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- PDB-6bft: Structure of Bevacizumab Fab mutant in complex with VEGF -

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Basic information

Entry
Database: PDB / ID: 6bft
TitleStructure of Bevacizumab Fab mutant in complex with VEGF
Components
  • Avastin Heavy Chain Fab fragment mutant
  • Avastin Light Chain Fab fragment mutant
  • Vascular endothelial growth factor A
KeywordsIMMUNE SYSTEM / Avastin / antibody
Function / homology
Function and homology information


basophil chemotaxis / cellular stress response to acid chemical / VEGF-A complex / Signaling by VEGF / lymph vessel morphogenesis / positive regulation of lymphangiogenesis / negative regulation of adherens junction organization / vascular endothelial growth factor receptor 1 binding / negative regulation of establishment of endothelial barrier / positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway ...basophil chemotaxis / cellular stress response to acid chemical / VEGF-A complex / Signaling by VEGF / lymph vessel morphogenesis / positive regulation of lymphangiogenesis / negative regulation of adherens junction organization / vascular endothelial growth factor receptor 1 binding / negative regulation of establishment of endothelial barrier / positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway / vascular endothelial growth factor receptor binding / VEGF ligand-receptor interactions / positive regulation of mast cell chemotaxis / post-embryonic camera-type eye development / primitive erythrocyte differentiation / positive regulation of protein kinase C signaling / positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway / negative regulation of blood-brain barrier permeability / VEGF-activated neuropilin signaling pathway / bone trabecula formation / positive regulation of vascular endothelial growth factor signaling pathway / coronary vein morphogenesis / cardiac vascular smooth muscle cell development / lung vasculature development / lymphangiogenesis / eye photoreceptor cell development / positive regulation of trophoblast cell migration / endothelial cell chemotaxis / motor neuron migration / positive regulation of epithelial tube formation / 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 protein localization to early endosome / vascular wound healing / regulation of hematopoietic progenitor cell differentiation / positive regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / positive regulation of branching involved in ureteric bud morphogenesis / camera-type eye morphogenesis / neuropilin binding / induction of positive chemotaxis / coronary artery morphogenesis / negative regulation of cell-cell adhesion mediated by cadherin / vascular endothelial growth factor receptor 2 binding / dopaminergic neuron differentiation / negative regulation of epithelial to mesenchymal transition / tube formation / commissural neuron axon guidance / positive regulation of vascular permeability / platelet-derived growth factor receptor binding / surfactant homeostasis / extracellular matrix binding / cell migration involved in sprouting angiogenesis / retinal ganglion cell axon guidance / cardiac muscle cell development / epithelial cell maturation / sprouting angiogenesis / positive regulation of positive chemotaxis / endothelial cell proliferation / Regulation of gene expression by Hypoxia-inducible Factor / positive regulation of leukocyte migration / vascular endothelial growth factor signaling pathway / positive regulation of p38MAPK cascade / positive regulation of endothelial cell chemotaxis / artery morphogenesis / positive regulation of DNA biosynthetic process / branching involved in blood vessel morphogenesis / positive regulation of cell migration involved in sprouting angiogenesis / positive regulation of neuroblast proliferation / negative regulation of fat cell differentiation / positive chemotaxis / transmembrane receptor protein tyrosine kinase activator activity / positive regulation of sprouting angiogenesis / outflow tract morphogenesis / chemoattractant activity / positive regulation of focal adhesion assembly / mesoderm development / monocyte differentiation / positive regulation of receptor internalization / macrophage differentiation / positive regulation of cell division / fibronectin binding / positive regulation of cell adhesion / neuroblast proliferation / positive regulation of blood vessel endothelial cell migration / mammary gland alveolus development / cellular response to vascular endothelial growth factor stimulus / vasculogenesis / immunoglobulin complex, circulating / immunoglobulin receptor binding / positive regulation of osteoblast differentiation / vascular endothelial growth factor receptor signaling pathway / heart morphogenesis / ovarian follicle development / cell maturation / homeostasis of number of cells within a tissue / positive regulation of protein autophosphorylation / positive regulation of endothelial cell proliferation / epithelial cell differentiation
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 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Ribbon / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Immunoglobulin gamma-1 heavy chain / Vascular endothelial growth factor A, long form / Ig-like domain-containing protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsChristie, M. / Christ, D.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)DE160100608 Australia
Australian Research Council (ARC)DP160104915 Australia
CitationJournal: To Be Published
Title: Stable human IgG antibody therapeutics with native framework structure
Authors: Christie, M. / Rouet, R. / Nevoltris, D. / Langley, D. / Schofield, P. / Fabri, L. / Tingey, K. / Lowe, D. / Jermutus, L. / Christ, D.
History
DepositionOct 27, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 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 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Avastin Light Chain Fab fragment mutant
A: Avastin Heavy Chain Fab fragment mutant
L: Avastin Light Chain Fab fragment mutant
H: Avastin Heavy Chain Fab fragment mutant
G: Vascular endothelial growth factor A
C: Vascular endothelial growth factor A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,34310
Polymers120,7616
Non-polymers5834
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14220 Å2
ΔGint-101 kcal/mol
Surface area47580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.279, 88.749, 106.676
Angle α, β, γ (deg.)90.00, 111.87, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules GC

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


Mass: 11933.665 Da / Num. of mol.: 2 / Fragment: UNP residues 214-315
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VEGFA, VEGF / Production host: Escherichia coli (E. coli) / References: UniProt: P15692

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Antibody , 2 types, 4 molecules BLAH

