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- PDB-4kzn: crystal structure of human VEGF-A receptor binding domain -

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Basic information

Entry
Database: PDB / ID: 4kzn
Titlecrystal structure of human VEGF-A receptor binding domain
ComponentsVascular endothelial growth factor A
KeywordsHORMONE / VEGF A / PDGF family / receptor binding
Function / homology
Function and homology information


basophil chemotaxis / positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway / cellular stress response to acid chemical / VEGF-A complex / Signaling by VEGF / lymph vessel morphogenesis / positive regulation of lymphangiogenesis / negative regulation of adherens junction organization / vascular endothelial growth factor receptor 1 binding / negative regulation of establishment of endothelial barrier ...basophil chemotaxis / positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway / cellular stress response to acid chemical / VEGF-A complex / Signaling by VEGF / lymph vessel morphogenesis / 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 / positive regulation of mast cell chemotaxis / post-embryonic camera-type eye development / 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 / cardiac vascular smooth muscle cell development / lung vasculature development / lymphangiogenesis / eye photoreceptor cell development / endothelial cell chemotaxis / motor neuron migration / positive regulation of trophoblast cell migration / positive regulation of epithelial tube formation / vascular endothelial growth factor receptor-2 signaling pathway / 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 / positive regulation of protein localization to early endosome / regulation of hematopoietic progenitor cell differentiation / 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 / 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 / tube formation / positive regulation of vascular permeability / dopaminergic neuron differentiation / commissural neuron axon guidance / negative regulation of epithelial to mesenchymal transition / platelet-derived growth factor receptor binding / surfactant homeostasis / extracellular matrix binding / cell migration involved in sprouting angiogenesis / cardiac muscle cell development / epithelial cell maturation / sprouting angiogenesis / positive regulation of positive chemotaxis / endothelial cell proliferation / Regulation of gene expression by Hypoxia-inducible Factor / positive regulation of leukocyte migration / vascular endothelial growth factor signaling pathway / positive regulation of p38MAPK cascade / positive regulation of endothelial cell chemotaxis / artery morphogenesis / branching involved in blood vessel morphogenesis / positive regulation of cell migration involved in sprouting angiogenesis / positive regulation of DNA biosynthetic process / retinal ganglion cell axon guidance / positive regulation of neuroblast proliferation / positive chemotaxis / negative regulation of fat cell differentiation / transmembrane receptor protein tyrosine kinase activator activity / positive regulation of sprouting angiogenesis / chemoattractant activity / outflow tract morphogenesis / positive regulation of focal adhesion assembly / mesoderm development / monocyte differentiation / positive regulation of receptor internalization / macrophage differentiation / fibronectin binding / positive regulation of cell division / positive regulation of cell adhesion / neuroblast proliferation / positive regulation of blood vessel endothelial cell migration / cellular response to vascular endothelial growth factor stimulus / mammary gland alveolus development / vasculogenesis / positive regulation of osteoblast differentiation / vascular endothelial growth factor receptor signaling pathway / heart morphogenesis / ovarian follicle development / cell maturation / homeostasis of number of cells within a tissue / positive regulation of protein autophosphorylation / positive regulation of endothelial cell proliferation / epithelial cell differentiation / lactation / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors
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 / Cystine Knot Cytokines, subunit B ...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
TRIETHYLENE GLYCOL / Vascular endothelial growth factor A, long form
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7114 Å
AuthorsLiaw, Y.C.
CitationJournal: to be published
Title: Structural Basis for the Bivalent Glycosylated Human VEGF-A121 and VEGF-A165 in recruiment of Receptor and Co-receptor
Authors: Shen, S.T. / Huang, P.T. / Shuau, Y.S. / Lee, Y.M. / Chen, Y.J. / Liaw, Y.C. / Lou, K.L.
History
DepositionMay 30, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 4, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vascular endothelial growth factor A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5924
Polymers12,2891
Non-polymers1,3033
Water1,13563
1
A: Vascular endothelial growth factor A
hetero molecules

A: Vascular endothelial growth factor A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1858
Polymers24,5782
Non-polymers2,6066
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5690 Å2
ΔGint-20 kcal/mol
Surface area12930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.573, 32.014, 42.981
Angle α, β, γ (deg.)90.000, 92.990, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Detailsbiological unit is a dimer. Half biological unit in the asym.

