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- PDB-4ckv: Crystal structure of VEGFR-1 domain 2 in presence of Zn -

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Basic information

Entry
Database: PDB / ID: 4ckv
TitleCrystal structure of VEGFR-1 domain 2 in presence of Zn
ComponentsVASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 1VEGF receptor
KeywordsRECEPTOR
Function / homology
Function and homology information


vascular endothelial growth factor receptor-1 signaling pathway / placental growth factor receptor activity / hyaloid vascular plexus regression / Neurophilin interactions with VEGF and VEGFR / VEGF binds to VEGFR leading to receptor dimerization / vascular endothelial growth factor receptor activity / embryonic morphogenesis / negative regulation of vascular endothelial cell proliferation / blood vessel morphogenesis / growth factor binding ...vascular endothelial growth factor receptor-1 signaling pathway / placental growth factor receptor activity / hyaloid vascular plexus regression / Neurophilin interactions with VEGF and VEGFR / VEGF binds to VEGFR leading to receptor dimerization / vascular endothelial growth factor receptor activity / embryonic morphogenesis / negative regulation of vascular endothelial cell proliferation / blood vessel morphogenesis / growth factor binding / monocyte chemotaxis / cellular response to vascular endothelial growth factor stimulus / vascular endothelial growth factor receptor signaling pathway / : / transmembrane receptor protein tyrosine kinase activity / cell surface receptor protein tyrosine kinase signaling pathway / positive regulation of MAP kinase activity / receptor protein-tyrosine kinase / peptidyl-tyrosine phosphorylation / positive regulation of angiogenesis / cell migration / actin cytoskeleton / angiogenesis / positive regulation of MAPK cascade / protein autophosphorylation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell differentiation / receptor complex / endosome / positive regulation of cell migration / focal adhesion / positive regulation of cell population proliferation / extracellular space / ATP binding / plasma membrane
Similarity search - Function
Vascular endothelial growth factor receptor 1 (VEGFR1) / 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 / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin I-set ...Vascular endothelial growth factor receptor 1 (VEGFR1) / 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 / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / 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 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.055 Å
AuthorsGaucher, J.-F. / Reille-Seroussi, M. / Gagey-Eilstein, N. / Broussy, S. / Coric, P. / Seijo, B. / Lascombe, M.-B. / Gautier, B. / Liu, W.-Q. / Huguenot, F. ...Gaucher, J.-F. / Reille-Seroussi, M. / Gagey-Eilstein, N. / Broussy, S. / Coric, P. / Seijo, B. / Lascombe, M.-B. / Gautier, B. / Liu, W.-Q. / Huguenot, F. / Inguimbert, N. / Bouaziz, S. / Vidal, M. / Broutin, I.
CitationJournal: Plos One / Year: 2016
Title: Biophysical Studies of the Induced Dimerization of Human Vegf R Receptor 1 Binding Domain by Divalent Metals Competing with Vegf-A
Authors: Gaucher, J.-F. / Reille-Seroussi, M. / Gagey-Eilstein, N. / Broussy, S. / Coric, P. / Seijo, B. / Lascombe, M.-B. / Gautier, B. / Liu, W.-Q. / Huguenot, F. / Inguimbert, N. / Bouaziz, S. / ...Authors: Gaucher, J.-F. / Reille-Seroussi, M. / Gagey-Eilstein, N. / Broussy, S. / Coric, P. / Seijo, B. / Lascombe, M.-B. / Gautier, B. / Liu, W.-Q. / Huguenot, F. / Inguimbert, N. / Bouaziz, S. / Vidal, M. / Broutin, I.
History
DepositionJan 9, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 28, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2017Group: Database references
Revision 2.0Mar 6, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Experimental preparation / Other
Category: atom_site / exptl_crystal_grow ...atom_site / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _atom_site.occupancy / _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 2.1May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.temp
Revision 2.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1196
Polymers10,8061
Non-polymers3145
Water1,45981
1
X: VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 1
hetero molecules

X: VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,23812
Polymers21,6112
Non-polymers62710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area2190 Å2
ΔGint-54.8 kcal/mol
Surface area11230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.730, 102.390, 27.470
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11X-1226-

ZN

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Components

#1: Protein VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 1 / VEGF receptor / VEGFR-1 / FMS-LIKE TYROSINE KINASE 1 / FLT-1 / TYROSINE-PROTEIN KINASE FRT / TYROSINE-PROTEIN ...VEGFR-1 / FMS-LIKE TYROSINE KINASE 1 / FLT-1 / TYROSINE-PROTEIN KINASE FRT / TYROSINE-PROTEIN KINASE RECEPTOR FLT / FLT / VASCULAR PERMEABILITY FACTOR RECEPTOR


