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- PDB-5fv1: Crystal structure of hVEGF in complex with VK domain antibody -

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Basic information

Entry
Database: PDB / ID: 5fv1
TitleCrystal structure of hVEGF in complex with VK domain antibody
Components
  • VASCULAR ENDOTHELIAL GROWTH FACTOR A
  • VK DOMAIN ANTIBODY
KeywordsIMMUNE SYSTEM / VEGF / DOMAIN ANTIBODY / VASCULAR ENDOTHELIAL GROWTH FACTOR
Function / homology
Function and homology information


basophil chemotaxis / positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway / VEGF-A complex / Signaling by VEGF / cellular stress response to acid chemical / positive regulation of lymphangiogenesis / vascular endothelial growth factor receptor 1 binding / negative regulation of establishment of endothelial barrier / vascular endothelial growth factor receptor binding / VEGF ligand-receptor interactions ...basophil chemotaxis / positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway / VEGF-A complex / Signaling by VEGF / cellular stress response to acid chemical / positive regulation of lymphangiogenesis / vascular endothelial growth factor receptor 1 binding / negative regulation of establishment of endothelial barrier / vascular endothelial growth factor receptor binding / VEGF ligand-receptor interactions / post-embryonic camera-type eye development / positive regulation of mast cell chemotaxis / lymph vessel morphogenesis / primitive erythrocyte differentiation / negative regulation of adherens junction organization / negative regulation of blood-brain barrier permeability / positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway / regulation of nitric oxide mediated signal transduction / VEGF-activated neuropilin signaling pathway / bone trabecula formation / coronary vein morphogenesis / cardiac vascular smooth muscle cell development / lymphangiogenesis / vascular endothelial growth factor receptor-2 signaling pathway / positive regulation of epithelial tube formation / VEGF binds to VEGFR leading to receptor dimerization / motor neuron migration / positive regulation of trophoblast cell migration / positive regulation of axon extension involved in axon guidance / lung vasculature development / vascular wound healing / eye photoreceptor cell development / regulation of hematopoietic progenitor cell differentiation / endothelial cell chemotaxis / positive regulation of protein localization to early endosome / camera-type eye morphogenesis / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / positive regulation of protein autophosphorylation / neuropilin binding / positive regulation of branching involved in ureteric bud morphogenesis / induction of positive chemotaxis / coronary artery morphogenesis / transmembrane receptor protein tyrosine kinase activator activity / negative regulation of cell-cell adhesion mediated by cadherin / commissural neuron axon guidance / positive regulation of vascular permeability / vascular endothelial growth factor receptor 2 binding / dopaminergic neuron differentiation / tube formation / positive regulation of vascular endothelial growth factor signaling pathway / positive regulation of blood vessel branching / surfactant homeostasis / platelet-derived growth factor receptor binding / sprouting angiogenesis / retinal ganglion cell axon guidance / cell migration involved in sprouting angiogenesis / extracellular matrix binding / endothelial cell proliferation / epithelial cell maturation / positive regulation of positive chemotaxis / positive regulation of leukocyte migration / cardiac muscle cell development / positive regulation of endothelial cell chemotaxis / Regulation of gene expression by Hypoxia-inducible Factor / positive regulation of cell migration involved in sprouting angiogenesis / vascular endothelial growth factor signaling pathway / artery morphogenesis / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of DNA biosynthetic process / negative regulation of epithelial to mesenchymal transition / branching involved in blood vessel morphogenesis / positive regulation of neuroblast proliferation / positive chemotaxis / negative regulation of fat cell differentiation / positive regulation of sprouting angiogenesis / chemoattractant activity / mesoderm development / outflow tract morphogenesis / fibronectin binding / positive regulation of cell division / monocyte differentiation / positive regulation of receptor internalization / macrophage differentiation / cellular response to vascular endothelial growth factor stimulus / mammary gland alveolus development / positive regulation of blood vessel endothelial cell migration / neuroblast proliferation / positive regulation of focal adhesion assembly / vascular endothelial growth factor receptor signaling pathway / positive regulation of osteoblast differentiation / vasculogenesis / heart morphogenesis / ovarian follicle development / cell maturation / lactation / positive regulation of endothelial cell proliferation / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / epithelial cell differentiation / extracellular matrix / positive regulation of endothelial cell migration
Similarity search - Function
Vascular endothelial growth factor, heparin-binding domain / Vascular endothelial growth factor, heparin-binding domain superfamily / VEGF heparin-binding 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 ...Vascular endothelial growth factor, heparin-binding domain / Vascular endothelial growth factor, heparin-binding domain superfamily / VEGF heparin-binding 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 / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Cystine-knot cytokine / Ribbon / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Vascular endothelial growth factor A, long form
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsChung, C. / Walker, A.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Novel Interaction Mechanism of a Domain Antibody Based Inhibitor of Human Vascular Endothelial Growth Factor with Greater Potency Than Ranibizumab and Bevacizumab and Improved Capacity Over Aflibercept.
Authors: Walker, A. / Chung, C. / Neu, M. / Burman, M. / Batuwangala, T. / Jones, G. / Tang, C. / Steward, M. / Mullin, M. / Tournier, N. / Lewis, A. / Korczynska, J. / Chung, V. / Catchpole, I.
History
DepositionFeb 2, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 17, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2016Group: Database references
Revision 1.2Apr 25, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_beamline
Revision 1.3May 15, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature
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 / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: VK DOMAIN ANTIBODY
M: VK DOMAIN ANTIBODY
V: VASCULAR ENDOTHELIAL GROWTH FACTOR A
W: VASCULAR ENDOTHELIAL GROWTH FACTOR A