#1: Antibody Avastin Light Chain Fab fragment mutant


Mass: 23527.969 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: Q8TCD0
#2: Antibody Avastin Heavy Chain Fab fragment mutant


Mass: 24918.730 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: P0DOX5

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Non-polymers , 3 types, 135 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 3.03 Å3/Da / Density % sol: 59.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 100 mM MES, 6.0, 225 mM ammonium sulfate, 13% PEG4000, 10% isopropanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.55→45 Å / Num. obs: 47223 / % possible obs: 99.8 % / Redundancy: 5.2 % / Rpim(I) all: 0.056 / Net I/σ(I): 11.6
Reflection shellResolution: 2.55→2.64 Å / Num. unique all: 4516 / CC1/2: 0.816

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1BJ1

1bj1


Resolution: 2.55→45 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 0.04 / Phase error: 23.56
RfactorNum. reflection% reflection
Rfree0.2199 2395 5.09 %
Rwork0.1702 --
obs0.1727 47199 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.55→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8194 0 34 131 8359
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018449
X-RAY DIFFRACTIONf_angle_d1.08211498
X-RAY DIFFRACTIONf_dihedral_angle_d15.3155033
X-RAY DIFFRACTIONf_chiral_restr0.0591251
X-RAY DIFFRACTIONf_plane_restr0.0061471
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5481-2.57710.381410.29442744X-RAY DIFFRACTION95
2.5771-2.60740.33921370.26822987X-RAY DIFFRACTION100
2.6074-2.63920.3151680.25712902X-RAY DIFFRACTION100
2.6392-2.67260.3531530.2492919X-RAY DIFFRACTION100
2.6726-2.70770.29662020.24312896X-RAY DIFFRACTION100
2.7077-2.74480.29711930.21742875X-RAY DIFFRACTION100
2.7448-2.7840.29411770.22112965X-RAY DIFFRACTION100
2.784-2.82560.27291390.22092926X-RAY DIFFRACTION100
2.8256-2.86970.32931500.21752927X-RAY DIFFRACTION100
2.8697-2.91680.26651750.21312885X-RAY DIFFRACTION100
2.9168-2.9670.28761440.21863033X-RAY DIFFRACTION100
2.967-3.0210.28531400.21292847X-RAY DIFFRACTION100
3.021-3.07910.27351400.21312983X-RAY DIFFRACTION100
3.0791-3.14190.23891680.20652882X-RAY DIFFRACTION100
3.1419-3.21020.28511560.20262966X-RAY DIFFRACTION100
3.2102-3.28490.25721210.20472988X-RAY DIFFRACTION100
3.2849-3.3670.25391810.19162894X-RAY DIFFRACTION100
3.367-3.4580.22241450.17782929X-RAY DIFFRACTION100
3.458-3.55970.22591670.172926X-RAY DIFFRACTION100
3.5597-3.67460.23541110.16652970X-RAY DIFFRACTION100
3.6746-3.80580.18861540.15382925X-RAY DIFFRACTION100
3.8058-3.95810.16891770.13992906X-RAY DIFFRACTION100
3.9581-4.13810.16211640.12982908X-RAY DIFFRACTION100
4.1381-4.35610.17421960.11632925X-RAY DIFFRACTION100
4.3561-4.62880.13831470.10952951X-RAY DIFFRACTION100
4.6288-4.98580.1351720.10452879X-RAY DIFFRACTION100
4.9858-5.48670.17151510.12082936X-RAY DIFFRACTION100
5.4867-6.27890.17571240.14962983X-RAY DIFFRACTION100
6.2789-7.90370.20391790.16022882X-RAY DIFFRACTION100
7.9037-45.00890.17491300.15392963X-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)
10.4761-0.0741-0.02650.4125-0.08260.50060.003-0.02450.03720.05330.0722-0.0811-0.07970.05350.00020.21030.0655-0.01180.2399-0.02950.15849.079612.8374164.3931
20.49220.0707-0.03650.240.24940.83920.06290.1141-0.11460.0576-0.02180.06390.095-0.0051-0.00020.1870.01970.00760.2103-0.00820.19756.1157-0.539151.9619
30.47990.15230.10310.50640.16610.5211-0.09640.069-0.0009-0.09420.0003-0.005-0.0046-0.1042-0.05280.1544-0.0050.01170.0654-0.0220.1217-96.4866-19.552997.1873
40.76140.35810.14630.40830.3750.4148-0.0231-0.09830.02940.0589-0.0309-0.01530.08430.041-0.00310.1879-0.00130.00040.10430.02060.1443-92.9318-17.2442115.9105
50.3706-0.1680.18750.2514-0.31680.3933-0.1202-0.39230.11560.04930.0003-0.02450.0326-0.0107-0.00550.20230.0498-0.01210.2817-0.08450.2647-41.56024.3919135.6483
60.1545-0.13120.08170.4129-0.19840.12010.03820.26870.1543-0.0332-0.08540.00070.12260.1673-0.00150.1880.01460.00550.2327-0.02140.2104-46.1438-2.5353121.6357
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'B' and resid 1 through 214)
2X-RAY DIFFRACTION2(chain 'A' and resid 1 through 230)
3X-RAY DIFFRACTION3(chain 'L' and resid 1 through 213)
4X-RAY DIFFRACTION4(chain 'H' and resid 1 through 223)
5X-RAY DIFFRACTION5(chain 'G' and resid 13 through 107)
6X-RAY DIFFRACTION6(chain 'C' and resid 14 through 107)

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