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- PDB-4wpb: Vascular endothelial growth factor in complex with alpha/beta-VEGF-1 -

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Basic information

Entry
Database: PDB / ID: 4wpb
TitleVascular endothelial growth factor in complex with alpha/beta-VEGF-1
Components
  • Vascular endothelial growth factor A
  • alpha/beta-VEGF-1
KeywordsPROTEIN BINDING / alpha/beta-peptide / foldamer
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 / Mainly Beta
Similarity search - Domain/homology
Vascular endothelial growth factor A, long form
Similarity search - Component
Biological speciesHomo sapiens (human)
Staphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.11 Å
AuthorsKreitler, D.F. / Checco, J.W. / Gellman, S.H. / Forest, K.T.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM056414 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM008349 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Targeting diverse protein-protein interaction interfaces with alpha / beta-peptides derived from the Z-domain scaffold.
Authors: Checco, J.W. / Kreitler, D.F. / Thomas, N.C. / Belair, D.G. / Rettko, N.J. / Murphy, W.L. / Forest, K.T. / Gellman, S.H.
History
DepositionOct 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2015Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_entity_src_syn / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Oct 11, 2017Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.6Jul 10, 2024Group: Data collection / Category: chem_comp / Item: _chem_comp.type

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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: Vascular endothelial growth factor A
C: alpha/beta-VEGF-1
D: alpha/beta-VEGF-1


Theoretical massNumber of molelcules
Total (without water)33,0844
Polymers33,0844
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5380 Å2
ΔGint-47 kcal/mol
Surface area13090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.100, 78.400, 56.500
Angle α, β, γ (deg.)90.000, 102.800, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1

Dom-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1GLUGLULYSLYSchain AAA13 - 1076 - 100
2VALVALPROPROchain BBB14 - 1067 - 99
3GLUGLUNH2NH2chain CCC8 - 408 - 40
4GLUGLUNH2NH2chain DDD8 - 408 - 40
Detailsbiological unit is the same as asym.

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Components

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


Mass: 11948.680 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: residues 8-109 / Source: (gene. exp.) Homo sapiens (human) / Gene: VEGFA, VEGF / Plasmid: pET-3d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P15692
#2: Protein/peptide alpha/beta-VEGF-1


Mass: 4593.250 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: This is a synthetic designed molecule based initially on the B domain of Staph aureus protein A.
Source: (synth.) Staphylococcus aureus (bacteria)

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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: 2.84 Å3/Da / Density % sol: 56.75 % / Description: crystals were parallelepiped plates
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1 M magnesium formate dihydrate, 15% (w/v) PEG3350, 30% (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 19, 2014
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 3.1→45.08 Å / Num. obs: 6096 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 44.01 Å2 / Rmerge F obs: 0.994 / Rmerge(I) obs: 0.083 / Rrim(I) all: 0.097 / Χ2: 0.984 / Net I/σ(I): 14.26 / Num. measured all: 22316
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
3.1-3.183.80.980.2437.4516894434470.283100
3.18-3.270.9810.1978.3117034574520.2398.9
3.27-3.360.990.1669.615714144140.193100
3.36-3.470.9920.1410.4715544124160.164100
3.47-3.580.9940.12111.1815524214150.14198.6
3.58-3.710.9890.12611.8113363673670.148100
3.71-3.850.9920.10612.814043823840.124100
3.85-40.9970.0914.3212823613560.10598.6
4-4.180.9970.0715.2912323423390.08399.1
4.18-4.380.9950.06516.9912463493470.07699.4
4.38-4.620.9960.06118.3410813002990.07199.7
4.62-4.90.9880.06418.6411113043010.07599
4.9-5.240.9970.06119.0110042742740.071100
5.24-5.660.980.06516.8210032772740.07798.9
5.66-6.20.9950.05518.518742372370.064100
6.2-6.930.9980.04719.597642182170.05599.5
6.93-8.010.9960.04420.917061971960.05299.5
8.01-9.80.9960.04521.845711661650.05399.4
9.8-13.870.9950.03922.144341291260.04797.7
13.870.9970.03720.5419973700.04595.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3 Å39.22 Å
Translation3 Å39.22 Å

