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- PDB-5x1o: PI(4,5)P2 lipid binding induced a reorientation of FGF2 molecules... -

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Basic information

Entry
Database: PDB / ID: 5x1o
TitlePI(4,5)P2 lipid binding induced a reorientation of FGF2 molecules near membrane surface to facilitate the unconventional oligomerization-dependent secretion process as revealed by a combined FTIR/NMR/X-ray study
ComponentsFibroblast growth factor 2Basic fibroblast growth factor
KeywordsPROTEIN BINDING / PI(4 / 5)P2 / Fibroblast growth factor 2
Function / homology
Function and homology information


growth factor dependent regulation of skeletal muscle satellite cell proliferation / positive regulation of inner ear auditory receptor cell differentiation / positive regulation of neuroepithelial cell differentiation / regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / positive regulation of lens fiber cell differentiation / positive regulation of cell fate specification / regulation of retinal cell programmed cell death / Formation of intermediate mesoderm / regulation of cell migration involved in sprouting angiogenesis / FGFRL1 modulation of FGFR1 signaling ...growth factor dependent regulation of skeletal muscle satellite cell proliferation / positive regulation of inner ear auditory receptor cell differentiation / positive regulation of neuroepithelial cell differentiation / regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / positive regulation of lens fiber cell differentiation / positive regulation of cell fate specification / regulation of retinal cell programmed cell death / Formation of intermediate mesoderm / regulation of cell migration involved in sprouting angiogenesis / FGFRL1 modulation of FGFR1 signaling / corticotropin hormone secreting cell differentiation / thyroid-stimulating hormone-secreting cell differentiation / chondroblast differentiation / lymphatic endothelial cell migration / chemokine binding / negative regulation of fibroblast growth factor receptor signaling pathway / POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation / positive regulation of cerebellar granule cell precursor proliferation / positive regulation of endothelial cell chemotaxis to fibroblast growth factor / cerebellar granule cell precursor proliferation / receptor-receptor interaction / positive regulation of stem cell differentiation / hyaluronan catabolic process / glial cell differentiation / regulation of endothelial cell chemotaxis to fibroblast growth factor / inner ear auditory receptor cell differentiation / negative regulation of wound healing / Signaling by activated point mutants of FGFR3 / FGFR3c ligand binding and activation / stem cell development / Phospholipase C-mediated cascade; FGFR3 / embryonic morphogenesis / FGFR2b ligand binding and activation / fibroblast growth factor receptor binding / angiogenesis involved in coronary vascular morphogenesis / FGFR2c ligand binding and activation / Activated point mutants of FGFR2 / positive regulation of epithelial tube formation / Phospholipase C-mediated cascade; FGFR2 / FGFR4 ligand binding and activation / FGFR1b ligand binding and activation / mammary gland epithelial cell differentiation / Phospholipase C-mediated cascade; FGFR4 / Signaling by activated point mutants of FGFR1 / FGFR1c ligand binding and activation / organ induction / Downstream signaling of activated FGFR1 / Phospholipase C-mediated cascade: FGFR1 / paracrine signaling / negative regulation of fibroblast migration / positive regulation of endothelial cell chemotaxis / endothelial cell proliferation / cell migration involved in sprouting angiogenesis / embryo development ending in birth or egg hatching / positive regulation of vascular endothelial cell proliferation / Signaling by FGFR2 IIIa TM / positive regulation of DNA biosynthetic process / Syndecan interactions / branching involved in ureteric bud morphogenesis / positive regulation of neuroblast proliferation / positive regulation of cell migration involved in sprouting angiogenesis / PI-3K cascade:FGFR3 / positive regulation of stem cell proliferation / positive regulation of sprouting angiogenesis / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR4 / PI-3K cascade:FGFR1 / chemoattractant activity / negative regulation of blood vessel endothelial cell migration / positive regulation of cell division / Non-integrin membrane-ECM interactions / neuroblast proliferation / PI3K Cascade / canonical Wnt signaling pathway / response to axon injury / positive regulation of blood vessel endothelial cell migration / fibroblast growth factor receptor signaling pathway / positive regulation of osteoblast differentiation / regulation of angiogenesis / SHC-mediated cascade:FGFR3 / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / SHC-mediated cascade:FGFR1 / negative regulation of stem cell proliferation / release of sequestered calcium ion into cytosol / FRS-mediated FGFR3 signaling / FRS-mediated FGFR2 signaling / positive regulation of cardiac muscle cell proliferation / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / FRS-mediated FGFR1 signaling / ERK1 and ERK2 cascade / positive regulation of vascular associated smooth muscle cell proliferation / Signaling by FGFR2 in disease / substantia nigra development / Signaling by FGFR1 in disease / positive regulation of endothelial cell proliferation / positive regulation of endothelial cell migration / nuclear receptor coactivator activity / phosphatidylinositol 3-kinase/protein kinase B signal transduction
Similarity search - Function
HBGF/FGF family signature. / Fibroblast growth factor family / Fibroblast growth factor / Acidic and basic fibroblast growth factor family. / Cytokine IL1/FGF / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Mainly Beta
Similarity search - Domain/homology
D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE / Fibroblast growth factor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsTsao, Y.H.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology, R.O.CMOST-103-2311-B-007-011-MY3 Taiwan
CitationJournal: To Be Published
Title: PI(4,5)P2 lipid binding induced a reorientation of FGF2 molecules near membrane surface to facilitate the unconventional oligomerization-dependent secretion process as revealed by a combined FTIR/NMR/X-ray study
Authors: Tsao, Y.H.
History
DepositionJan 26, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fibroblast growth factor 2
B: Fibroblast growth factor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7124
Polymers32,8722
Non-polymers8402
Water3,549197
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-6 kcal/mol
Surface area12990 Å2
Unit cell
Length a, b, c (Å)34.616, 67.346, 122.196
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Fibroblast growth factor 2 / Basic fibroblast growth factor / FGF-2 / Basic fibroblast growth factor / bFGF / Heparin-binding growth factor 2 / HBGF-2


