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- PDB-3s36: Structural basis for the function of two anti-VEGF receptor antibodies -

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Basic information

Entry
Database: PDB / ID: 3s36
TitleStructural basis for the function of two anti-VEGF receptor antibodies
Components
  • 1121B heavy chain
  • 1121B light chain
  • Vascular endothelial growth factor receptor 2VEGF receptor
KeywordsIMMUNE SYSTEM/Transferase / antibody / KDR / VEGF receptor / cancer / IMMUNE SYSTEM-Transferase complex
Function / homology
Function and homology information


blood vessel endothelial cell differentiation / cellular response to hydrogen sulfide / regulation of bone development / regulation of hematopoietic progenitor cell differentiation / Signaling by membrane-tethered fusions of PDGFRA or PDGFRB / endothelium development / Neurophilin interactions with VEGF and VEGFR / vascular endothelial growth factor binding / positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway / vascular endothelial growth factor receptor-2 signaling pathway ...blood vessel endothelial cell differentiation / cellular response to hydrogen sulfide / regulation of bone development / regulation of hematopoietic progenitor cell differentiation / Signaling by membrane-tethered fusions of PDGFRA or PDGFRB / endothelium development / Neurophilin interactions with VEGF and VEGFR / vascular endothelial growth factor binding / positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway / vascular endothelial growth factor receptor-2 signaling pathway / VEGF binds to VEGFR leading to receptor dimerization / endocardium development / vascular wound healing / vascular endothelial growth factor receptor activity / post-embryonic camera-type eye morphogenesis / endothelial cell differentiation / mesenchymal cell proliferation / positive regulation of vasculogenesis / lymph vessel development / positive regulation of BMP signaling pathway / surfactant homeostasis / epithelial cell maturation / anchoring junction / cell migration involved in sprouting angiogenesis / positive regulation of positive chemotaxis / embryonic hemopoiesis / vascular endothelial growth factor signaling pathway / positive regulation of mesenchymal cell proliferation / positive regulation of mitochondrial depolarization / positive regulation of mitochondrial fission / branching involved in blood vessel morphogenesis / positive regulation of cell migration involved in sprouting angiogenesis / lung alveolus development / positive regulation of stem cell proliferation / positive regulation of nitric-oxide synthase biosynthetic process / growth factor binding / sorting endosome / positive regulation of focal adhesion assembly / regulation of MAPK cascade / semaphorin-plexin signaling pathway / positive regulation of macroautophagy / : / positive regulation of blood vessel endothelial cell migration / cellular response to vascular endothelial growth factor stimulus / calcium ion homeostasis / cell fate commitment / vasculogenesis / Integrin cell surface interactions / vascular endothelial growth factor receptor signaling pathway / coreceptor activity / negative regulation of endothelial cell apoptotic process / peptidyl-tyrosine autophosphorylation / ovarian follicle development / positive regulation of endothelial cell proliferation / transmembrane receptor protein tyrosine kinase activity / positive regulation of endothelial cell migration / VEGFR2 mediated cell proliferation / epithelial cell proliferation / stem cell proliferation / Hsp90 protein binding / receptor protein-tyrosine kinase / VEGFA-VEGFR2 Pathway / peptidyl-tyrosine phosphorylation / cell surface receptor protein tyrosine kinase signaling pathway / positive regulation of angiogenesis / cell migration / integrin binding / cell junction / regulation of cell shape / angiogenesis / protein tyrosine kinase activity / negative regulation of neuron apoptotic process / positive regulation of MAPK cascade / protein autophosphorylation / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / early endosome / endosome / positive regulation of cell migration / cadherin binding / positive regulation of protein phosphorylation / membrane raft / external side of plasma membrane / negative regulation of gene expression / positive regulation of cell population proliferation / negative regulation of apoptotic process / Golgi apparatus / endoplasmic reticulum / extracellular region / ATP binding / identical protein binding / nucleus / plasma membrane
Similarity search - Function
Vascular endothelial growth factor receptor 2 (VEGFR2) / VEGFR-2, transmembrane domain / VEGFR-2 Transmembrane domain / Vascular endothelial growth factor receptor 1-like, Ig-like domain / Tyrosine-protein kinase, receptor class III, conserved site / Receptor tyrosine kinase class III signature. / Immunoglobulin domain / Immunoglobulin / Immunoglobulin domain / Immunoglobulin I-set ...Vascular endothelial growth factor receptor 2 (VEGFR2) / VEGFR-2, transmembrane domain / VEGFR-2 Transmembrane domain / Vascular endothelial growth factor receptor 1-like, Ig-like domain / Tyrosine-protein kinase, receptor class III, conserved site / Receptor tyrosine kinase class III signature. / Immunoglobulin domain / Immunoglobulin / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Immunoglobulin subtype / Immunoglobulin / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Vascular endothelial growth factor receptor 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsFranklin, M.C.
CitationJournal: Structure / Year: 2011
Title: The Structural Basis for the Function of Two Anti-VEGF Receptor 2 Antibodies.
Authors: Franklin, M.C. / Navarro, E.C. / Wang, Y. / Patel, S. / Singh, P. / Zhang, Y. / Persaud, K. / Bari, A. / Griffith, H. / Shen, L. / Balderes, P. / Kussie, P.
History
DepositionMay 17, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_scientific_name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: 1121B light chain
H: 1121B heavy chain
X: Vascular endothelial growth factor receptor 2


