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- PDB-1rv6: Crystal Structure of PlGF in Complex with Domain 2 of VEGFR1 -

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Basic information

Entry
Database: PDB / ID: 1rv6
TitleCrystal Structure of PlGF in Complex with Domain 2 of VEGFR1
Components
  • FLT1 protein
  • placenta growth factor (PlGF)
KeywordsHORMONE/GROWTH FACTOR/RECEPTOR / PlGF / VEGF family / cystine knot / growth factor / ligand-receptor complex / specificity / HORMONE-GROWTH FACTOR-RECEPTOR COMPLEX
Function / homology
Function and homology information


vascular endothelial growth factor receptor-1 signaling pathway / vascular endothelial growth factor receptor binding / VEGF ligand-receptor interactions / hyaloid vascular plexus regression / positive regulation of mast cell chemotaxis / Neurophilin interactions with VEGF and VEGFR / VEGF binds to VEGFR leading to receptor dimerization / embryonic morphogenesis / induction of positive chemotaxis / negative regulation of vascular endothelial cell proliferation ...vascular endothelial growth factor receptor-1 signaling pathway / vascular endothelial growth factor receptor binding / VEGF ligand-receptor interactions / hyaloid vascular plexus regression / positive regulation of mast cell chemotaxis / Neurophilin interactions with VEGF and VEGFR / VEGF binds to VEGFR leading to receptor dimerization / embryonic morphogenesis / induction of positive chemotaxis / negative regulation of vascular endothelial cell proliferation / sprouting angiogenesis / blood vessel morphogenesis / vascular endothelial growth factor signaling pathway / growth factor binding / chemoattractant activity / monocyte chemotaxis / positive regulation of cell division / cellular response to vascular endothelial growth factor stimulus / vascular endothelial growth factor receptor signaling pathway / transmembrane receptor protein tyrosine kinase activity / positive regulation of MAP kinase activity / cell surface receptor protein tyrosine kinase signaling pathway / growth factor activity / placental growth factor receptor activity / insulin receptor activity / vascular endothelial growth factor receptor activity / hepatocyte growth factor receptor activity / macrophage colony-stimulating factor receptor activity / platelet-derived growth factor alpha-receptor activity / platelet-derived growth factor beta-receptor activity / stem cell factor receptor activity / boss receptor activity / protein tyrosine kinase collagen receptor activity / brain-derived neurotrophic factor receptor activity / transmembrane-ephrin receptor activity / GPI-linked ephrin receptor activity / epidermal growth factor receptor activity / fibroblast growth factor receptor activity / insulin-like growth factor receptor activity / receptor protein-tyrosine kinase / peptidyl-tyrosine phosphorylation / positive regulation of angiogenesis / cell migration / cell-cell signaling / actin cytoskeleton / heparin binding / protein autophosphorylation / cell differentiation / response to hypoxia / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / positive regulation of MAPK cascade / endosome / positive regulation of cell migration / focal adhesion / positive regulation of cell population proliferation / signal transduction / extracellular space / extracellular region / ATP binding / membrane / plasma membrane / cytosol
Similarity search - Function
Vascular endothelial growth factor receptor 1 (VEGFR1) / VEGFR-2, transmembrane domain / : / : / : / VEGFR-2 Transmembrane domain / Vascular endothelial growth factor receptor 1-like, Ig-like domain / VEGFR1-3, N-terminal Ig-like domain / VEGFR-1-like, immunoglobulin-like domain / PDGF/VEGF domain ...Vascular endothelial growth factor receptor 1 (VEGFR1) / VEGFR-2, transmembrane domain / : / : / : / VEGFR-2 Transmembrane domain / Vascular endothelial growth factor receptor 1-like, Ig-like domain / VEGFR1-3, N-terminal Ig-like domain / VEGFR-1-like, immunoglobulin-like domain / PDGF/VEGF domain / Platelet-derived growth factor, conserved site / PDGF/VEGF domain / Platelet-derived growth factor (PDGF) family signature. / Platelet-derived growth factor (PDGF) family profile. / Platelet-derived and vascular endothelial growth factors (PDGF, VEGF) family / Tyrosine-protein kinase, receptor class III, conserved site / Receptor tyrosine kinase class III signature. / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Cystine-knot cytokine / Immunoglobulin / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / : / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / Ribbon / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Immunoglobulin subtype / Immunoglobulin / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Immunoglobulins / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Vascular endothelial growth factor receptor 1 / Placenta growth factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsChristinger, H.W. / Fuh, G. / de Vos, A.M. / Wiesmann, C.
Citation
Journal: J.Biol.Chem. / Year: 2004
Title: The crystal structure of placental growth factor in complex with domain 2 of vascular endothelial growth factor receptor-1.
Authors: Christinger, H.W. / Fuh, G. / de Vos, A.M. / Wiesmann, C.
#1: Journal: Cell(Cambridge,Mass.) / Year: 1997
Title: Crystal structure at 1.7 A resolution of VEGF in complex with domain 2 of the Flt-1 receptor
Authors: Wiesmann, C. / Fuh, G. / Christinger, C.H. / Eigenbrot, C. / Wells, J.A. / de Vos, A.M.
#2: Journal: J.Biol.Chem. / Year: 2001
Title: The crystal structure of human placenta growth factor-1 (PlGF-1), an angiogenic protein, at 2.0 A resolution.
Authors: Iyer, S. / Demetres, D. / Leonidas, G. / Swaminathan, J. / Maglione, D. / Battisti, M. / Tucci, M. / Persico, G. / Acharya, K.R.
History
DepositionDec 12, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
V: placenta growth factor (PlGF)
W: placenta growth factor (PlGF)
X: FLT1 protein
Y: FLT1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4035
Polymers46,1214
Non-polymers2821
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6190 Å2
ΔGint-50 kcal/mol
Surface area19630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.281, 71.979, 115.346
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 placenta growth factor (PlGF)


