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- PDB-1tzh: Crystal Structure of the Fab YADS1 Complexed with h-VEGF -

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Basic information

Entry
Database: PDB / ID: 1tzh
TitleCrystal Structure of the Fab YADS1 Complexed with h-VEGF
Components
  • Fab YADS1 Heavy Chain
  • Fab YADS1 Light Chain
  • Vascular endothelial growth factor A
KeywordsIMMUNE SYSTEM / phage display / antibody library / protein engineering
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 / Cystine Knot Cytokines, subunit B ...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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Vascular endothelial growth factor A, long form
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsFellouse, F.A. / Wiesmann, C. / Sidhu, S.S.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: Synthetic antibodies from a four-amino-acid code: A dominant role for tyrosine in antigen recognition
Authors: Fellouse, F.A. / Wiesmann, C. / Sidhu, S.S.
#1: Journal: J.Mol.Biol. / Year: 2004
Title: Phage-displayed antibody libraries of synthetic heavy chain complementarity determining regions
Authors: Sidhu, S.S. / Li, B. / Chen, Y. / Fellouse, F.A. / Eigenbrot, C. / Fuh, G.
History
DepositionJul 9, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Aug 23, 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
Remark 999SEQUENCE THE AUTHORS INFORMED THAT THE SEQUENCES OF Fab YADS1 Light Chain and Fab YADS1 heavy Chain ...SEQUENCE THE AUTHORS INFORMED THAT THE SEQUENCES OF Fab YADS1 Light Chain and Fab YADS1 heavy Chain are not yet available in any reference sequence database.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
V: Vascular endothelial growth factor A
W: Vascular endothelial growth factor A
A: Fab YADS1 Light Chain
B: Fab YADS1 Heavy Chain
L: Fab YADS1 Light Chain
H: Fab YADS1 Heavy Chain


Theoretical massNumber of molelcules
Total (without water)118,5706
Polymers118,5706
Non-polymers00
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12860 Å2
ΔGint-88 kcal/mol
Surface area46840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.269, 76.269, 112.497
Angle α, β, γ (deg.)90.00, 105.77, 90.00
Int Tables number4
Space group name H-MP1211
DetailsFor VEGF, the biological assembly is chain V and W, linked by a disulfide bridge. For the Fab VEGF complex, the biological assembly is all chains.

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Components

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


Mass: 11948.680 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VEGF, VEGFA / Production host: Escherichia coli (E. coli) / References: UniProt: P15692
#2: Antibody Fab YADS1 Light Chain


Mass: 23035.486 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: F / Production host: Escherichia coli (E. coli) / Strain (production host): 16C9
#3: Antibody Fab YADS1 Heavy Chain


Mass: 24300.898 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: F / Production host: Escherichia coli (E. coli) / Strain (production host): 16C9
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.8 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 3350, ammonium sulfate, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 6, 2003
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 41883 / Num. obs: 41828 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 54.378 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 16.8
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.423 / Mean I/σ(I) obs: 2.4 / Num. unique all: 4162 / Rsym value: 0.423 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: The VEGF from pdb entry 1VPF. The Fab from an in-house determined structure.

1vpf


Resolution: 2.6→20 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.884 / SU B: 12.721 / SU ML: 0.265 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.595 / ESU R Free: 0.325 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27105 2105 5 %RANDOM
Rwork0.21172 ---
all0.21478 39704 --
obs0.2147 39617 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.123 Å2
Baniso -1Baniso -2Baniso -3
1--2.16 Å20 Å2-2.47 Å2
2--0.56 Å20 Å2
3---0.26 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7994 0 0 110 8104
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0218195
X-RAY DIFFRACTIONr_bond_other_d0.0020.027062
X-RAY DIFFRACTIONr_angle_refined_deg1.3421.95211149
X-RAY DIFFRACTIONr_angle_other_deg0.815316586
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3351040
X-RAY DIFFRACTIONr_chiral_restr0.0810.21239
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029140
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021598
X-RAY DIFFRACTIONr_nbd_refined0.1950.21340
X-RAY DIFFRACTIONr_nbd_other0.2220.27976
X-RAY DIFFRACTIONr_nbtor_other0.0860.25119
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1950.2182
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2650.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2140.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1730.27
X-RAY DIFFRACTIONr_mcbond_it2.8272.55217
X-RAY DIFFRACTIONr_mcangle_it4.35158447
X-RAY DIFFRACTIONr_scbond_it3.062.52978
X-RAY DIFFRACTIONr_scangle_it4.54452702
LS refinement shellResolution: 2.6→2.655 Å / Total num. of bins used: 25
RfactorNum. reflection% reflection
Rfree0.407 124 -
Rwork0.29 2210 -
obs-2210 96.8 %
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)
1-0.1878-3.0196-1.276810.0867-2.31965.03040.3716-0.0838-0.4131-0.4435-0.27890.99010.9695-1.9194-0.09270.2303-0.3625-0.11951.3681-0.18210.290937.1694-6.4615120.5419
24.239-1.5216-0.14334.4217-1.08312.4814-0.0419-0.03480.42510.54690.29260.5983-0.5284-1.2168-0.25080.59360.42060.16361.4084-0.01520.552129.482518.5904145.0434
31.8167-0.315-0.07541.161.04744.96450.09780.1740.2905-0.1963-0.2799-0.1185-0.6657-1.5510.18210.27220.2332-0.04110.77690.0330.316247.403110.5997109.7901
42.02730.40261.89032.0803-1.36245.1111-0.0513-0.14550.07380.55540.22660.0485-0.5855-0.7198-0.17530.64720.4971-0.0070.9258-0.12360.379745.413920.7336141.8901
50.84230.2596-0.08461.16510.20933.8732-0.1277-0.1424-0.12990.1303-0.0771-0.14510.4518-0.21950.20480.3694-0.0225-0.01070.14180.00150.389620.804-13.903628.6984
61.90661.7215-0.05343.07910.22970.61070.03530.0725-0.0487-0.1352-0.0915-0.18670.02450.1060.05620.31130.0267-0.00780.1087-0.01010.437837.8637-2.4177-0.236
70.9906-0.0539-0.14420.81440.06893.9913-0.1046-0.30170.19230.1205-0.0375-0.0947-0.5239-0.16930.14210.46250.0844-0.14040.1753-0.08410.388620.69017.971934.5106
81.86310.3553-0.63791.7337-0.10792.2848-0.03950.2724-0.0405-0.04620.1328-0.1975-0.2188-0.2077-0.09340.30010.020900.13680.00330.405325.55927.49890.3653
91.96220.49763.49040.82620.46295.23840.2213-0.4580.0471-0.1873-0.1537-0.00580.2677-0.2841-0.06760.26990.03620.01280.4979-0.00150.247438.4751-5.053775.8914
103.0132-0.01062.61810.46390.24335.7033-0.1712-0.95080.0759-0.1127-0.12960.1161-0.1222-1.07070.30070.27990.083-0.03030.6031-0.06260.248723.0674-1.652171.3351
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L1 - 109
2X-RAY DIFFRACTION2L110 - 210
3X-RAY DIFFRACTION3H1 - 121
4X-RAY DIFFRACTION4H122 - 213
5X-RAY DIFFRACTION5A1 - 109
6X-RAY DIFFRACTION6A110 - 210
7X-RAY DIFFRACTION7B1 - 121
8X-RAY DIFFRACTION8B122 - 213
9X-RAY DIFFRACTION9V14 - 107
10X-RAY DIFFRACTION10W14 - 107

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