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- PDB-2xv7: Crystal structure of vascular endothelial growth factor D -

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Basic information

Entry
Database: PDB / ID: 2xv7
TitleCrystal structure of vascular endothelial growth factor D
ComponentsVASCULAR ENDOTHELIAL GROWTH FACTOR D
KeywordsHORMONE / ANGIOGENESIS / LYMPHANGIOGENESIS
Function / homology
Function and homology information


vascular endothelial growth factor receptor 3 binding / vascular endothelial growth factor receptor binding / VEGF ligand-receptor interactions / positive regulation of mast cell chemotaxis / platelet degranulation / VEGF binds to VEGFR leading to receptor dimerization / induction of positive chemotaxis / dopaminergic neuron differentiation / platelet-derived growth factor receptor binding / sprouting angiogenesis ...vascular endothelial growth factor receptor 3 binding / vascular endothelial growth factor receptor binding / VEGF ligand-receptor interactions / positive regulation of mast cell chemotaxis / platelet degranulation / VEGF binds to VEGFR leading to receptor dimerization / induction of positive chemotaxis / dopaminergic neuron differentiation / platelet-derived growth factor receptor binding / sprouting angiogenesis / vascular endothelial growth factor signaling pathway / chemoattractant activity / positive regulation of cell division / vascular endothelial growth factor receptor signaling pathway / positive regulation of endothelial cell proliferation / platelet alpha granule lumen / response to bacterium / growth factor activity / positive regulation of angiogenesis / Platelet degranulation / angiogenesis / cell population proliferation / response to hypoxia / positive regulation of protein phosphorylation / positive regulation of cell population proliferation / extracellular space / extracellular region / membrane / identical protein binding
Similarity search - Function
CXCXC repeat / CXCXC repeat / 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 ...CXCXC repeat / CXCXC repeat / 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 / Mainly Beta
Similarity search - Domain/homology
alpha-D-mannopyranose / Vascular endothelial growth factor D
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsLeppanen, V.-M. / Jeltsch, M. / Anisimov, A. / Tvorogov, D. / Aho, K. / Kalkkinen, N. / Toivanen, P. / Yla-Herttuala, S. / Ballmer-Hofer, K. / Alitalo, K.
CitationJournal: Blood / Year: 2011
Title: Structural Determinants of Vascular Endothelial Growth Factor-D - Receptor Binding and Specificity.
Authors: Leppanen, V.M. / Jeltsch, M. / Anisimov, A. / Tvorogov, D. / Aho, K. / Kalkkinen, N. / Toivanen, P. / Yla-Herttuala, S. / Ballmer-Hofer, K. / Alitalo, K.
History
DepositionOct 23, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VASCULAR ENDOTHELIAL GROWTH FACTOR D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0965
Polymers12,5621
Non-polymers1,5334
Water23413
1
A: VASCULAR ENDOTHELIAL GROWTH FACTOR D
hetero molecules

A: VASCULAR ENDOTHELIAL GROWTH FACTOR D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,19110
Polymers25,1252
Non-polymers3,0678
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_444-y-1,-x-1,-z-1/61
Buried area4960 Å2
ΔGint21.6 kcal/mol
Surface area15170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.720, 95.720, 70.940
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-2010-

HOH

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Components

#1: Protein VASCULAR ENDOTHELIAL GROWTH FACTOR D / C-FOS-INDUCED GROWTH FACTOR / VEGF-D / FIGF


Mass: 12562.252 Da / Num. of mol.: 1 / Fragment: VEGF HOMOLOGY DOMAIN, RESIDUES 92-195 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: N-GLYCOSYLATION AT ASN155 AND ASN185. / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PFASTBAC / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / Strain (production host): SF21 / References: UniProt: O43915
#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#3: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose / Mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, CYS 117 TO ALA
Sequence detailsFIRST TWO RESIDUES (ASP, PRO) ARE CLONING ARTEFACTS AND THERE IS A C-TERMINAL HEXAHISTIDINE TAG.

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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: 2.5 Å3/Da / Density % sol: 50 % / Description: NONE
Crystal growpH: 4.2
Details: A SINGLE VEGF-D CRYSTAL GREW IN 6 WEEKS AT ROOM TEMPERATURE OVER A RESERVOIR SOLUTION OF 0.1 M PHOSPHATE/CITRATE BUFFER AT PH 4.2, 40 % ETHANOL (V/V), 5 % PEG 1000 (W/V).

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 24, 2010
RadiationMonochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→80 Å / Num. obs: 36742 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 8.8 % / Biso Wilson estimate: 67.19 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 18
Reflection shellResolution: 2.9→3.05 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 3.8 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: VEGF-C FROM PDB ENTRY 2X1W

2x1w


Resolution: 2.9→19.893 Å / SU ML: 0.47 / σ(F): 1.99 / Phase error: 31.68 / Stereochemistry target values: ML
Details: THE SIDECHAINS OF THE RESIDUES TYR94, GLU97, LYS126, SER127, ASN129, SER169, VAL70, THR173, AND LYS190 ARE DISORDERED AND THE SIDECHAIN ATOMS WERE OMITTED FROM THE REFINEMENT.
RfactorNum. reflection% reflection
Rfree0.3325 454 10 %
Rwork0.2548 --
obs0.2626 4543 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.073 Å2 / ksol: 0.259 e/Å3
Displacement parametersBiso mean: 81.3 Å2
Baniso -1Baniso -2Baniso -3
1-2.8326 Å20 Å20 Å2
2--2.8326 Å20 Å2
3----5.6651 Å2
Refinement stepCycle: LAST / Resolution: 2.9→19.893 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms774 0 100 13 887
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01900
X-RAY DIFFRACTIONf_angle_d1.5431230
X-RAY DIFFRACTIONf_dihedral_angle_d33.883356
X-RAY DIFFRACTIONf_chiral_restr0.089166
X-RAY DIFFRACTIONf_plane_restr0.011143
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9002-3.31810.36451450.33921309X-RAY DIFFRACTION99
3.3181-4.17420.34761490.2411348X-RAY DIFFRACTION100
4.1742-19.8930.31221600.23621432X-RAY DIFFRACTION100
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)
11.7173-0.0933-0.71781.8608-2.51541.1530.412-0.04940.35170.27790.19990.0282-0.01930.267-0.37880.4331-0.02040.1903-0.00980.04950.1665-30.5644-30.3984-3.3104
20.92810.1498-0.25185.0111-1.18440.3538-0.3513-0.08851.08550.2769-0.2072-1.0457-1.7349-0.4917-0.33241.61030.43960.20780.57420.00760.8548-31.6475-14.39730.0723
32.0163-7.35513.51743.8979-4.41299.18420.05810.1385-3.31270.0746-0.2298-0.5304-0.7081.91720.16280.1854-0.1873-0.05620.8643-0.06841.0574-19.1024-32.8563.5458
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 91:194)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 400:404)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 500:502)

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