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- PDB-5hhc: Crystal Structure of Chemically Synthesized Heterochiral {RFX037 ... -

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Basic information

Entry
Database: PDB / ID: 5hhc
TitleCrystal Structure of Chemically Synthesized Heterochiral {RFX037 plus VEGF-A} Protein Complex in space group P21/n
Components
  • D- Vascular endothelial growth factor-A
  • Vascular endothelial growth factor A
KeywordsDE NOVO PROTEIN / HETEROCHIRAL PROTEIN-PROTEIN COMPLEX / D-PROTEIN ANTAGONIST / GROWTH FACTOR-INHIBITOR COMPLEX / RACEMIC PROTEIN CRYSTALLOGRAPHY
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 / vascular endothelial growth factor receptor 2 binding / negative regulation of cell-cell adhesion mediated by cadherin / 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 / cell migration involved in sprouting angiogenesis / endothelial cell proliferation / extracellular matrix binding / 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 / fibronectin binding / macrophage differentiation / positive regulation of cell division / positive regulation of receptor internalization / neuroblast proliferation / mammary gland alveolus development / 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
polypeptide(D) / polypeptide(D) (> 10) / Vascular endothelial growth factor A, long form
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsUppalapati, M. / Lee, D.J. / Mandal, K. / Kent, S.B.H. / Sidhu, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Center for Research Resources (NIH/NCRR)RR-15301 United States
CitationJournal: Acs Chem.Biol. / Year: 2016
Title: A Potent d-Protein Antagonist of VEGF-A is Nonimmunogenic, Metabolically Stable, and Longer-Circulating in Vivo.
Authors: Uppalapati, M. / Lee, D.J. / Mandal, K. / Li, H. / Miranda, L.P. / Lowitz, J. / Kenney, J. / Adams, J.J. / Ault-Riche, D. / Kent, S.B. / Sidhu, S.S.
History
DepositionJan 10, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Nov 13, 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
B: Vascular endothelial growth factor A
C: D- Vascular endothelial growth factor-A
D: D- Vascular endothelial growth factor-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6966
Polymers39,5124
Non-polymers1842
Water3,189177
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.290, 87.240, 81.344
Angle α, β, γ (deg.)90.00, 101.42, 90.00
Int Tables number14
Space group name H-MP121/n1

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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: obtained synthetically / Details: Chemical Synthesis / Source: (synth.) Homo sapiens (human) / References: UniProt: P15692
#2: Protein D- Vascular endothelial growth factor-A


Mass: 7807.466 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 2.34 Å3/Da / Density % sol: 47.46 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Proteins were dissolved in 0.01 M HEPES at pH 7.0 and crystallized against reservoir containing 0.1 M MgCl2, 0.1 M HEPES (pH 7.0), 11% (v/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 43802 / % possible obs: 99.2 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.128 / Net I/σ(I): 5.5
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.93 / Mean I/σ(I) obs: 1.625 / % possible all: 92.9

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Processing

Software
NameVersionClassification
PHENIXrefinement
SCALEPACKdata scaling
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GLN

4gln


Resolution: 2.1→49.62 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.307 2168 5.04 %Random selection
Rwork0.261 ---
obs0.263 43012 98.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.89 Å2
Refinement stepCycle: LAST / Resolution: 2.1→49.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2608 0 12 177 2797
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122784
X-RAY DIFFRACTIONf_angle_d1.2113760
X-RAY DIFFRACTIONf_dihedral_angle_d15.5441040
X-RAY DIFFRACTIONf_chiral_restr0.063395
X-RAY DIFFRACTIONf_plane_restr0.006501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0993-2.14810.43381210.3762448X-RAY DIFFRACTION88
2.1481-2.20180.41941380.3552736X-RAY DIFFRACTION99
2.2018-2.26140.38761630.32452712X-RAY DIFFRACTION99
2.2614-2.32790.32221280.30612741X-RAY DIFFRACTION99
2.3279-2.4030.36411490.30612759X-RAY DIFFRACTION99
2.403-2.48890.31561310.29992731X-RAY DIFFRACTION99
2.4889-2.58860.39891480.30362726X-RAY DIFFRACTION100
2.5886-2.70640.33471380.29092768X-RAY DIFFRACTION100
2.7064-2.84910.36251420.29112724X-RAY DIFFRACTION100
2.8491-3.02750.35461520.29222756X-RAY DIFFRACTION100
3.0275-3.26120.31961530.27982755X-RAY DIFFRACTION100
3.2612-3.58940.28421510.25662741X-RAY DIFFRACTION100
3.5894-4.10850.3111400.23272766X-RAY DIFFRACTION100
4.1085-5.17540.22041370.19742761X-RAY DIFFRACTION100
5.1754-49.63550.27881770.23892720X-RAY DIFFRACTION100
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)
10.573-0.2435-0.61140.19730.02381.1846-0.13050.0367-0.06210.04130.12760.0052-0.01440.17510.00020.3553-0.0609-0.04120.3995-0.01260.37114.985897.98410.7278
20.07990.0316-0.03480.1389-0.04040.0460.06760.51980.48330.1651-0.1245-0.1989-0.60980.1744-0.00090.7275-0.0893-0.070.653-0.00590.691621.6945116.5201-11.1899
30.8844-0.3618-1.23290.75270.21871.7671-0.0039-0.01220.02710.0402-0.0026-0.0296-0.27550.18760.00020.4052-0.1522-0.03640.50510.01210.384422.9135106.6287-1.6896
40.2089-0.37280.22890.8604-0.39390.25330.6509-0.53390.1032-0.1101-0.4922-0.231-0.31290.5460.01870.5432-0.1504-0.07930.74240.02630.586926.0322104.900514.7656
50.1735-0.11940.41630.412-0.34511.049-0.210.26150.0227-0.02780.0381-0.02060.1651-0.0950.00020.4501-0.0397-0.02850.4566-0.00560.40916.518197.5735-0.9757
60.74430.03520.77020.8237-0.51831.1617-0.15710.22870.1438-0.0496-0.03210.0795-0.4052-0.6267-0.00020.4350.0081-0.0470.4961-0.02490.414.421999.9898.9634
70.67540.0315-0.56720.6727-0.52450.8751-0.180.02690.19680.07510.2157-0.01010.1794-0.7762-0.00870.3424-0.0405-0.01720.5034-0.00490.36991.890894.592714.34
80.15320.0014-0.03760.12990.00480.0093-0.65030.9141-0.1096-0.7131-0.3011-0.30680.6412-0.1008-0.00160.5945-0.1911-0.01220.612-0.01050.47876.329490.4465-5.1535
91.0090.48451.0181.11680.13314.0683-0.1876-0.2281-0.0127-0.0062-0.0242-0.0511-0.22770.1521-00.47450.0178-0.02120.44180.01350.390312.850794.062934.289
100.5439-0.4946-0.20442.3972.54242.9349-0.10090.054-0.0519-0.0859-0.10150.10210.21650.01750.00020.5019-0.044-0.01410.56390.01940.443223.637193.8468-23.4857
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 6 THROUGH 31 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 32 THROUGH 38 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 39 THROUGH 92 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 93 THROUGH 96 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 6 THROUGH 31 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 32 THROUGH 58 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 59 THROUGH 92 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 93 THROUGH 96 )
9X-RAY DIFFRACTION9CHAIN 'C' AND (RESID 10 THROUGH 64 )
10X-RAY DIFFRACTION10CHAIN 'D' AND (RESID 10 THROUGH 64 )

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