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- PDB-2fjg: Structure of the G6 Fab, a phage derived Fab fragment, in complex... -

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Basic information

Entry
Database: PDB / ID: 2fjg
TitleStructure of the G6 Fab, a phage derived Fab fragment, in complex with VEGF
Components
  • Fab heavy chain
  • Fab light chain
  • Vascular endothelial growth factor A
KeywordsHORMONE/GROWTH FACTOR/IMMUNE SYSTEM / Protein Fab Complex / FAB / VEGF / Cystine knot / HORMONE-GROWTH FACTOR-IMMUNE SYSTEM COMPLEX
Function / homology
Function and homology information


basophil chemotaxis / positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway / 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 ...basophil chemotaxis / positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway / 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 / 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 / endothelial cell chemotaxis / motor neuron migration / positive regulation of trophoblast cell 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 / vascular wound healing / positive regulation of protein localization to early endosome / 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 / tube formation / positive regulation of vascular permeability / dopaminergic neuron differentiation / commissural neuron axon guidance / negative regulation of epithelial to mesenchymal transition / platelet-derived growth factor receptor binding / surfactant homeostasis / extracellular matrix binding / cell migration involved in sprouting angiogenesis / 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 / branching involved in blood vessel morphogenesis / positive regulation of cell migration involved in sprouting angiogenesis / positive regulation of DNA biosynthetic process / retinal ganglion cell axon guidance / positive regulation of neuroblast proliferation / positive chemotaxis / negative regulation of fat cell differentiation / transmembrane receptor protein tyrosine kinase activator activity / positive regulation of sprouting angiogenesis / chemoattractant activity / outflow tract morphogenesis / positive regulation of focal adhesion assembly / mesoderm development / monocyte differentiation / positive regulation of receptor internalization / macrophage differentiation / fibronectin binding / positive regulation of cell division / positive regulation of cell adhesion / neuroblast proliferation / positive regulation of blood vessel endothelial cell migration / cellular response to vascular endothelial growth factor stimulus / mammary gland alveolus development / vasculogenesis / 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 / lactation / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors
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: 2.8 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 ...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_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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
W: Vascular endothelial growth factor A
L: Fab light chain
H: Fab heavy chain
A: Fab light chain
B: Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,40613
Polymers118,7336
Non-polymers6727
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14880 Å2
ΔGint-175 kcal/mol
Surface area46000 Å2
MethodPISA
2
V: Vascular endothelial growth factor A
W: Vascular endothelial growth factor A
L: Fab light chain
H: Fab heavy chain
A: Fab light chain
B: Fab heavy chain
hetero molecules

V: Vascular endothelial growth factor A
W: Vascular endothelial growth factor A
L: Fab light chain
H: Fab heavy chain
A: Fab light chain
B: Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)238,81126
Polymers237,46612
Non-polymers1,34514
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area32480 Å2
ΔGint-368 kcal/mol
Surface area89280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.880, 117.880, 212.562
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11V
21W
12A
22L
13A
23L
14B
24H
15B
25H

NCS domain segments:

Component-ID: 1 / Refine code: 6

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALLYSLYSVA14 - 1087 - 101
21VALVALLYSLYSWB14 - 1077 - 100
12ASPASPTHRTHRAE1 - 1091 - 109
22ASPASPTHRTHRLC1 - 1091 - 109
13VALVALARGARGAE110 - 211110 - 211
23VALVALARGARGLC110 - 211110 - 211
14GLUGLUTHRTHRBF1 - 1231 - 123
24GLUGLUTHRTHRHD1 - 1231 - 123
15LYSLYSCYSCYSBF124 - 223124 - 223
25LYSLYSCYSCYSHD124 - 223124 - 223

NCS ensembles :
ID
1
2
3
4
5
DetailsChains V and W form a VEGF homodimer. Two Fabs are bound to this VEGF dimer. One fab is composed of chains L and H, the other of chains A and B

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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 (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 light chain


Mass: 23287.793 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PW0276 / Production host: Escherichia coli (E. coli)
#3: Antibody Fab heavy chain


Mass: 24130.092 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PW0276 / Production host: Escherichia coli (E. coli)
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.64 Å3/Da / Density % sol: 66.2 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2.0 M Ammonium sulfate, 5% Isopropanol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 27, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 42803 / Num. obs: 42763 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.8→2.9 Å / % possible all: 99.7

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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 the Fab was based on 2FJF.

