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

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Basic information

Entry
Database: PDB / ID: 5hhd
TitleCrystal Structure of Chemically Synthesized Heterochiral {RFX037 plus VEGF-A} Protein Complex in space group P21
Components
  • D-Peptide RFX037.D
  • D-Vascular endothelial growth factor
  • L-Peptide RFX037.L
  • Vascular endothelial growth factor A
KeywordsDE NOVO PROTEIN / HETEROCHIRAL PROTEIN-PROTEIN COMPLEX / D-PROTEIN ANTAGONIST / GROWTH FACTOR-INHIBITOR COMPLEX / RACEMIC 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 / Ubiquitin-like (UB roll) - #10 / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Cystine-knot cytokine / Ribbon / Ubiquitin-like (UB roll) / 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)
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 6, 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-Peptide RFX037.D
D: D-Peptide RFX037.D
E: D-Vascular endothelial growth factor
F: D-Vascular endothelial growth factor
G: L-Peptide RFX037.L
H: L-Peptide RFX037.L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,49713
Polymers79,0238
Non-polymers4745
Water6,179343
1
A: Vascular endothelial growth factor A
B: Vascular endothelial growth factor A
C: D-Peptide RFX037.D
D: D-Peptide RFX037.D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7897
Polymers39,5124
Non-polymers2763
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6170 Å2
ΔGint-47 kcal/mol
Surface area17100 Å2
MethodPISA
2
E: D-Vascular endothelial growth factor
F: D-Vascular endothelial growth factor
G: L-Peptide RFX037.L
H: L-Peptide RFX037.L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7086
Polymers39,5104
Non-polymers1982
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5840 Å2
ΔGint-41 kcal/mol
Surface area16830 Å2
MethodPISA
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 number4
Space group name H-MP1211

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Components

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Protein , 4 types, 8 molecules ABCDEFGH

#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-Peptide RFX037.D


Mass: 7807.466 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Protein D-Vascular endothelial growth factor


Mass: 11942.639 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Protein L-Peptide RFX037.L


Mass: 7812.501 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 348 molecules

#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.39 Å3/Da / Density % sol: 48.58 %
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 4, 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 % / Biso Wilson estimate: 33.78 Å2 / 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
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HHC

