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- PDB-3qtk: The crystal structure of chemically synthesized VEGF-A -

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Basic information

Entry
Database: PDB / ID: 3qtk
TitleThe crystal structure of chemically synthesized VEGF-A
ComponentsVascular endothelial growth factor A
KeywordsHORMONE / covalent dimer / cysteine knot protein / growth factor / X-ray crystal structure / human VEGF-A
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 / 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 / tube formation / 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 / sprouting angiogenesis / positive regulation of positive chemotaxis / 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 / retinal ganglion cell axon guidance / branching involved in blood vessel morphogenesis / 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 / positive regulation of focal adhesion assembly / outflow tract morphogenesis / mesoderm development / monocyte differentiation / positive regulation of receptor internalization / macrophage differentiation / fibronectin binding / positive regulation of cell division / neuroblast proliferation / mammary gland alveolus development / positive regulation of blood vessel endothelial cell migration / 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 / homeostasis of number of cells within a tissue / epithelial cell differentiation / 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 / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / trifluoroacetic acid / Vascular endothelial growth factor A, long form
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.849 Å
AuthorsMandal, K. / Kent, S.B.H.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2011
Title: Total chemical synthesis of biologically active vascular endothelial growth factor.
Authors: Mandal, K. / Kent, S.B.
History
DepositionFeb 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
D: Vascular endothelial growth factor A
B: Vascular endothelial growth factor A
C: Vascular endothelial growth factor A
E: Vascular endothelial growth factor A
F: Vascular endothelial growth factor A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,21724
Polymers71,6926
Non-polymers1,52518
Water7,494416
1
A: Vascular endothelial growth factor A
D: Vascular endothelial growth factor A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,65610
Polymers23,8972
Non-polymers7588
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-27 kcal/mol
Surface area11270 Å2
MethodPISA
2
B: Vascular endothelial growth factor A
C: Vascular endothelial growth factor A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3738
Polymers23,8972
Non-polymers4756
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-28 kcal/mol
Surface area11590 Å2
MethodPISA
3
E: Vascular endothelial growth factor A
F: Vascular endothelial growth factor A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1896
Polymers23,8972
Non-polymers2914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-29 kcal/mol
Surface area11410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)230.922, 44.008, 73.111
Angle α, β, γ (deg.)90.000, 99.930, 90.000
Int Tables number5
Space group name H-MC121

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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.: 6 / Fragment: UNP residues 34-135 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P15692
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-TFA / trifluoroacetic acid


Mass: 114.023 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2HF3O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 416 / 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: 2.55 Å3/Da / Density % sol: 51.8 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 45% v/v MPD, 0.2 M ammonium acetate, 0.1 M Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97919
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 19, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 1.849→50 Å / Num. obs: 61902 / % possible obs: 99.2 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.074 / Χ2: 1.427 / Net I/σ(I): 17.98
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.85-1.923.10.5741.8561581.16199.8
1.92-1.993.10.42362121.21199.9
1.99-2.083.10.28461631.25499.7
2.08-2.193.10.21861951.29999.9
2.19-2.333.10.16361541.33899.7
2.33-2.513.10.1362001.44199.6
2.51-2.763.10.10662061.60699.4
2.76-3.163.10.08362071.47999.2
3.16-3.9930.05561641.70898.2
3.99-503.10.0462431.7796.7

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIXdev_624refinement
PDB_EXTRACT3.1data extraction
ADSCdata collection
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VPF

