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- PDB-1mkk: Disulfide deficient mutant of vascular endothelial growth factor ... -

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Basic information

Entry
Database: PDB / ID: 1mkk
TitleDisulfide deficient mutant of vascular endothelial growth factor A (C61A and C104A)
ComponentsVascular Endothelial Growth Factor A
KeywordsHORMONE/GROWTH FACTOR / Cystine-knot growth factor / HORMONE-GROWTH FACTOR 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 / 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 protein autophosphorylation / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / 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 / retinal ganglion cell axon guidance / sprouting angiogenesis / 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 / artery morphogenesis / vascular endothelial growth factor signaling pathway / 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 / positive regulation of receptor internalization / macrophage differentiation / monocyte 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 / 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: 1.32 Å
AuthorsMuller, Y.A. / Heiring, C. / Misselwitz, R. / Welfle, K. / Welfle, H.
Citation
Journal: J.Biol.Chem. / Year: 2002
Title: The cystine knot promotes folding and not thermodynamic stability in vascular endothelial growth factor
Authors: Muller, Y.A. / Heiring, C. / Misselwitz, R. / Welfle, K. / Welfle, H.
#1: Journal: Protein Eng. / Year: 2001
Title: Folding Screening Assayed By Proteolysis: Application to Various Cystine Deletion Mutants of VasculaR Endothelial Growth Factor
Authors: Heiring, C. / Muller, Y.A.
History
DepositionAug 29, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Oct 27, 2021Group: Data collection / Database references / Category: database_2 / diffrn_source / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details
Revision 1.5Nov 20, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vascular Endothelial Growth Factor A
B: Vascular Endothelial Growth Factor A


Theoretical massNumber of molelcules
Total (without water)22,3922
Polymers22,3922
Non-polymers00
Water3,693205
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-25 kcal/mol
Surface area11370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.220, 75.470, 55.120
Angle α, β, γ (deg.)90.00, 97.25, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Vascular Endothelial Growth Factor A / VEGF-A / Vascular permeability factor / VPF


Mass: 11195.966 Da / Num. of mol.: 2 / Fragment: Residues 40-134, sequence database / Mutation: C61A,C104A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET-3d / Production host: Escherichia coli (E. coli) / Strain (production host): B843(DE3)pLysS / References: UniProt: P15692
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 2.6 Å3/Da / Density % sol: 52.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: isopropanol, PEG4000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15-6 mg/mlprotein1drop
210 mMTris-HCl1drop
350 mM1dropNaCl
40.05 Msodium citrate1drop
56 %(v/v)2-propanol1drop
614 %PEG40001drop
70.1 Msodium citrate1reservoir
812 %(v/v)2-propanol1reservoir
928 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8423 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 5, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8423 Å / Relative weight: 1
ReflectionResolution: 1.32→28 Å / Num. all: 53321 / Num. obs: 53321 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 22.06 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 12.08
Reflection shellResolution: 1.32→1.35 Å / Redundancy: 3.17 % / Rmerge(I) obs: 0.375 / Mean I/σ(I) obs: 2.48 / Num. unique all: 3498 / % possible all: 99.5

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Processing

Software
NameVersionClassification
MAR345data collection
XDSdata reduction
AMoREphasing
REFMAC5refinement
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VPF

2vpf


Resolution: 1.32→28 Å / SU B: 2.05958 / SU ML: 0.04509 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.0829 / ESU R Free: 0.07326 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.19515 5264 9.9 %Resolution shells
Rwork0.16543 ---
all0.16836 53318 --
obs0.16836 53318 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET'S PRINCIPLE
Displacement parametersBiso mean: 19.583 Å2
Baniso -1Baniso -2Baniso -3
1-1.32 Å20 Å20.03 Å2
2---0.86 Å20 Å2
3----0.46 Å2
Refinement stepCycle: LAST / Resolution: 1.32→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1528 0 0 205 1733
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONr_angle_refined_deg1.4031.971
X-RAY DIFFRACTIONr_bond_refined_d0.0110.021
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4323
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.09915
X-RAY DIFFRACTIONr_chiral_restr0.090.2
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02
X-RAY DIFFRACTIONr_xyhbond_nbd-refined
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_mcbond_it2.9594
X-RAY DIFFRACTIONr_mcangle_it4.2986
X-RAY DIFFRACTIONr_scbond_it4.7227
X-RAY DIFFRACTIONr_scangle_it6.799
X-RAY DIFFRACTIONr_rigid_bond_restr2.3314
X-RAY DIFFRACTIONr_sphericity_free13.1057
X-RAY DIFFRACTIONr_sphericity_bonded7.1447
Software
*PLUS
Name: REFMAC / Version: 5 / Classification: refinement
Refinement
*PLUS
σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.011
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.4
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scangle_it

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