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- PDB-1tzi: Crystal Structure of the Fab YADS2 Complexed with h-VEGF -

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Basic information

Entry
Database: PDB / ID: 1tzi
TitleCrystal Structure of the Fab YADS2 Complexed with h-VEGF
Components
  • Fab YADS2 Heavy Chain
  • Fab YADS2 Light Chain
  • Vascular endothelial growth factor A
KeywordsIMMUNE SYSTEM / phage display / antibody library / protein engineering
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 / negative regulation of cell-cell adhesion mediated by cadherin / vascular endothelial growth factor receptor 2 binding / 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 / endothelial cell proliferation / extracellular matrix binding / cell migration involved in sprouting angiogenesis / 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 / macrophage differentiation / fibronectin binding / positive regulation of cell division / positive regulation of receptor internalization / mammary gland alveolus development / neuroblast proliferation / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Vascular endothelial growth factor A, long form
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 10, 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 / 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
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE THE AUTHORS INFORMED THAT THE SEQUENCES OF Fab YADS2 Light Chain and Fab YADS2 heavy Chain ...SEQUENCE THE AUTHORS INFORMED THAT THE SEQUENCES OF Fab YADS2 Light Chain and Fab YADS2 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
A: Fab YADS2 Light Chain
B: Fab YADS2 Heavy Chain
V: Vascular endothelial growth factor A


Theoretical massNumber of molelcules
Total (without water)58,7133
Polymers58,7133
Non-polymers00
Water00
1
A: Fab YADS2 Light Chain
B: Fab YADS2 Heavy Chain
V: Vascular endothelial growth factor A

A: Fab YADS2 Light Chain
B: Fab YADS2 Heavy Chain
V: Vascular endothelial growth factor A


Theoretical massNumber of molelcules
Total (without water)117,4256
Polymers117,4256
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Unit cell
Length a, b, c (Å)96.504, 149.588, 117.421
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsFor VEGF, the biological assembly corresponds to two copies of chain V, related by a two fold symetry and physically linked by a disulfide bridge. The Fab VEGF complex, the biological assembly corresponds to all chains, related by a two fold symetry.

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Components

#1: Antibody Fab YADS2 Light Chain


Mass: 23387.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: F0771-B6 / Production host: Escherichia coli (E. coli) / Strain (production host): 16C9
#2: Antibody Fab YADS2 Heavy Chain


Mass: 23376.049 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: F0771-B6 / Production host: Escherichia coli (E. coli) / Strain (production host): 16C9
#3: Protein Vascular endothelial growth factor A / VEGF-A / Vascular permeability factor / VPF / h-vegf


Mass: 11948.680 Da / Num. of mol.: 1
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
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: 3.2 Å3/Da / Density % sol: 61.5 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: LITHIUM CHLORIDE, PEG 6000, MES, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 28, 2003
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 21429 / Num. obs: 20861 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 18.7
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 83.2 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.5 / Num. unique all: 2110 / Rsym value: 0.4 / % possible all: 82.92

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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 is from pdb entry 1VPF. The Fab is from an in-house determined structure.

1vpf


Resolution: 2.8→20 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.927 / SU B: 16.331 / SU ML: 0.299 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.685 / ESU R Free: 0.332 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25447 1023 4.9 %RANDOM
Rwork0.21786 ---
all0.2197 21229 --
obs0.2197 19702 97.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.845 Å2
Baniso -1Baniso -2Baniso -3
1--8.87 Å20 Å20 Å2
2--1.62 Å20 Å2
3---7.25 Å2
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4077 0 0 0 4077
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0214180
X-RAY DIFFRACTIONr_bond_other_d0.0010.023602
X-RAY DIFFRACTIONr_angle_refined_deg1.3341.9525685
X-RAY DIFFRACTIONr_angle_other_deg0.94538459
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5925530
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0760.2628
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024672
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02817
X-RAY DIFFRACTIONr_nbd_refined0.2030.2766
X-RAY DIFFRACTIONr_nbd_other0.2240.24141
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0860.22582
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.255
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3420.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2080.271
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1750.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it3.2112.52656
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.23154294
X-RAY DIFFRACTIONr_scbond_it2.8692.51524
X-RAY DIFFRACTIONr_scangle_it4.69651391
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.857 Å / Total num. of bins used: 25
RfactorNum. reflection
Rfree0.312 50
Rwork0.301 965
obs-965
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)
16.50560.3282-1.29433.73840.13171.06250.3033-0.9396-0.6390.5326-0.4492-0.53690.16740.12180.14590.3291-0.1912-0.08650.27850.15650.354141.467341.763816.5588
26.08871.6787-1.00765.94770.76411.2189-0.1119-0.7766-0.3798-0.24690.2676-0.18740.19940.8518-0.15560.16360.0865-0.09480.45-0.02110.279875.062950.97243.8372
36.8212.57210.55395.19790.76611.34790.4906-0.36580.31560.2345-0.50140.4575-0.07040.00940.01090.3471-0.07320.11230.2617-0.1080.069636.651763.087210.9753
44.1881-0.3574-1.63834.54812.56022.80930.02450.0944-0.1535-0.3304-0.04250.2049-0.14790.22740.0180.29340.0806-0.08670.2058-0.02820.246864.203956.9371-5.8362
56.34230.8842-5.44270.5995-1.18586.3566-0.2306-1.0282-0.8947-0.0424-0.17530.07150.12041.16450.40580.02390.08190.00130.49730.13280.30851.052553.281737.3582
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1091 - 109
2X-RAY DIFFRACTION2AA110 - 213110 - 213
3X-RAY DIFFRACTION3BB1 - 1211 - 128
4X-RAY DIFFRACTION4BB122 - 215129 - 222
5X-RAY DIFFRACTION5VC13 - 1096 - 102

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