Theoretical massNumber of molelcules
Total (without water)60,0743
Polymers60,0743
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5420 Å2
ΔGint-35 kcal/mol
Surface area24300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.864, 64.864, 263.161
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Antibody 1121B light chain


Mass: 23245.830 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens / Cell line (production host): MAMMALIAN KIDNEY CELLS HEK293 / Production host: Homo sapiens (human)
#2: Antibody 1121B heavy chain


Mass: 23324.131 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens / Cell line (production host): MAMMALIAN KIDNEY CELLS HEK293 / Production host: Homo sapiens (human)
#3: Protein Vascular endothelial growth factor receptor 2 / VEGF receptor / VEGFR-2 / Fetal liver kinase 1 / FLK-1 / Kinase insert domain receptor / Protein-tyrosine kinase ...VEGFR-2 / Fetal liver kinase 1 / FLK-1 / Kinase insert domain receptor / Protein-tyrosine kinase receptor flk-1


Mass: 13504.308 Da / Num. of mol.: 1 / Fragment: domain 3 of VEGF receptor 2, UNP residues 220-338
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FLK1, KDR / Cell line (production host): Hi5 / Production host: Spodoptera frugiperda
References: UniProt: P35968, receptor protein-tyrosine kinase

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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: 2.66 Å3/Da / Density % sol: 53.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M imidazole, pH 6.5; 0.1 M CaCl2, 40% PEG 1500, 10% isopropanol, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 12, 2009
RadiationMonochromator: Diamond 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→55 Å / Num. all: 11240 / Num. obs: 11083 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.2 % / Biso Wilson estimate: 91.7 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 20.8
Reflection shellResolution: 3.2→3.37 Å / Redundancy: 10.5 % / Rmerge(I) obs: 0.688 / Mean I/σ(I) obs: 3.2 / Num. unique all: 1602 / % possible all: 98.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→54.96 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.867 / SU B: 99.966 / SU ML: 0.711 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.678 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.33187 522 4.7 %RANDOM
Rwork0.27431 ---
obs0.27698 10548 97.76 %-
all-11324 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 124.403 Å2
Baniso -1Baniso -2Baniso -3
1-4.97 Å22.48 Å20 Å2
2--4.97 Å20 Å2
3----7.45 Å2
Refinement stepCycle: LAST / Resolution: 3.2→54.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4104 0 0 0 4104
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0224199
X-RAY DIFFRACTIONr_bond_other_d0.0010.022817
X-RAY DIFFRACTIONr_angle_refined_deg0.7541.9515701
X-RAY DIFFRACTIONr_angle_other_deg0.68636895
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4025536
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.6824.172163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.89715688
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.131518
X-RAY DIFFRACTIONr_chiral_restr0.0460.2645
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0214662
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02832
X-RAY DIFFRACTIONr_mcbond_it0.0371.52681
X-RAY DIFFRACTIONr_mcbond_other0.0061.51096
X-RAY DIFFRACTIONr_mcangle_it0.07124332
X-RAY DIFFRACTIONr_scbond_it0.09531518
X-RAY DIFFRACTIONr_scangle_it0.1714.51369
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.423 38 -
Rwork0.357 750 -
obs--98.25 %
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)
112.8342-1.828-0.4633.96870.065510.63161.44370.97980.7650.54340.2387-0.1122-2.833-2.1136-1.68241.25830.53340.56410.69950.34160.313446.820818.0356-30.9653
26.8024-2.90230.96475.6646-1.240411.63410.48830.56350.46860.407-0.6470.06470.2476-0.75040.15870.4045-0.25990.16340.3509-0.02480.178227.79228.5671-4.8133
34.1533-0.2689-3.58832.9057-2.014511.47380.2937-0.645-0.06230.5305-0.1914-0.0862-0.31991.5655-0.10240.2733-0.178-0.0390.36990.01610.062362.85294.3152-22.0317
49.9466-2.45182.74287.5439-3.12898.0350.23370.5243-0.73230.5175-0.79410.74270.9381-0.62160.56040.8584-0.53350.1820.4145-0.23810.24330.5501-7.223-7.7684
59.8008-0.4594-3.09565.57961.909412.3320.6189-0.15240.55430.4142-0.1287-0.8555-0.73551.7185-0.49020.4481-0.3330.01250.76730.15180.398479.353914.5117-44.128
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L1 - 108
2X-RAY DIFFRACTION2L109 - 214
3X-RAY DIFFRACTION3H2 - 116
4X-RAY DIFFRACTION4H117 - 221
5X-RAY DIFFRACTION5X219 - 330

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