537.4545
131.7246-0.81980.56651.105-1.66032.89720.0857-0.0876-0.11820.85090.0273-0.17560.0893-0.07470.09180.51250.0266-0.03840.1012-0.00840.26711.969-15.10847.8893
141.13190.25870.79932.07830.0661.2943-0.0063-0.1009-0.00650.62460.1375-0.26380.2270.2204-0.00540.43510.0859-0.09190.1897-0.04210.256210.3242-1.41252.8353
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 25 )
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 38 )
3X-RAY DIFFRACTION3chain 'A' and (resid 39 through 45 )
4X-RAY DIFFRACTION4chain 'A' and (resid 46 through 71 )
5X-RAY DIFFRACTION5chain 'A' and (resid 72 through 90 )
6X-RAY DIFFRACTION6chain 'A' and (resid 91 through 102 )
7X-RAY DIFFRACTION7chain 'A' and (resid 103 through 147 )
8X-RAY DIFFRACTION8chain 'B' and (resid 2 through 24 )
9X-RAY DIFFRACTION9chain 'B' and (resid 25 through 31 )
10X-RAY DIFFRACTION10chain 'B' and (resid 32 through 45 )
11X-RAY DIFFRACTION11chain 'B' and (resid 46 through 63 )
12X-RAY DIFFRACTION12chain 'B' and (resid 64 through 71 )
13X-RAY DIFFRACTION13chain 'B' and (resid 72 through 90 )
14X-RAY DIFFRACTION14chain 'B' and (resid 91 through 150 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more