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- PDB-3bdy: Dual specific bH1 Fab in complex with VEGF -

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Basic information

Entry
Database: PDB / ID: 3bdy
TitleDual specific bH1 Fab in complex with VEGF
Components
  • Fab Fragment -Heavy Chain
  • Fab Fragment -Light Chain
  • Vascular endothelial growth factor A
KeywordsHORMONE / Fab Complex / Angiogenesis / Developmental protein / Differentiation / Glycoprotein / Growth factor / Heparin-binding / Mitogen / Secreted
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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsBostrom, J.M. / Wiesmann, C. / Appleton, B.A.
CitationJournal: Science / Year: 2009
Title: Variants of the antibody herceptin that interact with HER2 and VEGF at the antigen binding site
Authors: Bostrom, J. / Yu, S.F. / Kan, D. / Appleton, B.A. / Lee, C.V. / Billeci, K. / Man, W. / Peale, F. / Ross, S. / Wiesmann, C. / Fuh, G.
History
DepositionNov 15, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 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_ref_seq / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: Fab Fragment -Heavy Chain
L: Fab Fragment -Light Chain
V: Vascular endothelial growth factor A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,5554
Polymers60,4633
Non-polymers921
Water84747
1
H: Fab Fragment -Heavy Chain
L: Fab Fragment -Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6063
Polymers48,5142
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-25 kcal/mol
Surface area20130 Å2
MethodPISA
2
V: Vascular endothelial growth factor A

V: Vascular endothelial growth factor A


Theoretical massNumber of molelcules
Total (without water)23,8972
Polymers23,8972
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545x,-y-1,-z1
Buried area2720 Å2
ΔGint-26 kcal/mol
Surface area11510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.600, 197.978, 77.650
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Antibody Fab Fragment -Heavy Chain


Mass: 24557.451 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Antibody Fab Fragment -Light Chain


Mass: 23956.588 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Protein Vascular endothelial growth factor A / VEGF-A / Vascular permeability factor / VPF


Mass: 11948.680 Da / Num. of mol.: 1 / Fragment: sequence database residues 27-135
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
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O
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: 3.17 Å3/Da / Density % sol: 61.14 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 7.5
Details: For crystallization of the Fab/VEGF (8-109) complex, equal volumes of protein complex solution (10.6 mg/ml protein, 300 mM NaCl, 25 mM Tris-HCl pH 7.5) and crystallization buffer containing ...Details: For crystallization of the Fab/VEGF (8-109) complex, equal volumes of protein complex solution (10.6 mg/ml protein, 300 mM NaCl, 25 mM Tris-HCl pH 7.5) and crystallization buffer containing 0.15 D, L Malic Acid pH 7.0, 20% PEG3350 were mixed and equilibrated at 19 C. Prior to data collection the crystals were cryo-protected by transfer between drops containing 5%, 10% and 15% Glycerol in artificial mother liquor, followed by flash freeze in liquid nitrogen, VAPOR DIFFUSION, 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 315 / Detector: CCD / Date: Jul 13, 2006
RadiationProtocol: 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: 24755 / Num. obs: 24705 / % possible obs: 99.8 % / Redundancy: 6.2 % / Rsym value: 0.09 / Χ2: 1.011 / Net I/σ(I): 16
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 3 / Num. unique all: 2419 / Rsym value: 0.658 / Χ2: 0.876 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1N8Z

1n8z


Resolution: 2.6→30 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.922 / SU B: 19.206 / SU ML: 0.194 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.41 / ESU R Free: 0.283 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1248 5.2 %RANDOM
Rwork0.194 ---
obs0.197 24225 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.479 Å2
Baniso -1Baniso -2Baniso -3
1--1.01 Å20 Å20 Å2
2---0.56 Å20 Å2
3---1.58 Å2
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4072 0 6 47 4125
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224184
X-RAY DIFFRACTIONr_bond_other_d0.0010.022829
X-RAY DIFFRACTIONr_angle_refined_deg1.2551.9545688
X-RAY DIFFRACTIONr_angle_other_deg0.8053.0046899
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1225524
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.83324.22173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.21915674
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4351518
X-RAY DIFFRACTIONr_chiral_restr0.0720.2624
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024644
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02826
X-RAY DIFFRACTIONr_nbd_refined0.1850.2607
X-RAY DIFFRACTIONr_nbd_other0.190.22648
X-RAY DIFFRACTIONr_nbtor_refined0.1810.21943
X-RAY DIFFRACTIONr_nbtor_other0.0840.22298
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.298
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3460.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.140.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0750.23
X-RAY DIFFRACTIONr_mcbond_it2.7692.53373
X-RAY DIFFRACTIONr_mcbond_other0.5172.51063
X-RAY DIFFRACTIONr_mcangle_it3.64554260
X-RAY DIFFRACTIONr_scbond_it2.672.51871
X-RAY DIFFRACTIONr_scangle_it3.82351428
LS refinement shellResolution: 2.6→2.653 Å / Total num. of bins used: 25
RfactorNum. reflection% reflection
Rfree0.413 93 -
Rwork0.304 1340 -
all-1433 -
obs--100 %
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)
13.8860.66621.17643.7232-0.39632.04110.0087-0.22490.12240.1727-0.0860.0037-0.09410.13190.0773-0.2637-0.0369-0.0034-0.1109-0.009-0.2229-25.4998-52.30421.7867
28.85730.020.35584.85580.12682.6832-0.0486-1.31770.1570.94930.0889-0.1741-0.31-0.4198-0.04030.23650.0188-0.03860.0986-0.1095-0.1399-45.5629-27.66916.8947
34.4846-0.8891.1811.2973-0.32771.49730.00870.1869-0.1329-0.02950.01130.03920.0637-0.0473-0.02-0.2283-0.0530.0169-0.1765-0.0209-0.2066-43.4596-58.8465-10.6603
45.72542.74561.25666.75180.78942.6788-0.41130.27461.0980.28080.35320.207-0.966-0.13750.05810.16540.06070.0316-0.08060.01650.0534-52.8848-21.8276-6.5557
50.35960.8805-0.40529.184-3.20931.156-0.1310.0398-0.1964-1.34290.0132-0.04830.62670.0130.11780.35510.0473-0.0175-0.0513-0.09990.2601-33.1874-95.9046-7.692
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1HA0 - 1153 - 123
2X-RAY DIFFRACTION2HA116 - 215124 - 223
3X-RAY DIFFRACTION3LB1 - 1091 - 113
4X-RAY DIFFRACTION4LB110 - 213114 - 217
5X-RAY DIFFRACTION5VC14 - 1087 - 101

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