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- PDB-4gls: Crystal Structure of Chemically Synthesized Heterochiral {D-Prote... -

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Basic information

Entry
Database: PDB / ID: 4gls
TitleCrystal Structure of Chemically Synthesized Heterochiral {D-Protein Antagonist plus VEGF-A} Protein Complex in space group P21
Components
  • D- RFX001
  • D- Vascular endothelial growth factor-A
  • L- RFX001
  • Vascular endothelial growth factor A
KeywordsGrowth Factor/Inhibitor / heterochiral protein-protein complex / D-protein antagonist / Growth Factor-Inhibitor complex
Function / homology
Function and homology information


basophil chemotaxis / cellular stress response to acid chemical / VEGF-A complex / Signaling by VEGF / lymph vessel morphogenesis / 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 ...basophil chemotaxis / cellular stress response to acid chemical / VEGF-A complex / Signaling by VEGF / lymph vessel morphogenesis / 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 / positive regulation of peptidyl-tyrosine autophosphorylation / negative regulation of adherens junction organization / post-embryonic camera-type eye development / primitive erythrocyte differentiation / positive regulation of protein kinase C signaling / 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 / positive regulation of vascular endothelial growth factor signaling pathway / coronary vein morphogenesis / cardiac vascular smooth muscle cell development / motor neuron migration / positive regulation of trophoblast cell migration / endothelial cell chemotaxis / positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway / eye photoreceptor cell development / 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 / positive regulation of cell migration by vascular endothelial growth factor signaling pathway / positive regulation of branching involved in ureteric bud morphogenesis / positive regulation of protein localization to early endosome / vascular wound healing / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / tube formation / camera-type eye morphogenesis / positive regulation of epithelial tube formation / negative regulation of cell-cell adhesion mediated by cadherin / neuropilin binding / induction of positive chemotaxis / coronary artery morphogenesis / vascular endothelial growth factor receptor 2 binding / commissural neuron axon guidance / positive regulation of vascular permeability / dopaminergic neuron differentiation / surfactant homeostasis / positive regulation of endothelial cell chemotaxis / platelet-derived growth factor receptor binding / extracellular matrix binding / cell migration involved in sprouting angiogenesis / retinal ganglion cell axon guidance / artery morphogenesis / cardiac muscle cell development / sprouting angiogenesis / positive regulation of positive chemotaxis / Regulation of gene expression by Hypoxia-inducible Factor / vascular endothelial growth factor signaling pathway / positive regulation of leukocyte migration / positive regulation of p38MAPK cascade / positive regulation of DNA biosynthetic process / branching involved in blood vessel morphogenesis / positive regulation of neuroblast proliferation / positive regulation of cell migration involved in sprouting angiogenesis / positive chemotaxis / transmembrane receptor protein tyrosine kinase activator activity / positive regulation of sprouting angiogenesis / outflow tract morphogenesis / activation of protein kinase activity / chemoattractant activity / positive regulation of focal adhesion assembly / mesoderm development / monocyte differentiation / positive regulation of receptor internalization / positive regulation of cell division / macrophage differentiation / fibronectin binding / positive regulation of cell adhesion / positive regulation of blood vessel endothelial cell migration / mammary gland alveolus development / cellular response to vascular endothelial growth factor stimulus / vasculogenesis / vascular endothelial growth factor receptor signaling pathway / heart morphogenesis / ovarian follicle development / cell maturation / positive regulation of protein autophosphorylation / epithelial cell differentiation / extracellular matrix / lactation / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / positive regulation of endothelial cell proliferation / positive regulation of endothelial cell migration / negative regulation of miRNA transcription / platelet alpha granule lumen / VEGFR2 mediated cell proliferation / secretory granule / kidney development / cytokine activity / positive regulation of epithelial cell proliferation
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 / Ubiquitin-like (UB roll) - #10 ...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 / Ubiquitin-like (UB roll) - #10 / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Cystine-knot cytokine / Ubiquitin-like (UB roll) / Ribbon / Roll / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / polypeptide(D) / polypeptide(D) (> 10) / polypeptide(D) (> 100) / Vascular endothelial growth factor A, long form
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsMandal, K. / Uppalapati, M. / Ault-Riche, D. / Kenney, J. / Lowitz, J. / Sidhu, S. / Kent, S.B.H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Chemical synthesis and X-ray structure of a heterochiral {D-protein antagonist plus vascular endothelial growth factor} protein complex by racemic crystallography.
Authors: Mandal, K. / Uppalapati, M. / Ault-Riche, D. / Kenney, J. / Lowitz, J. / Sidhu, S.S. / Kent, S.B.
History
DepositionAug 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2012Provider: repository / Type: Initial release
Revision 1.1May 29, 2013Group: Structure summary
Revision 1.2Nov 27, 2013Group: Database references
Revision 1.3Sep 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_comp_id / _struct_conn.ptnr1_label_seq_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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: D- Vascular endothelial growth factor-A
B: D- Vascular endothelial growth factor-A
C: L- RFX001
D: D- RFX001
E: Vascular endothelial growth factor A
F: Vascular endothelial growth factor A
H: D- RFX001
G: L- RFX001
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,49210
Polymers73,2948
Non-polymers1982
Water18,7721042
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.156, 88.322, 77.866
Angle α, β, γ (deg.)90.00, 99.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 4 types, 8 molecules ABCGDHEF