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Components

#1: Protein Vascular endothelial growth factor A / VEGF-A / Vascular permeability factor / VPF


Mass: 12289.062 Da / Num. of mol.: 1 / Fragment: receptor binding domain, UNP residues 39-135
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VEGFA, VEGF / Plasmid: pMT/V5-His / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): S2 / References: UniProt: P15692
#2: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1056.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-3-4/a4-b1_a6-f1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O

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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: 2.7 Å3/Da / Density % sol: 54.2 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Li2SO4, PEG200, Tris buffer, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSRRC BL13B111
SYNCHROTRONNSRRC BL13C121
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 3151CCDFeb 4, 2009monochromator
ADSC QUANTUM 3152CCDDec 23, 2008mirror
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1GRAPHITESINGLE WAVELENGTHMx-ray1
2GRAPHITESINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.71→30 Å / Num. obs: 12694 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 19.7817489644 Å2 / Rmerge(I) obs: 0.045 / Χ2: 1.163 / Net I/σ(I): 17.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.71-1.773.20.27112231.0041,296.4
1.77-1.843.60.22512521.0491,297.5
1.84-1.933.70.15312751.1461,297.8
1.93-2.033.70.11812681.2071,297.7
2.03-2.153.70.08812561.2141,297.9
2.15-2.323.60.06812901.2231,297.8
2.32-2.553.60.0612681.1321,298.3
2.55-2.923.60.05312881.2141,298
2.92-3.683.40.03712601.1311,297.1
3.68-303.30.02613141.2871,295.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å24.83 Å
Translation2.5 Å24.83 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.4.0phasing
RESOLVE2.15phasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb 1vpf

1vpf


Resolution: 1.7114→24.8338014786 Å / SU ML: 0.159239421364 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.38318867874 / σ(I): 0 / Phase error: 22.7181138622 / Stereochemistry target values: Engh & Huber
Details: MATTHEWS COEFFICIENT is calculated from both complete sequence and PDB.
RfactorNum. reflection% reflectionSelection details
Rfree0.218229685236 1275 10.051241624 %random
Rwork0.178919069691 ---
obs0.182783276428 12685 97.0691766146 %-
all-12685 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 5.51618585435 Å2
Refinement stepCycle: LAST / Resolution: 1.7114→24.8338014786 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms770 0 86 63 919
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0117018840049891
X-RAY DIFFRACTIONf_angle_d1.559122446991203
X-RAY DIFFRACTIONf_chiral_restr0.0983048194363141
X-RAY DIFFRACTIONf_plane_restr0.00608210773817145
X-RAY DIFFRACTIONf_dihedral_angle_d32.619799158380
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7114-1.77990.2854203157251350.2241613889651211X-RAY DIFFRACTION93.8633193863
1.7799-1.86090.2126093609671370.1871960163671266X-RAY DIFFRACTION97.4982626824
1.8609-1.95890.2106617199181410.1695237416191247X-RAY DIFFRACTION97.1988795518
1.9589-2.08160.2210622320261450.1709732565161269X-RAY DIFFRACTION97.8546712803
2.0816-2.24230.2186042901131420.1682774442661266X-RAY DIFFRACTION97.8457261987
2.2423-2.46770.224331261651460.1747896672831281X-RAY DIFFRACTION98.0756013746
2.4677-2.82440.2332700923931480.1791306876031284X-RAY DIFFRACTION98.2167352538
2.8244-3.55670.204714475331340.1881574233181286X-RAY DIFFRACTION97.1937029432
3.5567-24.83640.2124325096221470.1748100017961300X-RAY DIFFRACTION95.8913187541
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.157216181211.187934032163.76861988410.6002586395560.2261489463174.025515365020.0172720147214-0.06057156977490.0399825755467-0.0203662969681-0.0362686222322-0.04327029754270.1483286530.06621229153420.02262976327440.1825585093930.02330047196760.02433045321620.127017255424-0.002797397577220.166342436206-5.62740541872-8.329257573540.0906865831187
26.12898117435-0.739616507382-0.8477124741250.336249511023-0.02615402574390.959893392310.0202455179545-0.1758975684650.4181812231130.00748574804669-0.0222171493001-0.043592737203-0.1580842542970.04593232652020.03214328680930.189091179617-0.0135769873791-0.007053904120420.165604715074-0.01939652981530.1709639734455.92251044567-2.8496427608510.090001549
36.120700845590.5746072682390.2908256339641.01764322476-0.492907474580.4677945850630.179113224777-0.326952441177-0.322708492248-0.000606189059136-0.0849050577616-0.0862430747332-0.07978330432660.00434717658487-0.1039352039360.1965896650050.01741412950690.001273470279180.19178413382-0.04328713709610.1123890850886.80820862886-4.6287304314412.4166485487
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 13:38)
2X-RAY DIFFRACTION2(chain A and resid 39:84)
3X-RAY DIFFRACTION3(chain A and resid 85:107)

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