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- PDB-4gh7: Crystal structure of Anticalin N7A in complex with oncofetal fibr... -

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Basic information

Entry
Database: PDB / ID: 4gh7
TitleCrystal structure of Anticalin N7A in complex with oncofetal fibronectin fragment Fn7B8
Components
  • Fibronectin
  • Neutrophil gelatinase-associated lipocalin
KeywordsPROTEIN BINDING / lipocalin / anticalin / human fibronectin / Fn type III domain / oncofetal fibronectin splice variant P02751-7 / lipocalin-based binding protein / extra-domain B / EIIIB / ED-B / extracellular matrix
Function / homology
Function and homology information


positive regulation of iron ion import across plasma membrane / positive regulation of hippocampal neuron apoptotic process / positive regulation of endothelial tube morphogenesis / negative regulation of monocyte activation / negative regulation of hippocampal neuron apoptotic process / positive regulation of cell projection organization / negative regulation of transforming growth factor beta production / Extracellular matrix organization / Metal sequestration by antimicrobial proteins / positive regulation of substrate-dependent cell migration, cell attachment to substrate ...positive regulation of iron ion import across plasma membrane / positive regulation of hippocampal neuron apoptotic process / positive regulation of endothelial tube morphogenesis / negative regulation of monocyte activation / negative regulation of hippocampal neuron apoptotic process / positive regulation of cell projection organization / negative regulation of transforming growth factor beta production / Extracellular matrix organization / Metal sequestration by antimicrobial proteins / positive regulation of substrate-dependent cell migration, cell attachment to substrate / siderophore transport / response to kainic acid / Fibronectin matrix formation / calcium-independent cell-matrix adhesion / neural crest cell migration involved in autonomic nervous system development / response to mycotoxin / peptidase activator activity / cellular response to increased oxygen levels / response to blue light / fibrinogen complex / peptide cross-linking / response to fructose / integrin activation / cellular response to X-ray / ALK mutants bind TKIs / short-term memory / cellular response to interleukin-6 / cell-substrate junction assembly / enterobactin binding / proteoglycan binding / iron ion sequestering activity / response to herbicide / biological process involved in interaction with symbiont / extracellular matrix structural constituent / Molecules associated with elastic fibres / MET activates PTK2 signaling / response to iron(II) ion / Syndecan interactions / p130Cas linkage to MAPK signaling for integrins / response to muscle activity / endoplasmic reticulum-Golgi intermediate compartment / endodermal cell differentiation / positive regulation of reactive oxygen species biosynthetic process / regulation of protein phosphorylation / GRB2:SOS provides linkage to MAPK signaling for Integrins / basement membrane / Non-integrin membrane-ECM interactions / cellular response to interleukin-1 / long-term memory / ECM proteoglycans / Integrin cell surface interactions / endothelial cell migration / regulation of ERK1 and ERK2 cascade / positive regulation of axon extension / cellular response to nutrient levels / collagen binding / Degradation of the extracellular matrix / extrinsic apoptotic signaling pathway in absence of ligand / Integrin signaling / extracellular matrix / positive regulation of endothelial cell migration / substrate adhesion-dependent cell spreading / platelet alpha granule lumen / cell-matrix adhesion / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / integrin-mediated signaling pathway / acute-phase response / Cell surface interactions at the vascular wall / Post-translational protein phosphorylation / wound healing / Iron uptake and transport / cellular response to nerve growth factor stimulus / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / response to wounding / response to virus / specific granule lumen / cellular response to hydrogen peroxide / positive regulation of fibroblast proliferation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / cellular response to amyloid-beta / 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 / Signaling by BRAF and RAF1 fusions / integrin binding / Signaling by ALK fusions and activated point mutants / GPER1 signaling / Platelet degranulation / cellular response to tumor necrosis factor / nervous system development / heparin binding / regulation of cell shape / positive regulation of cold-induced thermogenesis / heart development / cellular response to lipopolysaccharide / protease binding / : / angiogenesis
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 ...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 / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Kringle-like fold / Calycin beta-barrel core domain / Calycin / Fibronectin type III domain / EGF-like domain signature 1. / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Lipocalin / Fibronectin type III / Fibronectin type III superfamily / Lipocalin signature. / Immunoglobulin-like fold / Immunoglobulins / Beta Barrel / Immunoglobulin-like / 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: 2.6 Å
AuthorsSchiefner, A. / Gebauer, M. / Skerra, A.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Combinatorial design of an Anticalin directed against the extra-domain b for the specific targeting of oncofetal fibronectin
Authors: Gebauer, M. / Schiefner, A. / Matschiner, G. / Skerra, A.
History
DepositionAug 7, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 8, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)105,9204
Polymers105,9204
Non-polymers00
Water2,954164
1
A: Neutrophil gelatinase-associated lipocalin
B: Fibronectin