Mass: 10805.559 Da / Num. of mol.: 1 / Fragment: DOMAIN-2, RESIDUES 132-225
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA-GAMI PLYSS
References: UniProt: P17948, receptor protein-tyrosine kinase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 3.06 Å3/Da / Density % sol: 59.8 % / Description: NONE
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.5
Details: VAPOR DIFFUSION METHOD, MOTHER LIQUOR:1MM VEGFR-1-D2,0.1%(W/V) DDM,4MM LAXAPHYCINE-A,5MM HEPES/NAOH PH 7.5. RESERVOIR:18% (W/V) PEG8000,100MM HEPES/NAOH PH 7.5, 18C

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 17, 2010
Details: CYLINDRICAL GRAZING INCIDENCE MIRROR BENT TO APPROXIMATE TO A TOROIDAL CURVATURE
RadiationMonochromator: LIQUID NITROGEN COOLED CHANNEL-CUT SILICON MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.05→47.86 Å / Num. obs: 8564 / % possible obs: 96.9 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 27.29 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.46
Reflection shellResolution: 2.06→2.13 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 3.97 / % possible all: 83.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FLT

1flt


Resolution: 2.055→47.865 Å / SU ML: 0.22 / σ(F): 1.94 / Phase error: 20.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2053 731 4.8 %
Rwork0.1628 --
obs0.165 8562 93.81 %
Solvent computationShrinkage radii: 0.5 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.7 Å2
Refinement stepCycle: LAST / Resolution: 2.055→47.865 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms759 0 17 81 857
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007835
X-RAY DIFFRACTIONf_angle_d1.0911131
X-RAY DIFFRACTIONf_dihedral_angle_d13.741323
X-RAY DIFFRACTIONf_chiral_restr0.076129
X-RAY DIFFRACTIONf_plane_restr0.006143
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0554-2.21410.26211320.18432562X-RAY DIFFRACTION82
2.2141-2.43690.20861480.17392979X-RAY DIFFRACTION97
2.4369-2.78940.24491540.17093026X-RAY DIFFRACTION97
2.7894-3.51430.19091400.15192989X-RAY DIFFRACTION97
3.5143-47.8780.18881570.15932977X-RAY DIFFRACTION96
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)
10.2139-0.048-0.01250.05350.02780.02080.1318-0.27990.18370.33130.3110.1254-0.27210.14280.03780.24320.06690.03630.2228-0.010.1548-17.0395-28.615712.0867
20.20670.0243-0.03260.1097-0.01090.0941-0.4786-0.17830.22550.28480.086-0.0276-0.09920.3652-0.01130.2867-0.0301-0.04190.322-0.02940.1954-6.8743-29.594810.5401
30.0840.03460.08590.01680.02960.37470.03710.3083-0.21240.27040.2945-0.40490.61170.59460.00180.27710.019-0.01280.2235-0.08270.4089-7.5716-45.41410.317
40.26630.20480.25890.39070.30250.29660.05360.10920.18660.18080.0022-0.00080.0299-0.16050.01540.16880.04060.01260.13720.02640.1526-18.9071-31.89333.9696
50.30640.11690.16670.7947-0.16560.15120.20640.11550.0731-0.2497-0.31180.21380.18240.4225-0.02040.1679-0.0136-0.01070.30950.01860.1551-12.5936-32.2397-7.443
60.0676-0.00660.2526-0.00110.00970.89910.04350.2118-0.26550.06120.0747-0.10590.5402-0.70510.04460.2343-0.00660.02780.1582-0.02980.1748-20.9227-38.2803-0.5648
70.5647-0.4235-0.00223.1161-1.41251.80530.01570.2161-0.4413-0.4090.4880.2255-0.23610.50540.87290.1483-0.0549-0.06660.2537-0.18840.1578-12.9329-42.1695-5.0924
80.02690.0070.03690.02120.00560.0337-0.19940.1783-0.1307-0.26850.465-0.0578-0.1251-0.161800.2109-0.0688-0.0090.3476-0.05120.2261-5.8522-36.0209-3.5873
90.011-0.035-0.00250.09730.09590.1077-0.00780.06920.1734-0.02360.098-0.1601-0.1281-0.0660.01010.20570.00550.01350.13930.00530.1814-15.7956-21.91035.4366
100.07840.0527-0.13090.0776-0.01650.2058-0.1271-0.0865-0.4251-0.2887-0.25220.0640.13550.5447-0.00660.20910.0780.01080.3024-0.06570.2926-4.1341-37.88442.8738
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN X AND RESID 132:137)
2X-RAY DIFFRACTION2(CHAIN X AND RESID 138:144)
3X-RAY DIFFRACTION3(CHAIN X AND RESID 145:153)
4X-RAY DIFFRACTION4(CHAIN X AND RESID 154:170)
5X-RAY DIFFRACTION5(CHAIN X AND RESID 171:182)
6X-RAY DIFFRACTION6(CHAIN X AND RESID 183:190)
7X-RAY DIFFRACTION7(CHAIN X AND RESID 191:199)
8X-RAY DIFFRACTION8(CHAIN X AND RESID 200:205)
9X-RAY DIFFRACTION9(CHAIN X AND RESID 206:218)
10X-RAY DIFFRACTION10(CHAIN X AND RESID 219:224)

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