1flt

2fjf


Resolution: 2.8→20 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.92 / SU B: 12.461 / SU ML: 0.236 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.565 / ESU R Free: 0.305 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23916 2152 5.1 %RANDOM
Rwork0.1987 ---
all0.21 40510 --
obs0.20077 40389 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.61 Å2
Baniso -1Baniso -2Baniso -3
1--1.16 Å2-0.58 Å20 Å2
2---1.16 Å20 Å2
3---1.75 Å2
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8031 0 35 0 8066
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0218273
X-RAY DIFFRACTIONr_bond_other_d0.0020.027160
X-RAY DIFFRACTIONr_angle_refined_deg1.551.95511263
X-RAY DIFFRACTIONr_angle_other_deg0.859316803
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.79751039
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_restr0.0850.21251
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029149
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021619
X-RAY DIFFRACTIONr_nbd_refined0.2050.21486
X-RAY DIFFRACTIONr_nbd_other0.2360.28247
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0910.25336
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.2136
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1370.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1660.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3040.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.1122.55219
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.84158468
X-RAY DIFFRACTIONr_scbond_it3.5942.53054
X-RAY DIFFRACTIONr_scangle_it5.61552795
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1439loose positional0.245
2A1564loose positional0.165
3A1479loose positional0.255
4B1782loose positional0.185
5B1323loose positional0.235
1A1439loose thermal1.8110
2A1564loose thermal1.9110
3A1479loose thermal2.0710
4B1782loose thermal1.8910
5B1323loose thermal1.9810
LS refinement shellResolution: 2.801→2.857 Å / Total num. of bins used: 25 /
RfactorNum. reflection
Rfree0.349 113
Rwork0.306 2325
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)
17.1812-1.2251-0.28520.4822-0.03721.7102-0.0202-0.1358-0.8568-0.2468-0.1902-0.12830.11080.03010.21040.52670.18130.1010.10030.07020.4452-88.8957133.518319.7218
23.07591.2483-0.87883.8204-2.39736.8256-0.30660.43940.15190.15830.0960.0068-0.612-0.34070.21060.43770.1665-0.10390.1752-0.050.1641-106.3871155.3332-3.2935
33.8664-0.41590.71611.16630.05642.87870.16720.5323-0.168-0.2871-0.0645-0.02190.07890.1522-0.10270.61120.28630.22080.15680.05020.4556-71.1322139.10318.3136
42.6723-0.8745-0.9015.17-0.23694.3334-0.04560.13330.2363-0.4561-0.2788-0.1638-0.15470.21350.32440.4880.1318-0.12060.25740.03140.2535-92.7925163.37040.6774
53.8149-1.79441.19311.9611-2.41294.2568-0.2031-0.08140.17440.42520.1624-0.0829-0.6674-0.46630.04080.52790.2731-0.00580.2119-0.02030.1302-25.355781.253938.3972
64.6687-0.0009-4.21652.32520.07247.033-0.1581-0.4119-0.10140.308-0.1652-0.6032-0.0251.08410.32340.24740.1098-0.06890.4670.1050.37018.223668.068732.8836
75.0118-0.6418-0.08922.0787-0.49061.9195-0.04230.01620.4474-0.10190.0719-0.1376-0.16560.1312-0.02960.42910.19540.02670.08930.0040.2345-24.828286.243617.1388
81.61671.2491-1.13877.2197-1.91133.3351-0.06050.0172-0.3376-0.0706-0.0408-0.22980.25180.33840.10130.2280.10990.09270.23780.03080.266-0.579263.363220.2056
91.7411-1.65410.17373.5561-0.13490.3979-0.0192-0.08580.40360.50750.0281-0.3956-0.0052-0.0316-0.00880.57640.19120.06710.14730.08660.4647-51.0415115.487828.2927
101.6959-1.4715-0.30323.94180.58371.01260.21770.1344-0.15450.0235-0.30810.66650.0266-0.14350.09030.45880.2520.08520.26050.00490.394-57.555102.272420.1331
11-73.5987-37.7232-62.86583.6334-100.095145.9570.1899-3.0256-1.3708-1.49423.4193-1.4633-3.1616-2.36-3.60930.4441-0.0470.07890.4388-0.09450.4784-40.973475.21719.1467
12-144.1312-30.858841.505628.9539-10.583-14.56-1.407910.059710.4666-1.20012.30290.3627-1.1286-1.8608-0.89490.42170.11310.10280.436-0.0070.4026-66.6992143.409326.8488
130000000000000000.4207000.420700.4207-60.558127.60618.6087
140000000000000000.4207000.420700.4207-33.90498.495814.2687
150000000000000000.4207000.420700.42071.368273.43776.0854
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1LC1 - 1091 - 109
2X-RAY DIFFRACTION2LC110 - 211110 - 211
3X-RAY DIFFRACTION3HD1 - 1211 - 121
4X-RAY DIFFRACTION4HD122 - 223122 - 223
5X-RAY DIFFRACTION5AE1 - 1091 - 109
6X-RAY DIFFRACTION6AE110 - 211110 - 211
7X-RAY DIFFRACTION7BF1 - 1211 - 121
8X-RAY DIFFRACTION8BF122 - 223122 - 223
9X-RAY DIFFRACTION9VA14 - 1087 - 101
10X-RAY DIFFRACTION10WB14 - 1077 - 100
11X-RAY DIFFRACTION11BG - H228 - 229
12X-RAY DIFFRACTION12HI - J228 - 229
13X-RAY DIFFRACTION13HK230
14X-RAY DIFFRACTION14BL230
15X-RAY DIFFRACTION15BM231

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