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- PDB-1bj1: VASCULAR ENDOTHELIAL GROWTH FACTOR IN COMPLEX WITH A NEUTRALIZING... -

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Basic information

Entry
Database: PDB / ID: 1bj1
TitleVASCULAR ENDOTHELIAL GROWTH FACTOR IN COMPLEX WITH A NEUTRALIZING ANTIBODY
Components
  • Fab fragment, heavy chain
  • Fab fragment, light chain
  • Vascular endothelial growth factor A
KeywordsIMMUNE SYSTEM / COMPLEX (ANTIBODY-ANTIGEN) / ANGIOGENIC FACTOR
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 / lymph vessel morphogenesis ...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 / lymph vessel morphogenesis / vascular endothelial growth factor receptor binding / VEGF ligand-receptor interactions / post-embryonic camera-type eye development / positive regulation of mast cell chemotaxis / 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 / positive regulation of vascular endothelial growth factor signaling pathway / endothelial cell chemotaxis / positive regulation of trophoblast cell migration / vascular endothelial growth factor receptor-2 signaling pathway / motor neuron migration / positive regulation of epithelial tube formation / VEGF binds to VEGFR leading to receptor dimerization / 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 / transmembrane receptor protein tyrosine kinase activator activity / neuropilin binding / coronary artery morphogenesis / induction of positive chemotaxis / vascular endothelial growth factor receptor 2 binding / tube formation / negative regulation of cell-cell adhesion mediated by cadherin / commissural neuron axon guidance / dopaminergic neuron differentiation / positive regulation of vascular permeability / platelet-derived growth factor receptor binding / surfactant homeostasis / cell migration involved in sprouting angiogenesis / endothelial cell proliferation / extracellular matrix binding / epithelial cell maturation / positive regulation of positive chemotaxis / positive regulation of leukocyte migration / cardiac muscle cell development / sprouting angiogenesis / Regulation of gene expression by Hypoxia-inducible Factor / positive regulation of p38MAPK cascade / positive regulation of endothelial cell chemotaxis / vascular endothelial growth factor signaling pathway / negative regulation of epithelial to mesenchymal transition / artery morphogenesis / positive regulation of cell migration involved in sprouting angiogenesis / 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 regulation of sprouting angiogenesis / positive chemotaxis / chemoattractant activity / mesoderm development / outflow tract morphogenesis / monocyte differentiation / macrophage differentiation / fibronectin binding / positive regulation of cell division / positive regulation of receptor internalization / neuroblast proliferation / mammary gland alveolus development / 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 / positive regulation of protein autophosphorylation / 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: 2.4 Å
AuthorsMuller, Y.A. / Christinger, H.W. / De Vos, A.M.
Citation
Journal: Structure / Year: 1998
Title: VEGF and the Fab fragment of a humanized neutralizing antibody: crystal structure of the complex at 2.4 A resolution and mutational analysis of the interface.
Authors: Muller, Y.A. / Chen, Y. / Christinger, H.W. / Li, B. / Cunningham, B.C. / Lowman, H.B. / de Vos, A.M.
#1: Journal: J.Biol.Chem. / Year: 1997
Title: Antibody Humanization Using Monovalent Phage Display
Authors: Baca, M. / Presta, L.G. / O'Connor, S.J. / Wells, J.A.
#2: Journal: Cancer Res. / Year: 1997
Title: Humanization of an Anti-Vascular Endothelial Growth Factor Monoclonal Antibody for the Therapy of Solid Tumors and Other Disorders
Authors: Presta, L.G. / Chen, H. / O'Connor, S.J. / Chisholm, V. / Meng, Y.G. / Krummen, L. / Winkler, M. / Ferrara, N.
History
DepositionJun 30, 1998Processing site: BNL
Revision 1.0Jan 13, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 26, 2018Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_prop / struct_keywords / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_name_com.name ..._entity.pdbx_description / _entity_name_com.name / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_seq_type / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _struct_keywords.pdbx_keywords / _struct_keywords.text / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.entity_id / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_db_isoform / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.pdbx_strand_id / _struct_ref_seq.ref_id / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end
Revision 1.4Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Fab fragment, light chain
H: Fab fragment, heavy chain
V: Vascular endothelial growth factor A
W: Vascular endothelial growth factor A
J: Fab fragment, light chain
K: Fab fragment, heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,8158
Polymers120,6236
Non-polymers1922
Water9,872548
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.860, 66.980, 140.510
Angle α, β, γ (deg.)90.00, 94.27, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
55
/ NCS ensembles :
ID
1
2
3
4
5

NCS oper:
IDCodeMatrixVector
1given(-0.71072, 0.64251, -0.28645), (0.64095, 0.42361, -0.64012), (-0.28994, -0.63854, -0.71288)54.82044, -28.79642, -9.24218
2given(-0.739628, 0.624519, -0.25085), (0.591152, 0.424688, -0.685696), (-0.321698, -0.655451, -0.683297)54.21593, -27.24564, -9.62751
3given(-0.735665, 0.630878, -0.246556), (0.594965, 0.42788, -0.680394), (-0.323749, -0.647234, -0.690126)54.00932, -27.26712, -9.39712
4given(-0.730897, 0.64445, -0.224663), (0.587447, 0.426486, -0.687761), (-0.347412, -0.63466, -0.690298)53.20964, -26.53706, -9.98252
5given(-0.736348, 0.63769, -0.226147), (0.593318, 0.447919, -0.668836), (-0.325214, -0.626673, -0.708178)53.07691, -27.89837, -8.75862