2vpf


Resolution: 1.849→32.509 Å / Occupancy max: 1 / Occupancy min: 0.1 / SU ML: 0.22 / σ(F): 0 / Phase error: 21.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2225 3137 5.07 %
Rwork0.1804 --
obs0.1825 61870 98.9 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.276 Å2 / ksol: 0.389 e/Å3
Displacement parametersBiso max: 133.27 Å2 / Biso mean: 38.9007 Å2 / Biso min: 6.68 Å2
Baniso -1Baniso -2Baniso -3
1--1.1036 Å20 Å2-5.3761 Å2
2--2.9554 Å20 Å2
3----1.8518 Å2
Refinement stepCycle: LAST / Resolution: 1.849→32.509 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4675 0 98 416 5189
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074989
X-RAY DIFFRACTIONf_angle_d1.0326706
X-RAY DIFFRACTIONf_chiral_restr0.07697
X-RAY DIFFRACTIONf_plane_restr0.005890
X-RAY DIFFRACTIONf_dihedral_angle_d14.4451957
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8485-1.87740.2631190.25242516263594
1.8774-1.90820.32251470.251226832830100
1.9082-1.94110.27091500.239426442794100
1.9411-1.97640.2841340.236526762810100
1.9764-2.01440.2741450.203726752820100
2.0144-2.05550.21081360.19126482784100
2.0555-2.10020.25261500.18912684283499
2.1002-2.1490.25291330.189426872820100
2.149-2.20280.20591380.190426842822100
2.2028-2.26230.2441370.177126532790100
2.2623-2.32890.25861430.185826922835100
2.3289-2.4040.23571310.177826862817100
2.404-2.48990.24491440.179426772821100
2.4899-2.58960.25691480.199126842832100
2.5896-2.70740.28241510.1942650280199
2.7074-2.850.22541520.18942689284199
2.85-3.02850.22521470.1772678282599
3.0285-3.26210.20681530.16452678283199
3.2621-3.590.19111390.16122667280698
3.59-4.10860.1941520.15472668282098
4.1086-5.1730.17151500.14642678282898
5.173-32.51360.24211380.21162736287495
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)
11.22830.00760.33480.5629-0.27140.2920.0246-0.0766-0.13750.09330.076-0.03860.0163-0.064-0.05310.1917-0.0115-0.01130.2517-0.00140.20621.35534.440338.657
20.36880.04990.07890.44670.28940.2069-0.1033-0.01950.1027-0.16410.0764-0.0598-0.13390.02020.01230.24170.0066-0.02490.1953-0.02270.225525.82112.935411.227
30.15420.1116-0.0090.3554-0.07670.0253-0.06920.03450.0716-0.15560.0472-0.0603-0.07240.05870.00080.25690.0005-0.02680.1974-0.04910.217428.0019-0.856512.698
40.0290.10160.05930.51640.10240.181-0.0241-0.00050.0166-0.02130.0543-0.0925-0.0290.0811-0.02510.1968-0.009-0.03730.1895-0.02610.253437.9831.359128.8948
50.2842-0.3125-0.07520.35430.15150.5541-0.063-0.03790.1020.0184-0.0163-0.014-0.077-0.20810.0530.17330.0039-0.03590.1822-0.03430.244217.72473.514217.7026
60.13140.0053-0.05380.11530.07840.15750.0518-0.07470.1855-0.0310.0542-0.0616-0.0809-0.0296-0.0310.23120.0654-0.00450.2649-0.07790.281622.149914.956627.4508
70.11540.0018-0.03270.0148-0.00050.00860.0607-0.20410.10640.1318-0.01460.0218-0.1524-0.02840.10220.0920.2906-0.01660.3124-0.13840.113416.966415.512130.7535
80.74540.4689-0.02810.35390.19770.7876-0.1280.0591-0.2251-0.0361-0.0042-0.08590.1313-0.10740.07960.2626-0.02940.03440.2392-0.07340.392941.742110.86627.8461
90.41420.1120.12880.02960.04580.43460.06720.12750.1159-0.2116-0.1698-0.0134-0.08310.07570.05930.24230.022-0.01220.17670.01830.277352.569234.140122.9065
100.3538-0.03320.20470.1333-0.10160.3772-0.03950.08360.0373-0.01890.0011-0.0834-0.16450.04440.00080.0830.0271-0.02670.0697-0.03570.141948.577931.966624.2023