Mass: 11609.339 Da / Num. of mol.: 2 / Fragment: Receptor binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P49763
#2: Protein FLT1 protein


Mass: 11451.219 Da / Num. of mol.: 2 / Fragment: domain-2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P17948
#3: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.68 Å3/Da / Density % sol: 53.73 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
125 %PEG40001reservoir
20.1 Mammonium sulfate1reservoir
30.02 %1reservoirNaN3
40.1 MBTP1reservoirpH6.5
56.5 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.45→25 Å / Num. all: 17048 / Num. obs: 15482 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Rsym value: 0.046 / Net I/σ(I): 16
Reflection shellResolution: 2.45→2.54 Å / Rsym value: 0.161 / % possible all: 99.2
Reflection
*PLUS
Lowest resolution: 25 Å / Num. measured all: 72785 / Rmerge(I) obs: 0.046
Reflection shell
*PLUS
% possible obs: 99.2 % / Rmerge(I) obs: 0.161

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Processing

Software
NameVersionClassification
REFMAC5.1.07refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FLT

1flt


Resolution: 2.45→20 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.886 / SU B: 8.654 / SU ML: 0.198 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / ESU R: 0.514 / ESU R Free: 0.295 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26022 1153 6.9 %RANDOM
Rwork0.19367 ---
all0.19843 16661 --
obs0.19843 15482 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.659 Å2
Baniso -1Baniso -2Baniso -3
1--0.78 Å20 Å20 Å2
2---0.95 Å20 Å2
3---1.74 Å2
Refinement stepCycle: LAST / Resolution: 2.45→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2985 0 19 161 3165
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0213078
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5561.9714184
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6865369
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.16822.632133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.71415533
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0831528
X-RAY DIFFRACTIONr_chiral_restr0.1030.2479
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022272
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2160.21185
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2180
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1730.256
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1470.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it3.0082.51867
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.64953070
X-RAY DIFFRACTIONr_scbond_it3.7492.51211
X-RAY DIFFRACTIONr_scangle_it5.40551114
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.45→2.5 Å / Total num. of bins used: 25 /
RfactorNum. reflection
Rfree0.297 59
Rwork0.246 845
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)
19.08220.9677-0.85031.40920.25590.90210.1207-0.38530.30490.1251-0.15150.079-0.0687-0.00040.03070.07830.0192-0.02140.06340.00690.01647.629132.825517.8849
28.72912.84520.42751.13550.45340.06430.1476-0.319-0.14550.1205-0.1544-0.0760.09320.00690.00680.10140.0112-0.00730.09540.0320.071822.291723.736419.5114
33.62240.688-0.11722.55490.87639.72490.037-0.0812-0.29240.07360.08970.11660.7811-0.4831-0.12670.2635-0.0617-0.0470.07490.04240.1206-4.98863.548412.7052
411.04440.0652-3.93526.2688-2.219210.51230.59860.40171.3665-0.3208-0.0489-0.6714-0.70680.2567-0.54970.3252-0.03510.11980.16220.10210.491135.583249.75.856
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1VA22 - 1154 - 97
2X-RAY DIFFRACTION2WB21 - 1153 - 97
3X-RAY DIFFRACTION3XC133 - 2244 - 95
4X-RAY DIFFRACTION4YD133 - 2244 - 95
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.26 / Rfactor Rwork: 0.198
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.013
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.6

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