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- PDB-3p9w: Crystal structure of an engineered human autonomous VH Domain in ... -

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Basic information

Entry
Database: PDB / ID: 3p9w
TitleCrystal structure of an engineered human autonomous VH Domain in complex with VEGF
Components
  • Vascular endothelial growth factor A
  • human VEGF
KeywordsSIGNALING PROTEIN/IMMUNE SYSTEM / VH / Cystine Knot Cytokine / VEGF-R / SIGNALING PROTEIN / SIGNALING PROTEIN-IMMUNE SYSTEM complex
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 / lymph vessel morphogenesis / positive regulation of lymphangiogenesis / negative regulation of adherens junction organization / negative regulation of establishment of endothelial barrier / vascular endothelial growth factor receptor 1 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 / lymph vessel morphogenesis / positive regulation of lymphangiogenesis / negative regulation of adherens junction organization / negative regulation of establishment of endothelial barrier / vascular endothelial growth factor receptor 1 binding / VEGF ligand-receptor interactions / vascular endothelial growth factor receptor binding / post-embryonic camera-type eye development / positive regulation of mast cell chemotaxis / primitive erythrocyte differentiation / positive regulation of protein kinase C signaling / positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway / negative regulation of blood-brain barrier permeability / VEGF-activated neuropilin signaling pathway / bone trabecula formation / positive regulation of vascular endothelial growth factor signaling pathway / coronary vein morphogenesis / lung vasculature development / cardiac vascular smooth muscle cell development / lymphangiogenesis / eye photoreceptor cell development / endothelial cell chemotaxis / positive regulation of trophoblast cell migration / positive regulation of epithelial tube formation / vascular endothelial growth factor receptor-2 signaling pathway / motor neuron migration / VEGF binds to VEGFR leading to receptor dimerization / regulation of nitric oxide mediated signal transduction / positive regulation of axon extension involved in axon guidance / vascular wound healing / regulation of hematopoietic progenitor cell differentiation / positive regulation of protein localization to early endosome / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / positive regulation of branching involved in ureteric bud morphogenesis / camera-type eye morphogenesis / tube formation / neuropilin binding / induction of positive chemotaxis / coronary artery morphogenesis / negative regulation of cell-cell adhesion mediated by cadherin / vascular endothelial growth factor receptor 2 binding / positive regulation of vascular permeability / dopaminergic neuron differentiation / commissural neuron axon guidance / platelet-derived growth factor receptor binding / surfactant homeostasis / extracellular matrix binding / cell migration involved in sprouting angiogenesis / cardiac muscle cell development / epithelial cell maturation / positive regulation of positive chemotaxis / sprouting angiogenesis / Regulation of gene expression by Hypoxia-inducible Factor / endothelial cell proliferation / positive regulation of leukocyte migration / vascular endothelial growth factor signaling pathway / positive regulation of endothelial cell chemotaxis / artery morphogenesis / positive regulation of p38MAPK cascade / negative regulation of epithelial to mesenchymal transition / positive regulation of cell migration involved in sprouting angiogenesis / positive regulation of DNA biosynthetic process / branching involved in blood vessel morphogenesis / retinal ganglion cell axon guidance / positive chemotaxis / positive regulation of neuroblast proliferation / transmembrane receptor protein tyrosine kinase activator activity / negative regulation of fat cell differentiation / positive regulation of sprouting angiogenesis / chemoattractant activity / mesoderm development / positive regulation of receptor internalization / positive regulation of focal adhesion assembly / outflow tract morphogenesis / monocyte differentiation / positive regulation of cell division / fibronectin binding / macrophage differentiation / neuroblast proliferation / positive regulation of blood vessel endothelial cell migration / mammary gland alveolus development / cellular response to vascular endothelial growth factor stimulus / vasculogenesis / vascular endothelial growth factor receptor signaling pathway / positive regulation of osteoblast differentiation / heart morphogenesis / ovarian follicle development / cell maturation / positive regulation of protein autophosphorylation / epithelial cell differentiation / 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 / 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: 2.41 Å
AuthorsMa, X. / Wiesmann, C.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Design of Synthetic Autonomous VH Domain Libraries and Structural Analysis of a VH Domain Bound to Vascular Endothelial Growth Factor.
Authors: Ma, X. / Barthelemy, P.A. / Rouge, L. / Wiesmann, C. / Sidhu, S.S.
History
DepositionOct 18, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2012Group: Other
Revision 1.2Mar 27, 2013Group: Database references
Revision 1.3Apr 3, 2013Group: Database references
Revision 1.4Jun 12, 2013Group: Database references
Revision 1.5Jun 19, 2013Group: Database references
Revision 1.6Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Vascular endothelial growth factor A
B: human VEGF
C: Vascular endothelial growth factor A
D: human VEGF
E: Vascular endothelial growth factor A
F: human VEGF
G: Vascular endothelial growth factor A
H: human VEGF


Theoretical massNumber of molelcules
Total (without water)103,5178
Polymers103,5178
Non-polymers00
Water7,909439
1
A: Vascular endothelial growth factor A
B: human VEGF


Theoretical massNumber of molelcules
Total (without water)25,8792
Polymers25,8792
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Vascular endothelial growth factor A
D: human VEGF


Theoretical massNumber of molelcules
Total (without water)25,8792
Polymers25,8792
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Vascular endothelial growth factor A
F: human VEGF


Theoretical massNumber of molelcules
Total (without water)25,8792
Polymers25,8792
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Vascular endothelial growth factor A
H: human VEGF


Theoretical massNumber of molelcules
Total (without water)25,8792
Polymers25,8792
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.727, 132.908, 175.481
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
Vascular endothelial growth factor A / engineered human autonomous VH Domain / VEGF-A / Vascular permeability factor / VPF


Mass: 12421.224 Da / Num. of mol.: 4 / Fragment: unp residues 7-110
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RP1-261G23.1-009, VEGF, VEGFA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P15692
#2: Antibody
human VEGF


Mass: 13457.903 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 439 / 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: 2.97 Å3/Da / Density % sol: 58.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10 %(w/v) PEG 4000, 20 %(w/v) Isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 18, 2008
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 44934 / % possible obs: 92.5 % / Redundancy: 4 % / Biso Wilson estimate: 47.8 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.058 / Net I/σ(I): 19.5
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 4 % / Mean I/σ(I) obs: 3.6 / Num. unique all: 4512 / Rsym value: 0.326 / % possible all: 94.9

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Processing

Software
NameVersionClassification
DNAdata collection
PHASESphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.41→50 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.92 / SU B: 6.448 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R Free: 0.245 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23332 2277 5.1 %RANDOM
Rwork0.19341 ---
obs0.19548 42491 91.65 %-
all-44896 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.099 Å2
Baniso -1Baniso -2Baniso -3
1-0.99 Å20 Å20 Å2
2--0.31 Å20 Å2
3----1.31 Å2
Refinement stepCycle: LAST / Resolution: 2.41→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6911 0 0 439 7350
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0227104
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0141.959625
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5625867
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.23823.503334
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.127151162
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9031544
X-RAY DIFFRACTIONr_chiral_restr0.0820.2999
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0215474
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_it1.2431.54327
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.35826976
X-RAY DIFFRACTIONr_scbond_it3.41432777
X-RAY DIFFRACTIONr_scangle_it5.4334.52649
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.406→2.469 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 159 -
Rwork0.292 2871 -
obs--85.45 %

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