110.34310.12850.36590.25970.2280.4288-0.05780.13760.0243-0.08-0.00140.0444-0.08770.02510.01680.2850.0565-0.03960.2658-0.05690.22537.932731.17847.1466
120.4181-0.00290.10920.43060.10180.1421-0.03410.1088-0.05230.0938-0.06830.1360.10180.05640.05750.17360.02290.01360.16740.00360.233351.805622.009123.7164
130.0519-0.1532-0.07050.490.17510.1514-0.0428-0.0188-0.05110.00910.02080.03220.0197-0.04190.00470.33370.06850.1340.70880.04130.53455.517216.5359-5.9165
140.14190.12320.16120.23810.29150.45410.03380.1055-0.0105-0.05140.084-0.0873-0.03540.1812-0.09910.22280.03590.02050.269-0.07260.262454.604519.981413.496
150.08370.0419-0.07470.0764-0.01520.1054-0.12790.0012-0.1889-0.06380.04580.01530.17330.0994-0.12130.26590.11890.01620.375-0.22380.377955.408412.98427.8015
160.0127-0.01180.08260.18170.00750.5853-0.04220.00280.1010.0167-0.090.0442-0.0479-0.09840.04780.2734-0.0591-0.02170.34920.03930.28733.702830.1248-21.2879
170.18030.03860.28110.35490.11910.4460.05510.20730.0141-0.21740.1072-0.05310.13770.3708-0.08190.3022-0.03860.0260.4406-0.02840.216532.283729.0754-18.5953
180.33070.2817-0.14030.5817-0.13570.8394-0.09960.2792-0.0327-0.24990.1571-0.0806-0.0210.29290.03390.2565-0.12650.01790.32590.02370.190729.835133.3108-19.8818
190.087-0.00410.02860.03640.0030.010.0379-0.13220.0030.01230.04430.00410.03620.002-0.04150.2818-0.0932-0.0080.2588-0.0380.15629.643636.0189-5.9087
200.13950.0145-0.02620.0588-0.08610.12420.0088-0.0220.0052-0.07480.0061-0.02010.1457-0.038-0.01430.3175-0.1145-0.02050.29510.03280.216414.587722.3915-17.3604
210.0253-0.0152-0.00630.05250.01090.0329-0.0620.0321-0.077-0.05650.0372-0.09870.1359-0.03590.01570.2574-0.10660.00680.25120.03750.170514.203319.1503-18.5892
220.0892-0.0489-0.03560.05980.05320.0373-0.05120.0998-0.0930.0107-0.03560.03010.1695-0.1025-0.00950.2911-0.1701-0.03190.40260.07450.23456.224418.609-18.0802
230.1322-0.0058-0.12530.0393-0.06080.2719-0.0345-0.053-0.02040.1003-0.0543-0.01450.0510.01320.04080.3825-0.0596-0.02260.31620.07690.292423.265317.0037-3.0105
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 7:19)A0
2X-RAY DIFFRACTION2chain 'A' and (resseq 20:51)A0
3X-RAY DIFFRACTION3chain 'A' and (resseq 52:92)A0
4X-RAY DIFFRACTION4chain 'A' and (resseq 93:102)A0
5X-RAY DIFFRACTION5chain 'D' and (resseq 6:31)D0
6X-RAY DIFFRACTION6chain 'D' and (resseq 32:58)D0
7X-RAY DIFFRACTION7chain 'D' and (resseq 59:100)D0
8X-RAY DIFFRACTION8chain 'B' and (resseq 6:19)B0
9X-RAY DIFFRACTION9chain 'B' and (resseq 20:38)B0
10X-RAY DIFFRACTION10chain 'B' and (resseq 39:92)B0
11X-RAY DIFFRACTION11chain 'B' and (resseq 93:102)B0
12X-RAY DIFFRACTION12chain 'C' and (resseq 5:31)C0
13X-RAY DIFFRACTION13chain 'C' and (resseq 32:38)C0
14X-RAY DIFFRACTION14chain 'C' and (resseq 39:58)C0
15X-RAY DIFFRACTION15chain 'C' and (resseq 59:100)C0
16X-RAY DIFFRACTION16chain 'E' and (resseq 6:19)E0
17X-RAY DIFFRACTION17chain 'E' and (resseq 20:37)E0
18X-RAY DIFFRACTION18chain 'E' and (resseq 38:100)E0
19X-RAY DIFFRACTION19chain 'F' and (resseq 6:19)F0
20X-RAY DIFFRACTION20chain 'F' and (resseq 20:31)F0
21X-RAY DIFFRACTION21chain 'F' and (resseq 32:58)F0
22X-RAY DIFFRACTION22chain 'F' and (resseq 59:92)F0
23X-RAY DIFFRACTION23chain 'F' and (resseq 93:102)F0

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