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- PDB-2fjh: Structure of the B20-4 Fab, a phage derived Fab fragment, in comp... -

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Basic information

Entry
Database: PDB / ID: 2fjh
TitleStructure of the B20-4 Fab, a phage derived Fab fragment, in complex with VEGF
Components
  • Fab fragment heavy chainFragment antigen-binding
  • Fab fragment light chainFragment antigen-binding
  • Vascular endothelial growth factor A
KeywordsHORMONE/GROWTH FACTOR/IMMUNE SYSTEM / VEGF / Fab / Protein Fab complex / Cystine knot / HORMONE-GROWTH FACTOR-IMMUNE SYSTEM 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 / 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 / Vascular endothelial growth factor A, long form
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsWiesmann, C.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Structure-function studies of two synthetic anti-vascular endothelial growth factor Fabs and comparison with the Avastin Fab.
Authors: Fuh, G. / Wu, P. / Liang, W.C. / Ultsch, M. / Lee, C.V. / Moffat, B. / Wiesmann, C.
History
DepositionJan 2, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 30, 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 Fab fragment of an antibody was derived using phage display. Therefore there is no ...SEQUENCE The Fab fragment of an antibody was derived using phage display. Therefore there is no match for the deposited FAB sequences in any sequence database.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
V: Vascular endothelial growth factor A
L: Fab fragment light chain
H: Fab fragment heavy chain
W: Vascular endothelial growth factor A
A: Fab fragment light chain
B: Fab fragment heavy chain


Theoretical massNumber of molelcules
Total (without water)118,8016
Polymers118,8016
Non-polymers00
Water0
1
V: Vascular endothelial growth factor A
L: Fab fragment light chain
H: Fab fragment heavy chain

V: Vascular endothelial growth factor A
L: Fab fragment light chain
H: Fab fragment heavy chain


Theoretical massNumber of molelcules
Total (without water)118,8016
Polymers118,8016
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x+y,y,-z+1/31
2
W: Vascular endothelial growth factor A
A: Fab fragment light chain
B: Fab fragment heavy chain

W: Vascular endothelial growth factor A
A: Fab fragment light chain
B: Fab fragment heavy chain


Theoretical massNumber of molelcules
Total (without water)118,8016
Polymers118,8016
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_575x,x-y+2,-z1
Unit cell
Length a, b, c (Å)165.538, 165.538, 150.548
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Space group name H-MP3112
DetailsThe crystallographic two-fold axis generates two NCS related complexes comprising a homodimer of VEGF bound to 2 Fab moleucles

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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 / Fragment: Receptor binding domain of VEGF (residues 34-135)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pB2105 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96NW5, UniProt: P15692*PLUS
#2: Antibody Fab fragment light chain / Fragment antigen-binding


Mass: 23253.875 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PW0357-4 / Production host: Escherichia coli (E. coli)
#3: Antibody Fab fragment heavy chain / Fragment antigen-binding


Mass: 24198.023 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PW0357-4 / Production host: Escherichia coli (E. coli)

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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: 5.046684 Å3/Da / Density % sol: 75.627563 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1 M Sodium acetate, 1.6 M Ammonium sulfate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 14, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. all: 42840 / Num. obs: 42755 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 3.1→3.21 Å / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Search model for VEGF was based on 1FLT, search model for Fab was based on 2FJF.

1flt

2fjf


Resolution: 3.1→30 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.927 / SU B: 15.736 / SU ML: 0.267 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.657 / ESU R Free: 0.343 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2394 2120 5 %RANDOM
Rwork0.19829 ---
all0.21 42910 --
obs0.20038 39869 97.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.043 Å2
Baniso -1Baniso -2Baniso -3
1-2.32 Å21.16 Å20 Å2
2--2.32 Å20 Å2
3----3.48 Å2
Refinement stepCycle: LAST / Resolution: 3.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8103 0 0 0 8103
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0218311
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.421.94711304
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.78651050
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_restr0.0980.21257
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026270
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2230.23338
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2240
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2370.2111
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1160.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.342.55271
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.71658539
X-RAY DIFFRACTIONr_scbond_it3.7872.53040
X-RAY DIFFRACTIONr_scangle_it6.16352765
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.1→3.163 Å / Total num. of bins used: 25 /
RfactorNum. reflection
Rfree0.41 138
Rwork0.315 2354
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)
14.3710.29140.16381.2834-0.5022.07040.16950.2106-0.7658-0.19520.1789-0.0410.1380.1347-0.34840.27050.0301-0.02590.2161-0.08090.04681.775673.348517.6586
21.7379-0.3585-0.26895.9527-3.73864.3014-0.0209-0.16030.09060.26380.0561-0.1502-0.5849-0.0963-0.03520.18820.08050.06360.2278-0.03780.0847-14.871898.41513.0664
39.0625-4.7317-0.84345.31150.26734.2331-0.0245-0.6040.86650.44710.62090.7048-1.2729-0.6808-0.59630.78920.51780.33540.41140.17380.7031-38.5581125.25783.7744
45.1901-1.69540.26744.341-0.65254.1730.1191-0.3707-0.25230.3870.40550.6042-0.4405-0.8967-0.52460.13580.12470.14940.51910.1850.17-32.219889.782423.9394
54.53810.4319-2.24396.0136-1.11619.99280.01530.02710.21440.06390.73741.0092-0.6446-1.2783-0.75270.27110.46070.29380.87830.36820.7333-46.6539111.12274.1606
62.9056-0.9484-1.19162.7447-1.509910.21950.43780.5309-0.75840.116-0.05040.66351.4857-0.3826-0.38751.16160.3286-0.0560.3457-0.16810.8864-69.7062142.63413.4594
713.6151-4.3405-1.68583.6766-1.72064.48780.0483-1.45950.9950.02790.277-0.4398-0.58580.4119-0.32540.7760.34360.04820.6827-0.41580.4777-44.1838149.9972-11.1331
88.33552.1761-3.88623.4133-2.36236.71470.3048-0.73522.0433-0.1546-0.0388-0.6787-1.43510.9063-0.2661.0804-0.04910.47760.4847-0.19091.5581-13.0756153.2304-30.9539
98.4067-1.4439-2.41286.3115-1.27277.0370.67830.92870.899-0.8359-0.3026-0.2704-0.5142-1.0851-0.37560.82460.60370.08320.5601-0.03410.4946-54.4309153.6617-30.5196
108.5533-5.0976-0.5179.7221-2.07724.3380.61770.58661.3371-0.3935-0.3127-0.6194-1.1797-0.3044-0.3050.93160.29820.47270.38950.27970.8788-24.9142146.4231-40.094
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1VA12 - 1095 - 102
2X-RAY DIFFRACTION2LB1 - 1091 - 109
3X-RAY DIFFRACTION3LB110 - 213110 - 213
4X-RAY DIFFRACTION4HC1 - 1211 - 121
5X-RAY DIFFRACTION5HC122 - 224122 - 224
6X-RAY DIFFRACTION6WD13 - 1096 - 102
7X-RAY DIFFRACTION7AE1 - 1091 - 109
8X-RAY DIFFRACTION8AE110 - 211110 - 211
9X-RAY DIFFRACTION9BF1 - 1211 - 121
10X-RAY DIFFRACTION10BF122 - 224122 - 224

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