#1: Protein D- Vascular endothelial growth factor-A


Mass: 11942.639 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemical Synthesis
#2: Protein L- RFX001


Mass: 6379.902 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemical Synthesis
#3: Protein D- RFX001


Mass: 6375.875 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemical Synthesis
#4: 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

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Non-polymers , 3 types, 1044 molecules

#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1042 / 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: 2.64 Å3/Da / Density % sol: 53.43 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: Proteins were dissolved in 0.01 M HEPES, 50 mM NaCl at pH 8.4 and crystallized against reservoir containing 0.1 M MgCl2, 0.1 M HEPES, 12.5% PEG3350, 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: 0.97916 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 9, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 1.6→35 Å / Num. all: 97962 / Num. obs: 97962 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 2.1 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 17.8
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 2 % / Rmerge(I) obs: 0.365 / Mean I/σ(I) obs: 1.77 / Num. unique all: 9622 / % possible all: 96.2

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: dev_1128)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 3QTK, 2QMT

3qtk

2qmt


Resolution: 1.6→34.604 Å / SU ML: 0.15 / σ(F): 1.35 / Phase error: 27.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2313 4886 4.99 %
Rwork0.1901 --
obs0.1922 97836 97.65 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.56 Å2
Refinement stepCycle: LAST / Resolution: 1.6→34.604 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4892 0 13 1042 5947
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065209
X-RAY DIFFRACTIONf_angle_d1.0157059
X-RAY DIFFRACTIONf_dihedral_angle_d14.3951924
X-RAY DIFFRACTIONf_chiral_restr0.072764
X-RAY DIFFRACTIONf_plane_restr0.005930
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.61880.25821510.20863017X-RAY DIFFRACTION95
1.6188-1.63790.23621630.19913050X-RAY DIFFRACTION97
1.6379-1.65790.24071750.19223036X-RAY DIFFRACTION96
1.6579-1.67880.2631760.1923048X-RAY DIFFRACTION97
1.6788-1.70090.28341310.19573078X-RAY DIFFRACTION97
1.7009-1.72420.22841700.19193051X-RAY DIFFRACTION97
1.7242-1.74890.2721300.18583094X-RAY DIFFRACTION97
1.7489-1.7750.29081740.19443084X-RAY DIFFRACTION97
1.775-1.80270.23751820.18473056X-RAY DIFFRACTION98
1.8027-1.83230.27051460.18243103X-RAY DIFFRACTION98
1.8323-1.86380.25471630.17673091X-RAY DIFFRACTION98
1.8638-1.89770.221690.17473098X-RAY DIFFRACTION98
1.8977-1.93420.21051300.17593115X-RAY DIFFRACTION98
1.9342-1.97370.22251610.1683127X-RAY DIFFRACTION98
1.9737-2.01660.20611700.17083074X-RAY DIFFRACTION98
2.0166-2.06350.23251760.1633121X-RAY DIFFRACTION98
2.0635-2.11510.22651730.16413112X-RAY DIFFRACTION98
2.1151-2.17230.21561820.17523063X-RAY DIFFRACTION98
2.1723-2.23620.23451680.17383104X-RAY DIFFRACTION98
2.2362-2.30840.22311620.18063131X-RAY DIFFRACTION98
2.3084-2.39090.26631660.18813110X-RAY DIFFRACTION98
2.3909-2.48660.24321590.19593132X-RAY DIFFRACTION98
2.4866-2.59970.25921580.20083129X-RAY DIFFRACTION98
2.5997-2.73670.23051790.20633089X-RAY DIFFRACTION99
2.7367-2.90810.23981590.20263127X-RAY DIFFRACTION98
2.9081-3.13250.27191500.21173150X-RAY DIFFRACTION99
3.1325-3.44750.21031670.20043141X-RAY DIFFRACTION98
3.4475-3.94570.21321760.19193152X-RAY DIFFRACTION99
3.9457-4.96880.18961610.16863146X-RAY DIFFRACTION98
4.9688-34.6040.23981590.22693121X-RAY DIFFRACTION96

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