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- PDB-5fv2: Crystal structure of hVEGF in complex with VH domain antibody -

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Basic information

Entry
Database: PDB / ID: 5fv2
TitleCrystal structure of hVEGF in complex with VH domain antibody
Components
  • VASCULAR ENDOTHELIAL GROWTH FACTOR
  • VH DOMAIN ANTIBODY
KeywordsHORMONE / GROWTH FACTOR RECEPTOR / 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 / negative regulation of adherens junction organization / vascular endothelial growth factor receptor 1 binding / negative regulation of establishment of endothelial barrier / vascular endothelial growth factor receptor binding ...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 / negative regulation of adherens junction organization / 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 blood-brain barrier permeability / positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway / VEGF-activated neuropilin signaling pathway / bone trabecula formation / coronary vein morphogenesis / lung vasculature development / cardiac vascular smooth muscle cell development / lymphangiogenesis / endothelial cell chemotaxis / positive regulation of trophoblast cell migration / 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 / regulation of nitric oxide mediated signal transduction / positive regulation of protein localization to early endosome / eye photoreceptor cell development / positive regulation of axon extension involved in axon guidance / vascular wound healing / regulation of hematopoietic progenitor cell differentiation / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / camera-type eye morphogenesis / positive regulation of branching involved in ureteric bud morphogenesis / neuropilin binding / coronary artery morphogenesis / induction of positive chemotaxis / transmembrane receptor protein tyrosine kinase activator activity / negative regulation of cell-cell adhesion mediated by cadherin / vascular endothelial growth factor receptor 2 binding / commissural neuron axon guidance / dopaminergic neuron differentiation / tube formation / positive regulation of vascular endothelial growth factor signaling pathway / positive regulation of vascular permeability / positive regulation of blood vessel branching / platelet-derived growth factor receptor binding / surfactant homeostasis / endothelial cell proliferation / extracellular matrix binding / cell migration involved in sprouting angiogenesis / epithelial cell maturation / positive regulation of leukocyte migration / positive regulation of positive chemotaxis / cardiac muscle cell development / sprouting angiogenesis / Regulation of gene expression by Hypoxia-inducible Factor / positive regulation of endothelial cell chemotaxis / vascular endothelial growth factor signaling pathway / artery morphogenesis / negative regulation of epithelial to mesenchymal transition / positive regulation of cell migration involved in sprouting angiogenesis / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of DNA biosynthetic process / retinal ganglion cell axon guidance / branching involved in blood vessel morphogenesis / positive regulation of neuroblast proliferation / negative regulation of fat cell differentiation / positive chemotaxis / positive regulation of sprouting angiogenesis / chemoattractant activity / mesoderm development / outflow tract morphogenesis / positive regulation of protein autophosphorylation / monocyte differentiation / macrophage differentiation / fibronectin binding / positive regulation of cell division / positive regulation of receptor internalization / mammary gland alveolus development / neuroblast proliferation / cellular response to vascular endothelial growth factor stimulus / positive regulation of focal adhesion assembly / positive regulation of blood vessel endothelial cell migration / vascular endothelial growth factor receptor signaling pathway / positive regulation of osteoblast differentiation / vasculogenesis / heart morphogenesis / cell maturation / ovarian follicle development / homeostasis of number of cells within a tissue / positive regulation of endothelial cell proliferation / lactation / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / epithelial cell differentiation / 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: 3.45 Å
AuthorsChung, C. / Batuwangala, T.
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 1.2May 15, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.3Nov 20, 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
A: VH DOMAIN ANTIBODY
B: VH DOMAIN ANTIBODY
C: VH DOMAIN ANTIBODY
V: VASCULAR ENDOTHELIAL GROWTH FACTOR
W: VASCULAR ENDOTHELIAL GROWTH FACTOR
X: VASCULAR ENDOTHELIAL GROWTH FACTOR


Theoretical massNumber of molelcules
Total (without water)78,8816
Polymers78,8816
Non-polymers00
Water00
1
B: VH DOMAIN ANTIBODY
C: VH DOMAIN ANTIBODY
V: VASCULAR ENDOTHELIAL GROWTH FACTOR
W: VASCULAR ENDOTHELIAL GROWTH FACTOR


Theoretical massNumber of molelcules
Total (without water)52,5884
Polymers52,5884
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6200 Å2
ΔGint-49.2 kcal/mol
Surface area21270 Å2
MethodPISA
2
A: VH DOMAIN ANTIBODY
X: VASCULAR ENDOTHELIAL GROWTH FACTOR

A: VH DOMAIN ANTIBODY
X: VASCULAR ENDOTHELIAL GROWTH FACTOR


Theoretical massNumber of molelcules
Total (without water)52,5884
Polymers52,5884
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area6220 Å2
ΔGint-45.4 kcal/mol
Surface area21200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.108, 130.397, 81.178
Angle α, β, γ (deg.)90.00, 106.53, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody VH DOMAIN ANTIBODY


Mass: 12745.378 Da / Num. of mol.: 3 / Fragment: VH DOMAIN ANTIBODY
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 / VEGF-A / VASCULAR PERMEABILITY FACTOR / VPF / VASCULAR ENDOTHELIAL GROWTH FACTOR


Mass: 13548.438 Da / Num. of mol.: 3 / Fragment: VEGF UNP 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
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: 1

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Sample preparation

CrystalDensity Matthews: 3.44 Å3/Da / Density % sol: 64.29 % / Description: NONE
Crystal growTemperature: 293 K / pH: 8.5 / Details: 0.1M TRIS PH 8.5, 7%PEG6000, 0.2M MGCL2 20C

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Type: ESRF / Wavelength: 0.9395
DetectorDate: Jun 19, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9395 Å / Relative weight: 1
ReflectionResolution: 3.45→51.34 Å / Num. obs: 14048 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.01 / Net I/σ(I): 7.8
Reflection shellResolution: 3.45→3.64 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.7 / % possible all: 99.9

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Processing

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

Resolution: 3.45→39.62 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.888 / SU B: 32.857 / SU ML: 0.457 / Cross valid method: THROUGHOUT / ESU R Free: 0.567 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2627 706 5 %RANDOM
Rwork0.21244 ---
obs0.21484 13340 99.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 108.524 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20 Å20.6 Å2
2---0.78 Å2-0 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 3.45→39.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5022 0 0 0 5022
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0195151
X-RAY DIFFRACTIONr_bond_other_d0.0010.024727
X-RAY DIFFRACTIONr_angle_refined_deg0.7891.9586970
X-RAY DIFFRACTIONr_angle_other_deg0.967310940
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5665631
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.58823.966232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.5815878
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.171530
X-RAY DIFFRACTIONr_chiral_restr0.0470.2736
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0215794
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021170
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_it2.25914.5192542
X-RAY DIFFRACTIONr_mcbond_other2.25814.5172541
X-RAY DIFFRACTIONr_mcangle_it4.04732.6423167
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.07714.8262609
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: 3.45→3.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 54 -
Rwork0.333 990 -
obs--99.81 %

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