Mass: 16435.857 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FGF2, FGFB / Production host: Escherichia coli (E. coli) / References: UniProt: P09038
#2: Chemical ChemComp-I3P / D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE / Inositol trisphosphate


Mass: 420.096 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15O15P3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O

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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: 2.17 Å3/Da / Density % sol: 43.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1M Sodium citrate, 0.2M Ammonium acetate, 30% PEG 4000

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.975 Å
DetectorType: ADSC QUANTUM 315r / Detector: DIFFRACTOMETER / Date: Dec 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 1.9→24.14 Å / Num. obs: 21395 / % possible obs: 92 % / Redundancy: 4.1 % / Net I/σ(I): 2.49

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementResolution: 1.9→24.137 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.02
RfactorNum. reflection% reflection
Rfree0.2763 1096 5.12 %
Rwork0.2247 --
obs0.2274 21393 91.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→24.137 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2046 0 48 197 2291
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082137
X-RAY DIFFRACTIONf_angle_d1.2192876
X-RAY DIFFRACTIONf_dihedral_angle_d17.4461281
X-RAY DIFFRACTIONf_chiral_restr0.066300
X-RAY DIFFRACTIONf_plane_restr0.009360
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9005-1.98690.34641000.27911853X-RAY DIFFRACTION69
1.9869-2.09160.31481250.28162352X-RAY DIFFRACTION87
2.0916-2.22260.35881240.27082518X-RAY DIFFRACTION92
2.2226-2.3940.28851420.25832571X-RAY DIFFRACTION94
2.394-2.63470.3471460.27012649X-RAY DIFFRACTION96
2.6347-3.01530.31231490.2342681X-RAY DIFFRACTION98
3.0153-3.79660.24841530.19862781X-RAY DIFFRACTION99
3.7966-24.13880.20651570.17622892X-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)
10.2619-0.0773-0.03182.2046-0.33810.5612-0.0289-0.0682-0.1688-0.1431-0.0012-0.16710.11610.04180.11920.199-0.0503-0.05740.17220.18550.481826.8505-5.0023256.9183
24.7631-0.6694-0.3813.01710.80764.37080.0730.2922-0.1501-0.5472-0.13820.3901-0.0507-0.16130.10010.21460.0216-0.0760.19760.03830.174526.46413.6033250.8463
32.6288-0.76011.40762.806-0.49054.54720.0542-0.1328-0.23410.1779-0.1275-0.32140.40640.503-0.02630.22510.0602-0.02990.13160.13870.276638.4473-2.3264258.1246
42.0534-1.7434-1.77732.99931.74443.2646-0.0136-0.3452-0.0157-0.24230.0671-0.2978-0.22740.2741-0.04740.1716-0.00730.01290.16830.05960.130536.5079.4552257.4453
51.1420.4701-0.13712.6302-1.47511.87910.0845-0.1623-0.3097-0.10130.16790.39250.1783-0.2815-0.04830.1935-0.0203-0.02330.37560.23610.341834.1949-1.8229266.3081
60.3802-0.33490.46440.3261-0.53081.07730.1041-0.2475-0.26480.023-0.0115-0.02240.07190.01130.1420.1538-0.0215-0.05070.33830.21760.181527.25853.0978265.6539
70.75970.44510.45280.93520.42332.49590.11580.0207-0.52010.1748-0.0434-0.00010.303-0.0497-0.14070.2052-0.0078-0.01970.1854-0.12830.305738.5687-0.1217232.637
82.35531.6971-1.04071.9302-0.62211.16930.16850.2810.040.33280.03740.2948-0.1665-0.1785-0.13320.17670.01490.03480.1429-0.05110.134932.336210.185230.7865
91.1701-0.6842-0.49171.84270.90392.1213-0.00810.1586-0.2238-0.0370.1269-0.24060.30510.27640.11430.12610.05970.03690.4293-0.25640.248136.5056-0.6636220.3148
100.2740.23980.2130.36770.47750.70030.02080.2899-0.19710.0048-0.01320.01090.1128-0.0914-0.03730.1246-0.0179-0.0140.4163-0.20530.154842.91535.213222.6853
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 18 through 30 )
2X-RAY DIFFRACTION2chain 'A' and (resid 31 through 48 )
3X-RAY DIFFRACTION3chain 'A' and (resid 49 through 67 )
4X-RAY DIFFRACTION4chain 'A' and (resid 68 through 87 )
5X-RAY DIFFRACTION5chain 'A' and (resid 88 through 103 )
6X-RAY DIFFRACTION6chain 'A' and (resid 104 through 144 )
7X-RAY DIFFRACTION7chain 'B' and (resid 18 through 67 )
8X-RAY DIFFRACTION8chain 'B' and (resid 68 through 89 )
9X-RAY DIFFRACTION9chain 'B' and (resid 90 through 108 )
10X-RAY DIFFRACTION10chain 'B' and (resid 109 through 144 )

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