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- PDB-6l4o: Crystal structure of API5-FGF2 complex -

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Basic information

Entry
Database: PDB / ID: 6l4o
TitleCrystal structure of API5-FGF2 complex
Components
  • Apoptosis inhibitor 5
  • Fibroblast growth factor 2
KeywordsSTRUCTURAL PROTEIN / API5 / FGF2 / complex
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 lens fiber cell differentiation / positive regulation of neuroepithelial cell differentiation / regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / response to wortmannin / positive regulation of endothelial cell chemotaxis to fibroblast growth factor / TGFBR3 regulates FGF2 signaling / positive regulation of cell fate specification / regulation of retinal cell programmed cell death ...growth factor dependent regulation of skeletal muscle satellite cell proliferation / positive regulation of inner ear auditory receptor cell differentiation / positive regulation of lens fiber cell differentiation / positive regulation of neuroepithelial cell differentiation / regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / response to wortmannin / positive regulation of endothelial cell chemotaxis to fibroblast growth factor / TGFBR3 regulates FGF2 signaling / 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 / negative regulation of fibroblast growth factor receptor signaling pathway / chemokine binding / POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation / positive regulation of cerebellar granule cell precursor proliferation / cerebellar granule cell precursor proliferation / Formation of the nephric duct / positive regulation of epithelial tube formation / receptor-receptor interaction / regulation of endothelial cell chemotaxis to fibroblast growth factor / inner ear auditory receptor cell differentiation / hyaluronan catabolic process / negative regulation of wound healing / positive regulation of stem cell differentiation / Signaling by activated point mutants of FGFR3 / FGFR3c ligand binding and activation / Phospholipase C-mediated cascade; FGFR3 / histone H3K9me2/3 reader activity / glial cell differentiation / stem cell development / embryonic morphogenesis / FGFR2b ligand binding and activation / behavioral response to ethanol / fibroblast growth factor receptor binding / FGFR2c ligand binding and activation / Activated point mutants of FGFR2 / FGFR4 ligand binding and activation / Phospholipase C-mediated cascade; FGFR2 / FGFR1b ligand binding and activation / mammary gland epithelial cell differentiation / Phospholipase C-mediated cascade; FGFR4 / angiogenesis involved in coronary vascular morphogenesis / 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 apoptotic process / Developmental Lineage of Pancreatic Acinar Cells / positive regulation of blood vessel branching / negative regulation of fibroblast migration / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / endothelial cell proliferation / cell migration involved in sprouting angiogenesis / embryo development ending in birth or egg hatching / fibroblast apoptotic process / positive regulation of vascular endothelial cell proliferation / positive regulation of endothelial cell chemotaxis / positive regulation of cell migration involved in sprouting angiogenesis / positive regulation of DNA biosynthetic process / branching involved in ureteric bud morphogenesis / Signaling by FGFR2 IIIa TM / PI-3K cascade:FGFR3 / Syndecan interactions / PI-3K cascade:FGFR2 / positive regulation of neuroblast proliferation / PI-3K cascade:FGFR4 / PI-3K cascade:FGFR1 / positive regulation of stem cell proliferation / positive regulation of sprouting angiogenesis / chemoattractant activity / fibroblast growth factor binding / negative regulation of blood vessel endothelial cell migration / positive regulation of cell division / Non-integrin membrane-ECM interactions / PI3K Cascade / neuroblast proliferation / positive regulation of blood vessel endothelial cell migration / fibroblast growth factor receptor signaling pathway / response to axon injury / regulation of angiogenesis / canonical Wnt signaling pathway / positive regulation of osteoblast differentiation / SHC-mediated cascade:FGFR3 / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / negative regulation of stem cell proliferation / SHC-mediated cascade:FGFR1 / FRS-mediated FGFR3 signaling / positive regulation of cardiac muscle cell proliferation / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / positive regulation of vascular associated smooth muscle cell proliferation
Similarity search - Function
Apoptosis inhibitory 5 / Apoptosis inhibitory protein 5 (API5) / 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 ...Apoptosis inhibitory 5 / Apoptosis inhibitory protein 5 (API5) / 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 / Armadillo-like helical / Armadillo-type fold / Mainly Beta
Similarity search - Domain/homology
Fibroblast growth factor 2 / Apoptosis inhibitor 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLee, B.I. / Bong, S.M.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (Korea)NRF-2015R1A2A2A01003004 Korea, Republic Of
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Regulation of mRNA export through API5 and nuclear FGF2 interaction.
Authors: Bong, S.M. / Bae, S.H. / Song, B. / Gwak, H. / Yang, S.W. / Kim, S. / Nam, S. / Rajalingam, K. / Oh, S.J. / Kim, T.W. / Park, S. / Jang, H. / Lee, B.I.
History
DepositionOct 18, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.year
Revision 1.2Jun 24, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Apoptosis inhibitor 5
B: Fibroblast growth factor 2


