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- PDB-5n48: Structure of Anticalin N9B in complex with extra-domain B of huma... -

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Basic information

Entry
Database: PDB / ID: 5n48
TitleStructure of Anticalin N9B in complex with extra-domain B of human oncofetal fibronectin
Components
  • Fibronectin
  • Neutrophil gelatinase-associated lipocalin
KeywordsPROTEIN BINDING / LIPOCALIN / ANTICALIN / LIPOCALIN-BASED BINDING PROTEIN / HUMAN FIBRONECTIN / ONCOFETAL SPLICE VARIANT / FN TYPE III DOMAIN / EXTRA-DOMAIN B / EIIIB / ED-B / EXTRACELLULAR MATRIX
Function / homology
Function and homology information


negative regulation of monocyte activation / calcium-independent cell-matrix adhesion / negative regulation of transforming growth factor beta production / siderophore transport / Fibronectin matrix formation / Extracellular matrix organization / Metal sequestration by antimicrobial proteins / positive regulation of substrate-dependent cell migration, cell attachment to substrate / neural crest cell migration involved in autonomic nervous system development / peptidase activator activity ...negative regulation of monocyte activation / calcium-independent cell-matrix adhesion / negative regulation of transforming growth factor beta production / siderophore transport / Fibronectin matrix formation / Extracellular matrix organization / Metal sequestration by antimicrobial proteins / positive regulation of substrate-dependent cell migration, cell attachment to substrate / neural crest cell migration involved in autonomic nervous system development / peptidase activator activity / fibrinogen complex / peptide cross-linking / integrin activation / ALK mutants bind TKIs / cell-substrate junction assembly / iron ion sequestering activity / enterobactin binding / biological process involved in interaction with symbiont / Molecules associated with elastic fibres / proteoglycan binding / extracellular matrix structural constituent / MET activates PTK2 signaling / Syndecan interactions / p130Cas linkage to MAPK signaling for integrins / endodermal cell differentiation / small molecule binding / GRB2:SOS provides linkage to MAPK signaling for Integrins / Non-integrin membrane-ECM interactions / Signaling by ALK fusions and activated point mutants / basement membrane / ECM proteoglycans / endoplasmic reticulum-Golgi intermediate compartment / positive regulation of axon extension / Integrin cell surface interactions / Nuclear events stimulated by ALK signaling in cancer / collagen binding / extracellular matrix / Degradation of the extracellular matrix / Integrin signaling / substrate adhesion-dependent cell spreading / cell-matrix adhesion / regulation of ERK1 and ERK2 cascade / platelet alpha granule lumen / integrin-mediated signaling pathway / Post-translational protein phosphorylation / acute-phase response / Cell surface interactions at the vascular wall / Iron uptake and transport / regulation of protein phosphorylation / Signaling by high-kinase activity BRAF mutants / wound healing / MAP2K and MAPK activation / response to wounding / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / GPER1 signaling / specific granule lumen / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / positive regulation of fibroblast proliferation / Signaling by BRAF and RAF1 fusions / integrin binding / Platelet degranulation / heparin binding / nervous system development / positive regulation of cold-induced thermogenesis / heart development / regulation of cell shape / collagen-containing extracellular matrix / angiogenesis / blood microparticle / Interleukin-4 and Interleukin-13 signaling / protease binding / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell adhesion / defense response to bacterium / iron ion binding / apical plasma membrane / endoplasmic reticulum lumen / signaling receptor binding / innate immune response / apoptotic process / positive regulation of cell population proliferation / Neutrophil degranulation / positive regulation of gene expression / extracellular space / extracellular exosome / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Neutrophil gelatinase-associated lipocalin/epididymal-specific lipocalin-12 / Fibronectin type I domain / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. ...Neutrophil gelatinase-associated lipocalin/epididymal-specific lipocalin-12 / Fibronectin type I domain / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. / Fibronectin type 2 domain / Lipocalin / Lipocalin family conserved site / Calycin beta-barrel core domain / Kringle-like fold / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / EGF-like domain signature 1. / Fibronectin type III domain / Calycin / Lipocalin / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Lipocalin signature. / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
Fibronectin / Neutrophil gelatinase-associated lipocalin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSchiefner, A. / Skerra, A.
CitationJournal: Structure / Year: 2018
Title: Anticalins Reveal High Plasticity in the Mode of Complex Formation with a Common Tumor Antigen.
Authors: Schiefner, A. / Gebauer, M. / Richter, A. / Skerra, A.
History
DepositionFeb 10, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2018Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 11, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: Neutrophil gelatinase-associated lipocalin
B: Fibronectin
C: Neutrophil gelatinase-associated lipocalin
D: Fibronectin


Theoretical massNumber of molelcules
Total (without water)65,9884
Polymers65,9884
Non-polymers00
Water5,332296
1
A: Neutrophil gelatinase-associated lipocalin
B: Fibronectin