Theoretical massNumber of molelcules
Total (without water)51,1844
Polymers51,1844
Non-polymers00
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4920 Å2
ΔGint-44 kcal/mol
Surface area21340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.221, 147.128, 175.171
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Antibody VK DOMAIN ANTIBODY


Mass: 12043.541 Da / Num. of mol.: 2 / Fragment: VK DOMAIN ANTIBODY, RESIDUES 1-108
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli)
#2: Protein VASCULAR ENDOTHELIAL GROWTH FACTOR A / VEGF-A / VASCULAR PERMEABILITY FACTOR / VPF / VASCULAR ENDOTHE LIAL GROWTH FACTOR


Mass: 13548.438 Da / Num. of mol.: 2 / Fragment: VEGF RESIDUES 27-136
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P15692
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsRESIDUAL C-TERMINAL POLYHIS PURIFICATION TAG

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.85 Å3/Da / Density % sol: 68.08 % / Description: NONE
Crystal growTemperature: 277 K / pH: 8.5
Details: 20% PEG3350, 0.1M BIS TRIS PROPANE PH 8.5, 0.2M NA CITRATE 4C

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Type: DIAMOND / Wavelength: 0.92
DetectorDate: Apr 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.7→73.56 Å / Num. obs: 22056 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 6.6 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 18.5
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 3.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NONE

Resolution: 2.7→73.56 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.929 / SU B: 11.601 / SU ML: 0.233 / Cross valid method: THROUGHOUT / ESU R: 0.374 / ESU R Free: 0.286 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26056 1125 5.1 %RANDOM
Rwork0.20536 ---
obs0.20819 20930 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 73.629 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å2-0 Å2-0 Å2
2--1.84 Å20 Å2
3----1.32 Å2
Refinement stepCycle: LAST / Resolution: 2.7→73.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3256 0 0 73 3329
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0193350
X-RAY DIFFRACTIONr_bond_other_d0.0010.023068
X-RAY DIFFRACTIONr_angle_refined_deg1.2021.954529
X-RAY DIFFRACTIONr_angle_other_deg0.71237126
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.795406
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.87324.474152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.46415579
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2261514
X-RAY DIFFRACTIONr_chiral_restr0.070.2476
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213728
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02758
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_it5.2649.4541635
X-RAY DIFFRACTIONr_mcbond_other5.2619.4521634
X-RAY DIFFRACTIONr_mcangle_it7.88621.2462036
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.19310.2651715
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 2.702→2.772 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 73 -
Rwork0.317 1547 -
obs--99.94 %

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