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- PDB-2xac: Structural Insights into the Binding of VEGF-B by VEGFR-1D2: Reco... -

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Basic information

Entry
Database: PDB / ID: 2xac
TitleStructural Insights into the Binding of VEGF-B by VEGFR-1D2: Recognition and Specificity
Components
  • VASCULAR ENDOTHELIAL GROWTH FACTOR B
  • VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 1
KeywordsTRANSFERASE/SIGNALING PROTEIN / TRANSFERASE-SIGNALING PROTEIN COMPLEX / ANGIOGENESIS / CYSTEINE-KNOT PROTEIN / MITOGEN / TRANSFERASE / SIGNALING PROTEIN
Function / homology
Function and homology information


vascular endothelial growth factor receptor-1 signaling pathway / placental growth factor receptor activity / positive regulation of vascular wound healing / vascular endothelial growth factor receptor 1 binding / vascular endothelial growth factor receptor binding / VEGF ligand-receptor interactions / positive regulation of mast cell chemotaxis / hyaloid vascular plexus regression / Neurophilin interactions with VEGF and VEGFR / VEGF binds to VEGFR leading to receptor dimerization ...vascular endothelial growth factor receptor-1 signaling pathway / placental growth factor receptor activity / positive regulation of vascular wound healing / vascular endothelial growth factor receptor 1 binding / vascular endothelial growth factor receptor binding / VEGF ligand-receptor interactions / positive regulation of mast cell chemotaxis / hyaloid vascular plexus regression / Neurophilin interactions with VEGF and VEGFR / VEGF binds to VEGFR leading to receptor dimerization / vascular endothelial growth factor receptor activity / embryonic morphogenesis / induction of positive chemotaxis / protein O-linked glycosylation / coronary vasculature development / sprouting angiogenesis / blood vessel morphogenesis / positive regulation of vascular endothelial growth factor receptor signaling pathway / negative regulation of vascular endothelial cell proliferation / vascular endothelial growth factor signaling pathway / positive regulation of peptidyl-tyrosine phosphorylation / growth factor binding / chemoattractant activity / positive regulation of MAP kinase activity / monocyte chemotaxis / positive regulation of cell division / cellular response to vascular endothelial growth factor stimulus / vascular endothelial growth factor receptor signaling pathway / cardiac muscle contraction / positive regulation of endothelial cell proliferation / transmembrane receptor protein tyrosine kinase activity / cell surface receptor protein tyrosine kinase signaling pathway / platelet alpha granule lumen / peptidyl-tyrosine phosphorylation / growth factor activity / receptor protein-tyrosine kinase / positive regulation of angiogenesis / cell migration / Platelet degranulation / heparin binding / actin cytoskeleton / protein autophosphorylation / negative regulation of neuron apoptotic process / cell differentiation / response to hypoxia / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / endosome / positive regulation of MAPK cascade / positive regulation of cell migration / negative regulation of gene expression / focal adhesion / positive regulation of cell population proliferation / negative regulation of apoptotic process / extracellular space / extracellular region / ATP binding / identical protein 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 / Ribbon / Immunoglobulin V-set domain / 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 / Vascular endothelial growth factor B
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å
AuthorsIyer, S. / Darley, P. / Acharya, K.R.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Structural Insights Into the Binding of Vegf-B by Vegfr-1D2: Recognition and Specificity
Authors: Iyer, S. / Darley, P. / Acharya, K.R.
History
DepositionMar 30, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 19, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 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
A: VASCULAR ENDOTHELIAL GROWTH FACTOR B
B: VASCULAR ENDOTHELIAL GROWTH FACTOR B
C: VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 1
X: VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8265
Polymers44,7344
Non-polymers921
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6020 Å2
ΔGint-45.2 kcal/mol
Surface area20920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.212, 65.526, 82.824
Angle α, β, γ (deg.)90.00, 90.26, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein VASCULAR ENDOTHELIAL GROWTH FACTOR B / VEGF-B / VEGF-RELATED FACTOR / VRF


Mass: 11157.050 Da / Num. of mol.: 2 / Fragment: RECEPTOR-BINDING DOMAIN, RESIDUES 31-129
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET-32 XA/LIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTAGAMI B (DE3) PLYSS / References: UniProt: P49765
#2: Protein VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 1 / VEGFR-1 / VASCULAR PERMEABILITY FACTOR RECEPTOR / TYROSINE-PROTEIN KINASE RECEPTOR FLT / TYROSINE- ...VEGFR-1 / VASCULAR PERMEABILITY FACTOR RECEPTOR / TYROSINE-PROTEIN KINASE RECEPTOR FLT / TYROSINE-PROTEIN KINASE FRT / FLT-1 / FMS-LIKE TYROSINE KINASE 1


Mass: 11209.933 Da / Num. of mol.: 2 / Fragment: DOMAIN 2, RESIDUES 129-226
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) CODONPLUS-RIPL
References: UniProt: P17948, receptor protein-tyrosine kinase
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.42 Å3/Da / Density % sol: 49.2 % / Description: NONE
Crystal growpH: 8
Details: 14% PEG 4000, 0.1M SODIUM CITRATE, PH 5.6 AND 0.2M LICL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979
DetectorType: ADSC CCD / Detector: CCD / Date: May 17, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.71→40 Å / Num. obs: 11510 / % possible obs: 85 % / Observed criterion σ(I): 0 / Redundancy: 11.8 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 12.5
Reflection shellResolution: 2.71→2.85 Å / Redundancy: 2 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 2.6 / % possible all: 47.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERFOR MRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2C7W AND 1FLT

2c7w

1flt


Resolution: 2.71→32.76 Å / Cor.coef. Fo:Fc: 0.871 / Cor.coef. Fo:Fc free: 0.801 / SU B: 25.128 / SU ML: 0.519 / Cross valid method: THROUGHOUT / ESU R Free: 0.606 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.364 476 4.9 %RANDOM
Rwork0.282 ---
obs0.286 9289 85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.42 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20.06 Å2
2--0.04 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.71→32.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2974 0 6 33 3013
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223050
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1131.9794140
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8035384
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.1723.534116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.88415537
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6631522
X-RAY DIFFRACTIONr_chiral_restr0.0670.2475
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212246
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3171.51928
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.58323149
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.58131122
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.0344.5991
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.71→2.78 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.5 18 -
Rwork0.445 330 -
obs--41.78 %

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