Theoretical massNumber of molelcules
Total (without water)80,9662
Polymers80,9662
Non-polymers00
Water63135
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: surface plasmon resonance, API5-FGF2 complex structure include monomer form of API5 and monomer form of FGF2
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint6 kcal/mol
Surface area27350 Å2
Unit cell
Length a, b, c (Å)46.862, 76.523, 208.158
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Apoptosis inhibitor 5 / API-5 / Antiapoptosis clone 11 protein / AAC-11 / Cell migration-inducing gene 8 protein / ...API-5 / Antiapoptosis clone 11 protein / AAC-11 / Cell migration-inducing gene 8 protein / Fibroblast growth factor 2-interacting factor / FIF / Protein XAGL


Mass: 61250.801 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: API5, MIG8 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BZZ5
#2: Protein Fibroblast growth factor 2 / FGF-2 / Basic fibroblast growth factor / bFGF / Heparin-binding growth factor 2 / HBGF-2


Mass: 19715.398 Da / Num. of mol.: 1 / Mutation: C211S,C229S
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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 2.3 Å3/Da / Density % sol: 46.63 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 100mM Na-HEPES (pH 7.5), 100mM potassium chloride, 10% (v/v) polyethylene glycol (PEG) 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 22727 / % possible obs: 94.5 % / Redundancy: 4.4 % / Biso Wilson estimate: 45.42 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 15.7
Reflection shellResolution: 2.6→2.64 Å / Rmerge(I) obs: 0.375 / Num. unique obs: 22727

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3U0R, 1BAS

3u0r

1bas


Resolution: 2.6→37.63 Å / SU ML: 0.4212 / Cross valid method: FREE R-VALUE / σ(F): 1.47 / Phase error: 28.7567
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2615 1162 5.12 %
Rwork0.224 21534 -
obs0.226 22696 94.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.5 Å2
Refinement stepCycle: LAST / Resolution: 2.6→37.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4442 0 0 35 4477
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00134519
X-RAY DIFFRACTIONf_angle_d0.38626094
X-RAY DIFFRACTIONf_chiral_restr0.0336697
X-RAY DIFFRACTIONf_plane_restr0.0035780
X-RAY DIFFRACTIONf_dihedral_angle_d12.5432781
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.710.38771190.36072385X-RAY DIFFRACTION85.43
2.71-2.860.34511400.32352541X-RAY DIFFRACTION91.13
2.86-3.040.36821300.30052595X-RAY DIFFRACTION92.56
3.04-3.270.32721380.26842671X-RAY DIFFRACTION94.58
3.27-3.60.31921620.23842729X-RAY DIFFRACTION96.33
3.6-4.120.25071270.19872808X-RAY DIFFRACTION98.46
4.12-5.190.19461610.17282863X-RAY DIFFRACTION99.34
5.19-37.630.21211850.18742942X-RAY DIFFRACTION97.96

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