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Processing

Software
NameVersionClassification
XDSNovember 11, 2013data reduction
XSCALEJanuary 10, 2014data scaling
PHASER2.5.6phasing
PHENIX1.9-1692refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.11→45.078 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 35.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2983 506 8.41 %random
Rwork0.2405 5511 --
obs0.2454 6017 99.29 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 112.05 Å2 / Biso mean: 66.8012 Å2 / Biso min: 43.87 Å2
Refinement stepCycle: final / Resolution: 3.11→45.078 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1909 0 0 0 1909
Num. residues----254
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0251995
X-RAY DIFFRACTIONf_angle_d1.4752682
X-RAY DIFFRACTIONf_chiral_restr0.059295
X-RAY DIFFRACTIONf_plane_restr0.011352
X-RAY DIFFRACTIONf_dihedral_angle_d13.519666
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A953X-RAY DIFFRACTION11.739TORSIONAL
12B953X-RAY DIFFRACTION11.739TORSIONAL
13C953X-RAY DIFFRACTION11.739TORSIONAL
14D953X-RAY DIFFRACTION11.739TORSIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1101-3.4230.36051260.26791366X-RAY DIFFRACTION99
3.423-3.9180.32541250.25841376X-RAY DIFFRACTION100
3.918-4.93530.27421260.22091371X-RAY DIFFRACTION99
4.9353-45.080.27831290.23371398X-RAY DIFFRACTION99
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)
12.97521.59761.11024.7537-2.4510.60350.50210.28450.5005-0.08720.2809-0.0986-0.1495-0.0511-0.61341.38530.0240.27590.49150.05760.261317.8996-13.818927.0333
22.40631.5973-2.44261.0858-1.62742.4545-0.24920.60020.4381-0.23010.61450.61-0.9062-1.11-0.39931.6525-0.07380.40130.5730.04120.315210.63645.21984.6995
30.4072-0.41020.10772.97690.16290.0691-0.1951-0.0796-0.11070.47210.1490.46740.2034-0.10860.01521.33040.05920.41690.3466-0.17070.516912.99594.077615.4635
41.6430.7612-0.16114.2027-2.14033.2673-0.26130.02090.0417-0.0577-0.02870.1696-0.0453-0.27020.23620.93970.03640.27080.26550.02340.448813.58568.459910.9411
50.78680.5312-0.32944.1271-1.70781.9651-0.11740.22440.1008-0.73170.0933-0.51710.3877-0.00960.0191.1420.06120.35820.30340.02960.612223.60621.851.8052
60.87290.8132-0.45511.9599-1.11572.9359-0.21840.2869-0.0835-0.08140.04710.09310.0611-0.26880.13971.130.13070.53470.57770.12040.433611.1128-12.440314.9487
71.55410.8640.87699.5531-4.91463.70930.013-0.3717-0.1748-0.30461.03781.06880.5279-0.7583-1.04931.1217-0.31130.20471.13630.12420.54030.3448-21.688521.8339
80.2687-0.28410.05722.13110.23760.052-0.10870.12520.0686-0.50690.09970.5455-0.2241-0.46540.05411.6370.15380.42930.3514-0.18490.306912.442-15.159613.5631
91.41930.07820.35193.4071-2.6425.456-0.13020.15820.145-0.61170.1925-0.0562-0.0414-0.6685-0.13321.05630.02150.11460.3421-0.0140.341311.9538-19.633916.0686
104.00782.6046-2.51446.1665-3.27192.18040.541-0.63030.04691.4596-0.2868-0.1548-0.85510.1766-0.27760.9864-0.07840.03670.57030.05740.343418.218-19.508937.6187
110.02120.2778-0.24327.1292-3.05162.7370.2524-0.2560.48212.1764-0.0220.6385-1.2253-0.3101-0.26261.82710.1878-0.06550.5337-0.08360.71125.3511-14.34941.4365
120.0882-0.04980.31582.71960.06171.1621-0.0195-0.4112-0.01870.7855-0.03390.1717-0.6984-0.1125-0.01141.8491-0.02160.13850.65250.36960.230410.8108-9.135138.8466
131.8126-0.1827-0.84362.3224-0.47350.52740.5908-0.53050.44561.9668-0.3443-0.4703-0.8080.4272-0.20461.9154-0.2145-0.33140.60970.05461.209619.9323-8.62237.1402
142.0001222220.5937-1.7361-1.4224-1.54171.73355.244-0.43160.6305-2.32421.7876-0.1607-0.3021.0496-0.04810.63826.1156-11.486735.4041
150.8932-0.21010.8040.0499-0.19140.7221-0.0107-0.09-0.1309-0.2206-0.1504-0.29640.16990.35430.14060.9479-0.04150.61990.77710.34030.668732.15578.1098-3.4724
160.4584-0.0214-0.26550.5730.22130.2347-0.29460.4288-0.2506-0.3719-0.21260.06050.5078-0.40630.32011.5896-0.03080.6770.4361-0.1450.48822.22933.0769-12.2176
170.81451.1791-0.06534.6757-2.1651.9926-0.0740.2318-0.3957-1.7201-0.07-1.41830.96450.2870.19481.65220.1970.74070.69670.27171.322529.9488-2.6729-4.8045
182.0003222.000122.00011.88641.62917.7844-7.8885-9.4701-3.469-5.2194-2.85487.58810.89430.11280.25050.24910.20411.015835.22261.0298-1.5952
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'D' and (resid 39 through 39 )D39
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 50 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 51 through 84 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 85 through 107 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid 14 through 26 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 27 through 38 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 39 through 45 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 46 through 84 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 85 through 106 )B0
10X-RAY DIFFRACTION10chain 'C' and (resid 8 through 20 )C0
11X-RAY DIFFRACTION11chain 'C' and (resid 21 through 25 )C0
12X-RAY DIFFRACTION12chain 'C' and (resid 26 through 31 )C0
13X-RAY DIFFRACTION13chain 'C' and (resid 32 through 38 )C0
14X-RAY DIFFRACTION14chain 'C' and (resid 39 through 39 )C0
15X-RAY DIFFRACTION15chain 'D' and (resid 8 through 14 )D0
16X-RAY DIFFRACTION16chain 'D' and (resid 15 through 31 )D0
17X-RAY DIFFRACTION17chain 'D' and (resid 32 through 38 )D0
18X-RAY DIFFRACTION18chain 'D' and (resid 39 through 39 )D0

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