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- PDB-4qaf: Crystal structure of an engineered lipocalin (Anticalin) in compl... -

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Basic information

Entry
Database: PDB / ID: 4qaf
TitleCrystal structure of an engineered lipocalin (Anticalin) in complex with VEGF(8-109)
Components
  • Lipocalin-1
  • Vascular endothelial growth factor A
KeywordsTRANSPORT PROTEIN/SIGNALING PROTEIN / beta-barrel / binding protein / engineered lipocalin / TRANSPORT PROTEIN-SIGNALING PROTEIN complex
Function / homology
Function and homology information


Transport of fatty acids / 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 ...Transport of fatty acids / 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 / vascular endothelial growth factor receptor binding / VEGF ligand-receptor interactions / post-embryonic camera-type eye development / positive regulation of mast cell chemotaxis / lymph vessel morphogenesis / 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 / endothelial cell chemotaxis / positive regulation of trophoblast cell migration / vascular endothelial growth factor receptor-2 signaling pathway / positive regulation of epithelial tube formation / VEGF binds to VEGFR leading to receptor dimerization / motor neuron migration / 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 / neuropilin binding / coronary artery morphogenesis / induction of positive chemotaxis / transmembrane receptor protein tyrosine kinase activator activity / negative regulation of cell-cell adhesion mediated by cadherin / vascular endothelial growth factor receptor 2 binding / commissural neuron axon guidance / dopaminergic neuron differentiation / tube formation / positive regulation of vascular endothelial growth factor signaling pathway / positive regulation of vascular permeability / positive regulation of blood vessel branching / platelet-derived growth factor receptor binding / surfactant homeostasis / endothelial cell proliferation / extracellular matrix binding / cell migration involved in sprouting angiogenesis / epithelial cell maturation / positive regulation of leukocyte migration / positive regulation of positive chemotaxis / cardiac muscle cell development / sprouting angiogenesis / Regulation of gene expression by Hypoxia-inducible Factor / positive regulation of endothelial cell chemotaxis / vascular endothelial growth factor signaling pathway / chloride ion binding / artery morphogenesis / negative regulation of epithelial to mesenchymal transition / positive regulation of cell migration involved in sprouting angiogenesis / positive regulation of peptidyl-tyrosine phosphorylation / 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 chemotaxis / positive regulation of sprouting angiogenesis / chemoattractant activity / mesoderm development / outflow tract morphogenesis / positive regulation of protein autophosphorylation / monocyte differentiation / macrophage differentiation / fibronectin binding / positive regulation of cell division / positive regulation of receptor internalization / cysteine-type endopeptidase inhibitor activity / mammary gland alveolus development / neuroblast proliferation / 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 / ovarian follicle development / homeostasis of number of cells within a tissue / positive regulation of endothelial cell proliferation / lactation
Similarity search - Function
von Ebner's gland protein/ Bos/Can allergen / 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. ...von Ebner's gland protein/ Bos/Can allergen / 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 / Lipocalin / Cystine-knot cytokine / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Ribbon / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Chem-OMA / Vascular endothelial growth factor A, long form / Lipocalin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD, MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGiese, T. / Skerra, A.
CitationJournal: To be Published
Title: Crystal structure of an Anticalin with specific blocking activity towards human vascular endothelial growth factor (VEGF) reveals plasticity of the lipocalin fold
Authors: Giese, T. / Skerra, A.
History
DepositionMay 4, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lipocalin-1
C: Vascular endothelial growth factor A
D: Vascular endothelial growth factor A
B: Lipocalin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,60310
Polymers58,6674
Non-polymers9366
Water3,783210
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7340 Å2
ΔGint-104 kcal/mol
Surface area19670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.210, 88.210, 103.421
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein Lipocalin-1 / Tear lipocalin / Tlc / Tear prealbumin / TP / Von Ebner gland protein / VEG protein


Mass: 16184.311 Da / Num. of mol.: 2 / Fragment: UNP residues 23-174
Mutation: R26V,E27G,F28A,P29L,E30R,M31C,N32L,L33A,E34G,T37I,M39T,L56H,S58K,C61S,E69S,K76I,D80I,K83I,Y87K,I89G,C101S,E104C,H106S,K108V,R111P,K114W,C153S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: engineered variant, LCN1 / Plasmid: pTLc99 / Production host: Escherichia coli (E. coli) / Strain (production host): JM83 / References: UniProt: P31025
#2: Protein Vascular endothelial growth factor A / VEGF-A / Vascular permeability factor / VPF


Mass: 13148.979 Da / Num. of mol.: 2 / Fragment: UNP residues 34-135
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VEGFA, VEGF / Plasmid: pVEGFs / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P15692

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Non-polymers , 4 types, 216 molecules

#3: Chemical ChemComp-OMA / 10-{(1R,2R)-2-[(2E)-hex-2-en-1-yl]cyclopropyl}decanoic acid


Mass: 294.472 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H34O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 1.98 Å3/Da / Density % sol: 37.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.5
Details: 1 M sodium chloride, 0.2 M lithium sulfate, 7.5% w/v dextran sulfate, pH 3.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 29, 2009 / Details: mirrors
RadiationMonochromator: sagittally bent Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.8→35 Å / Num. all: 43626 / Num. obs: 43539 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.75 % / Biso Wilson estimate: 33.05 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 23.88
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.8-1.850.4263.95185113189199.9
1.85-1.90.3055.44179133086199.9
1.9-1.950.2247.25175723027199.9
1.95-2.010.1898.641704729471100
2.01-2.080.14211.11652728361100
2.08-2.150.11913.231617927891100
2.15-2.230.09615.98154232631199.9
2.23-2.320.07619.14148902578199.7
2.32-2.430.06521.76144572471199.9
2.43-2.550.05824.52136042342199.9
2.55-2.680.04629.491308322581100
2.68-2.850.04233.531235421371100
2.85-3.040.03737.89116622012199.9
3.04-3.290.03144.44107161870199.9
3.29-3.60.02950.197801723199.8
3.6-4.020.02852.7289271593199.8
4.02-4.650.02656.5577901398199.8
4.65-5.690.02556.5466371194199.9
5.69-8.050.02455.615176953199.7
8.05-350.02848.482217505191

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
MAR345dtbdata collection
XDSdata reduction
Auto-Rickshawphasing
RefinementMethod to determine structure: SAD, MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BJ1

1bj1


Resolution: 1.8→34.47 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.934 / WRfactor Rfree: 0.2579 / WRfactor Rwork: 0.215 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8466 / SU B: 2.565 / SU ML: 0.081 / SU R Cruickshank DPI: 0.1282 / SU Rfree: 0.1258 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2421 2195 5 %RANDOM
Rwork0.2033 ---
obs0.2053 41384 99.91 %-
all-43626 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 114.42 Å2 / Biso mean: 33.7489 Å2 / Biso min: 9.38 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→34.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3029 0 61 210 3300
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.023191
X-RAY DIFFRACTIONr_angle_refined_deg2.2141.984323
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1315392
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.33324.58131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.05715550
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.9811513
X-RAY DIFFRACTIONr_chiral_restr0.1650.2484
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212341
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 152 -
Rwork0.31 2839 -
all-2991 -
obs--100 %

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