5hhc


Resolution: 2.1→49.62 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.282 2203 5.06 %
Rwork0.222 --
obs0.225 43521 98.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.77 Å2
Refinement stepCycle: LAST / Resolution: 2.1→49.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5088 0 31 343 5462
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085406
X-RAY DIFFRACTIONf_angle_d1.067279
X-RAY DIFFRACTIONf_dihedral_angle_d15.5961977
X-RAY DIFFRACTIONf_chiral_restr0.064779
X-RAY DIFFRACTIONf_plane_restr0.005954
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0993-2.14490.36971220.30862274X-RAY DIFFRACTION87
2.1449-2.19480.38071340.29082574X-RAY DIFFRACTION98
2.1948-2.24970.33511340.25932548X-RAY DIFFRACTION98
2.2497-2.31050.2961290.2442595X-RAY DIFFRACTION99
2.3105-2.37850.34161600.23422570X-RAY DIFFRACTION99
2.3785-2.45530.30881500.23212547X-RAY DIFFRACTION99
2.4553-2.5430.33311380.23612620X-RAY DIFFRACTION99
2.543-2.64490.27771240.23482605X-RAY DIFFRACTION99
2.6449-2.76520.31861440.23962589X-RAY DIFFRACTION99
2.7652-2.9110.34881320.24142606X-RAY DIFFRACTION99
2.911-3.09340.34361200.24732616X-RAY DIFFRACTION99
3.0934-3.33210.28971350.23262620X-RAY DIFFRACTION99
3.3321-3.66740.26691460.22932628X-RAY DIFFRACTION99
3.6674-4.19780.2571210.19082635X-RAY DIFFRACTION100
4.1978-5.28790.22421660.17012620X-RAY DIFFRACTION100
5.2879-49.63550.24551480.22012671X-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)
10.0102-0.00010.00740.00280.00420.0073-0.2526-0.0658-0.07350.1960.0039-0.029-0.22530.21020.00030.3531-0.0026-0.00130.3094-0.00970.3653-23.343110.9035-0.3536
20.0398-0.09790.02790.2208-0.10760.1256-0.0097-0.0329-0.09810.2005-0.02450.0332-0.0825-0.01830.00350.3248-0.2008-0.03650.4593-0.01530.287-16.983320.5624-22.7612
30.0144-0.05430.02950.0147-0.05930.0478-0.29990.2835-0.0123-0.1590.01610.0948-0.1055-0.0329-0.00010.3963-0.12330.00480.3897-0.01110.3495-23.412913.7122-20.2944
40.0841-0.07990.12550.2203-0.17210.2756-0.125-0.01680.0780.12560.23770.09660.0629-0.34520.23860.0923-0.21760.04650.0752-0.06380.2713-35.433711.0859-6.0303
50.0751-0.05130.05240.0361-0.03480.0378-0.06480.04860.0692-0.0308-0.03130.0125-0.0104-0.0001-0.07120.4069-0.3389-0.02720.3466-0.02720.3566-30.9686.7741-25.1474
60.0050.00260.01080.0108-0.00150.011-0.0284-0.0102-0.190.12020.0409-0.00080.1149-0.04760.00010.39270.0640.00650.4248-0.02950.2566-25.49767.873520.0655
70.0068-0.0165-0.00930.03670.03120.0181-0.08760.0577-0.0459-0.0194-0.0711-0.00980.1595-0.00550.00010.3576-0.05440.03130.24350.05140.3071-10.50968.79-48.5194
80.1278-0.1515-0.09620.2010.02010.0796-0.132-0.1755-0.0429-0.04170.1614-0.00440.2505-0.1373-0.00850.3515-0.0647-0.01710.3920.0340.3296-4.6648-16.4566-18.5313
90.1796-0.1716-0.01860.1673-0.04350.26320.2745-0.0729-0.2933-0.0126-0.2820.0879-0.09720.3150.00330.3101-0.0429-0.01080.45310.03120.355213.7857-5.8504-29.3088
100.00780.010.00370.00960.00510.0040.0305-0.0366-0.023-0.0280.09740.1383-0.0554-0.04250.00010.2762-0.08880.04960.38020.18960.38912.758-1.0923-56.9129
110.02590.015-0.01070.00850.00080.0064-0.05330.0466-0.0341-0.0794-0.0690.0103-0.12710.0924-00.3965-0.1024-0.04460.5750.04550.38918.2896-0.1028-62.5049
120.01810.01370.02740.011-0.00360.06360.21120.0997-0.042-0.0838-0.02050.06630.35350.2422-00.37910.0234-0.04160.3510.00350.29017.2871-5.4334-52.1705
130.1607-0.06990.0220.03060.00090.12780.0615-0.00350.01910.00260.05030.0518-0.0814-0.06830.00770.2820.24460.0160.67110.06770.3472-2.80021.5215-51.1057
140.0226-0.0113-0.00390.03850.01980.0307-0.08020.04740.1101-0.0812-0.0329-0.0481-0.1156-0.0114-0.00010.5423-0.10310.06570.5844-0.01940.402-9.7262-2.49957.7437
150.00920.0031-0.00090.002-0.00180.001-0.0329-0.042-0.0580.09410.05250.0798-0.0260.00060.00010.658-0.07890.05880.5497-0.13440.3755-7.51570.941610.4063
160.0211-0.0164-0.0120.05030.05460.04320.02530.04990.04260.22570.22720.03010.14390.0489-0.00010.51040.0581-0.12010.7285-0.03070.4671-4.4247-6.2322.1907
170.0032-0.00750.00340.0131-0.00990.00780.04380.03910.0033-0.0469-0.00270.0065-0.0436-0.00270.00050.6380.1479-0.01020.33760.01930.3351-6.28715.3598-1.6295
180.006-0.0003-0.00080.02520.01470.05040.1561-0.1114-0.05080.02170.12090.0247-0.002-0.04360.07780.3257-0.22730.00580.4508-0.04230.3522-18.169821.0905-18.3772
190.06350.0007-0.06580.0127-0.01480.06170.1256-0.0458-0.080.1520.0063-0.0265-0.05190.11640.10570.2673-0.2739-0.0140.46850.0120.3093-12.173624.0697-20.952
200.04390.0159-0.00790.01310.00880.02320.0955-0.25360.00950.1006-0.1443-0.1347-0.0372-0.019-0.01750.3415-0.4134-0.04750.5010.03860.4145-12.449324.1891-28.2533
210.0123-0.0042-0.00250.0339-0.02610.0151-0.25810.16350.0836-0.11190.04450.0128-0.0372-0.03760.00010.3366-0.0514-0.05540.2693-0.04030.3562-29.344613.7075-8.9506
220.0355-0.00280.06190.0149-0.02730.1204-0.1145-0.0061-0.090.02470.0541-0.0467-0.09170.1346-00.42510.0096-0.00350.2512-0.02980.3423-25.064111.447412.1404
23-0.0015-0.0036-0.00010.07610.090.0899-0.0184-0.08840.0154-0.0247-0.21260.12050.0660.083900.3925-0.10590.08080.27330.00090.3827-14.875411.4389-41.396
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 10 THROUGH 19 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 39 THROUGH 52 )
3X-RAY DIFFRACTION3CHAIN 'B' AND (RESID 10 THROUGH 31 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 59 THROUGH 92 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 93 THROUGH 96 )
6X-RAY DIFFRACTION6CHAIN 'C' AND (RESID 10 THROUGH 24 )
7X-RAY DIFFRACTION7CHAIN 'D' AND (RESID 10 THROUGH 24 )
8X-RAY DIFFRACTION8CHAIN 'E' AND (RESID 51 THROUGH 85 )
9X-RAY DIFFRACTION9CHAIN 'F' AND (RESID 51 THROUGH 85 )
10X-RAY DIFFRACTION10CHAIN 'G' AND (RESID 10 THROUGH 15 )
11X-RAY DIFFRACTION11CHAIN 'G' AND (RESID 16 THROUGH 24 )
12X-RAY DIFFRACTION12CHAIN 'G' AND (RESID 30 THROUGH 54 )
13X-RAY DIFFRACTION13CHAIN 'G' AND (RESID 55 THROUGH 60 )
14X-RAY DIFFRACTION14CHAIN 'H' AND (RESID 10 THROUGH 19 )
15X-RAY DIFFRACTION15CHAIN 'H' AND (RESID 20 THROUGH 24 )
16X-RAY DIFFRACTION16CHAIN 'H' AND (RESID 30 THROUGH 54 )
17X-RAY DIFFRACTION17CHAIN 'H' AND (RESID 55 THROUGH 60 )
18X-RAY DIFFRACTION18CHAIN 'A' AND (RESID 20 THROUGH 31 )
19X-RAY DIFFRACTION19CHAIN 'A' AND (RESID 59 THROUGH 77 )
20X-RAY DIFFRACTION20CHAIN 'A' AND (RESID 78 THROUGH 96 )
21X-RAY DIFFRACTION21CHAIN 'B' AND (RESID 40 THROUGH 52 )
22X-RAY DIFFRACTION22CHAIN 'C' AND (RESID 30 THROUGH 60 )
23X-RAY DIFFRACTION23CHAIN 'D' AND (RESID 30 THROUGH 60 )

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