Theoretical massNumber of molelcules
Total (without water)32,9942
Polymers32,9942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint-7 kcal/mol
Surface area13330 Å2
MethodPISA
2
C: Neutrophil gelatinase-associated lipocalin
D: Fibronectin


Theoretical massNumber of molelcules
Total (without water)32,9942
Polymers32,9942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-6 kcal/mol
Surface area13260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.456, 67.801, 76.806
Angle α, β, γ (deg.)90.000, 90.060, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Neutrophil gelatinase-associated lipocalin / NGAL / 25 kDa alpha-2-microglobulin-related subunit of MMP-9 / Lipocalin-2 / Oncogene 24p3 / ...NGAL / 25 kDa alpha-2-microglobulin-related subunit of MMP-9 / Lipocalin-2 / Oncogene 24p3 / Siderocalin LCN2 / p25


Mass: 21659.764 Da / Num. of mol.: 2
Mutation: Q28H, L36R, A40M, I41R, Q49A, Y52V, S68K, L70M, R72Q, K73R, D77K, W79M, R81N, C87S, N96A, Y100P, L103P, Y106T, K125H, S127F, K134H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LCN2, HNL, NGAL / Plasmid: pNGAL98-N9B / Production host: Escherichia coli (E. coli) / Strain (production host): TG1 / References: UniProt: P80188
#2: Protein Fibronectin / / FN / Cold-insoluble globulin / CIG


Mass: 11334.474 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FN1, FN / Plasmid: pASK35(+)-EDB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P02751
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 296 / 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: 2.07 Å3/Da / Density % sol: 40.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 29 % (w/v) PEG4000, 0.1 M Na-malonate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91741 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 7, 2011
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91741 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.51
11h,-k,-l20.49
ReflectionResolution: 1.6→28.47 Å / Num. obs: 70827 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4.18 % / Biso Wilson estimate: 25.453 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.057 / Rrim(I) all: 0.065 / Χ2: 0.978 / Net I/σ(I): 14.85 / Num. measured all: 296035 / Scaling rejects: 5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.6-1.74.1720.4233.33117140.8790.48599.8
1.7-1.84.190.275.0692600.9460.3199.8
1.8-24.1930.149.17134480.9850.1699.6
2-2.54.1820.07317.27177010.9930.08399.7
2.5-34.1730.0524.6678020.9960.05799.7
3-44.1710.04130.6462760.9970.04799.6
4-64.1820.03433.0332390.9980.03999.8
6-84.1510.03532.527940.9980.0499.6
8-104.1170.02832.782910.9980.03399.3
10-28.473.8940.03231.993020.9980.03793.2

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.8.0155refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GH7

4gh7


Resolution: 1.6→28.47 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.449 / SU ML: 0.044 / SU R Cruickshank DPI: 0.0176 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.018 / ESU R Free: 0.019
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2078 3545 5 %RANDOM
Rwork0.1688 ---
obs0.1707 67277 99.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 54.83 Å2 / Biso mean: 22.795 Å2 / Biso min: 11.09 Å2
Baniso -1Baniso -2Baniso -3
1--10.75 Å2-0 Å21.05 Å2
2--27.05 Å20 Å2
3----16.31 Å2
Refinement stepCycle: final / Resolution: 1.6→28.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4217 0 0 296 4513
Biso mean---30.59 -
Num. residues----534
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0194321
X-RAY DIFFRACTIONr_bond_other_d0.0020.024097
X-RAY DIFFRACTIONr_angle_refined_deg1.9181.9585873
X-RAY DIFFRACTIONr_angle_other_deg1.13639459
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5085530
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.34324.421190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.06315721
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6421520
X-RAY DIFFRACTIONr_chiral_restr0.1170.2666
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0214828
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02972
LS refinement shellResolution: 1.598→1.64 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 240 -
Rwork0.213 4769 -
all-5009 -
obs--96.25 %
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)
10.4069-0.01160.15810.0953-0.18860.42890.02080.0051-0.0092-0.00150.00480.01870.0175-0.0039-0.02560.16420.00680.00140.0022-0.00810.145553.58294.541837.1738
20.8966-0.0423-0.21220.3445-0.71381.58760.0917-0.09290.0243-0.0494-0.06350.02160.06160.1662-0.02820.1405-0.0150.01360.0422-0.01160.112370.01741.489454.6294
30.34440.0142-0.18510.04030.16410.99030.01590.01920.01020.01040.0076-0.0187-0.0027-0.0309-0.02360.14610.00850.0180.02590.00140.121141.09932.0944-1.3041
40.777-0.06360.04740.25820.61691.55040.11770.0049-0.0029-0.0045-0.0731-0.03190.0121-0.2089-0.04460.1299-0.00720.01850.0824-0.00150.088624.55015.423516.3733
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 177
2X-RAY DIFFRACTION2B1266 - 1357
3X-RAY DIFFRACTION3C4 - 177
4X-RAY DIFFRACTION4D1265 - 1357

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