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Components

#1: Antibody Fab fragment, light chain / FAB-12


Mass: 23471.949 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: HUMANIZED VERSION OF A MONOCLONAL MURINE ANTI-VEGF ANTIBODY
Source: (gene. exp.) Mus musculus (house mouse)
Description: HUMANIZED VERSION OF A MONOCLONAL MURINE ANTI-VEGF ANTIBODY
Production host: Escherichia coli (E. coli)
#2: Antibody Fab fragment, heavy chain / FAB-12


Mass: 24890.764 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: HUMANIZED VERSION OF A MONOCLONAL MURINE ANTI-VEGF ANTIBODY
Source: (gene. exp.) Mus musculus (house mouse)
Description: HUMANIZED VERSION OF A MONOCLONAL MURINE ANTI-VEGF ANTIBODY
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.: 2 / Fragment: RECEPTOR BINDING DOMAIN
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
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 548 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE NUMBERING OF THE LIGHT CHAINS L AND J AS WELL AS OF THE HEAVY CHAINS H AND K IS SEQUENTIAL. ...THE NUMBERING OF THE LIGHT CHAINS L AND J AS WELL AS OF THE HEAVY CHAINS H AND K IS SEQUENTIAL. CONVERSION TO THE KABAT NUMBERING (E.A. KABAT, T.T. WU, M. REID-MILLER, H.M. PERRY, K.S. GOTTESMAN (1991) SEQUENCES OF PROTEINS OF IMMUNOLOGICAL INTEREST, 5TH ED, NATIONAL INSTITUTES OF HEALTH, BETHESDA, MD) IS GIVEN BELOW: SEQUENTIAL NUMBERING KABAT NUMBERING LIGHT CHAIN 1 - 213 1 - 213 HEAVY CHAIN 1 - 52 1 - 52 53 52A 54 - 83 53 - 82 84 - 86 82A - 82C 87 - 104 83 - 100 105 - 110 100A - 100F 111 - 226 101 - 216

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.6 Å3/Da / Density % sol: 66 %
Crystal growpH: 6 / Details: pH 6.0
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Details: drop solution was mixed with an equal volume of reservoir solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17.8 A280protein1drop
230 mMTris-HCl1drop
30.4 Msodium chloride1drop
415 %PEG1reservoir
510 %isopropanol1reservoir
60.2 Mammonium sulfate1reservoir
70.2 MMES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.914
DetectorType: ADSC QUANTUM / Detector: CCD / Date: Mar 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.914 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 63147 / % possible obs: 96 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 8.6
Reflection shellResolution: 2.4→2.48 Å / Rmerge(I) obs: 0.128 / Mean I/σ(I) obs: 3.5 / % possible all: 81.3
Reflection shell
*PLUS
% possible obs: 81.3 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.8model building
X-PLOR3.8refinement
X-PLOR3.8phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VPF AND 1FVD

2vpf

1fvd


Resolution: 2.4→8 Å / Rfactor Rfree error: 0.0035 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE MODEL IS UNUSUAL IN REGARD TO THE HIGH AVERAGE TEMPERATURE FACTOR OF 100 A2 OF THE CONSTANT DOMAIN OF THE SECOND FAB MOLECULE. HOWEVER THE USE OF NON-CRYSTALLOGRAPHIC SYMMETRY RESTRAINTS ...Details: THE MODEL IS UNUSUAL IN REGARD TO THE HIGH AVERAGE TEMPERATURE FACTOR OF 100 A2 OF THE CONSTANT DOMAIN OF THE SECOND FAB MOLECULE. HOWEVER THE USE OF NON-CRYSTALLOGRAPHIC SYMMETRY RESTRAINTS GREATLY RESTRICTS THE CONFORMATIONAL FREEDOM OF THIS PORTION TO THE WELL-DEFINED CONSTANT DOMAIN OF THE FIRST FAB FRAGMENT. MORE DETAILS CAN BE FOUND IN THE PRIMARY PUBLICATION.
RfactorNum. reflection% reflectionSelection details
Rfree0.266 5908 9.8 %THIN RESOLUTION SHELLS
Rwork0.196 ---
obs0.196 60401 94.8 %-
Displacement parametersBiso mean: 42 Å2
Baniso -1Baniso -2Baniso -3
1-3.7 Å20 Å2-0.31 Å2
2---8.5 Å20 Å2
3---4.8 Å2
Refine analyzeLuzzati sigma a obs: 0.35 Å
Refinement stepCycle: LAST / Resolution: 2.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8136 0 10 548 8694
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.66
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.97
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.47
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.61.5
X-RAY DIFFRACTIONx_mcangle_it4.12
X-RAY DIFFRACTIONx_scbond_it52
X-RAY DIFFRACTIONx_scangle_it7.32.5
Refine LS restraints NCS
Ens-IDDom-IDNCS model detailsRefine-IDRms dev position (Å)Weight position
11RESTRAINTSX-RAY DIFFRACTION0.23120
22X-RAY DIFFRACTION0.2220
33X-RAY DIFFRACTION0.22720
44X-RAY DIFFRACTION0.4235
55X-RAY DIFFRACTION0.3985
LS refinement shellResolution: 2.4→2.48 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.341 389 7.9 %
Rwork0.312 4550 -
obs--78.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 54493
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.97
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.47
LS refinement shell
*PLUS
Rfactor obs: 0.312

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