Theoretical massNumber of molelcules
Total (without water)52,9602
Polymers52,9602
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Neutrophil gelatinase-associated lipocalin
D: Fibronectin


Theoretical massNumber of molelcules
Total (without water)52,9602
Polymers52,9602
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.126, 107.126, 233.156
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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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: 21993.904 Da / Num. of mol.: 2 / Fragment: Lcn2, UNP residues 21-198
Mutation: Q28H, L36K, A40H, I41D, Q49R, Y52Q, S68N, L70R, R72V, K73H, D77N, W79R, R81W, C87S, Y100W, Y106W, K125R, S127Y, Y132L, K134E, S146N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HNL, LCN2, NGAL / Production host: Escherichia coli (E. coli) / Strain (production host): TG1/F- / References: UniProt: P80188
#2: Protein Fibronectin / FN


Mass: 30966.117 Da / Num. of mol.: 2 / Fragment: Fn7B8, UNP residues 1173-1448
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FN1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P02751
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS SEQUENCE CORRESPONDS TO THE ISOFORM 7 FOUND IN UNP P02751

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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: 3.16 Å3/Da / Density % sol: 61.05 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 17-19%(w/v) PEG3350, 0.1M Na-citrate, pH 5.5-6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
PH range: 5.5-6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 2, 2010 / Details: Double Crystal
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.6→35 Å / Num. all: 42537 / Num. obs: 42537 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 55.042 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 20.04
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.6-2.70.5730.742.7332714447844760.795100
2.7-2.80.4250.5353.7828246385038500.575100
2.8-30.2620.3365.945810626262590.361100
3-3.50.1110.14113.077389610165101640.152100
3.5-40.0510.06925.6941228577257700.074100
4-50.030.04238.7539518574657250.04599.6
5-60.0250.03742.7717346260425940.0499.6
6-80.0230.03243.5913906210220930.03599.6
8-100.0160.02551.9347497727650.02799.1
10-150.0130.02353.1734415955890.02599
150.0140.02249.3413002852520.02488.4

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
MAR345data collection
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QQS, 3T1W

1qqs

3t1w


Resolution: 2.6→30 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.898 / WRfactor Rfree: 0.2406 / WRfactor Rwork: 0.198 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8263 / SU B: 21.068 / SU ML: 0.225 / SU R Cruickshank DPI: 0.4611 / SU Rfree: 0.2899 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.461 / ESU R Free: 0.29 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.259 2149 5.1 %RANDOM
Rwork0.218 ---
obs0.22 42523 99.85 %-
all-42523 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 229.37 Å2 / Biso mean: 57.7581 Å2 / Biso min: 17.88 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7094 0 0 164 7258
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0227276
X-RAY DIFFRACTIONr_angle_refined_deg1.0811.9599958
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0145897
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.61724.802329
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.142151156
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1871536
X-RAY DIFFRACTIONr_chiral_restr0.070.21142
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0225574
X-RAY DIFFRACTIONr_mcbond_it0.3541.54517
X-RAY DIFFRACTIONr_mcangle_it0.752.57440
X-RAY DIFFRACTIONr_scbond_it1.5743.52759
X-RAY DIFFRACTIONr_scangle_it2.902102518
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 147 -
Rwork0.307 2928 -
all-3075 -
obs-2928 99.94 %
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)
15.4610.2315-0.08014.5646-1.960510.78490.2148-0.17970.11450.2756-0.29640.21050.2195-0.24820.08150.2852-0.07560.02860.0548-0.06670.187612.4222-47.7508-17.7039
27.69334.1219-3.36165.22451.11294.39590.06620.5522-0.03460.5434-0.48630.65130.5006-1.0920.42010.5222-0.25870.07150.42180.02150.60132.4194-58.2251-18.9901
31.40690.3940.17314.02972.71694.07870.1359-0.15410.00940.3066-0.33620.3169-0.2424-0.41480.20030.2139-0.01680.07270.2495-0.00630.2398.8865-49.3475-20.1457
43.197-0.8586-1.90741.63570.59472.50450.08140.1924-0.0269-0.3304-0.1017-0.1460.21310.10010.02020.29720.0050.00840.14820.00590.122429.5514-80.1122-47.5321
511.0098-1.9909-0.30850.62190.05131.59020.1247-0.20630.3533-0.06350.14190.2031-0.0631-0.492-0.26660.1143-0.05870.0070.28180.11150.3778-5.9234-70.7153-32.6553
612.9453-0.8644.29559.3113-1.68958.95190.01570.73020.7016-1.68950.07810.5118-0.9501-0.8129-0.09390.5740.1526-0.03110.57720.24890.4695-25.2436-63.6175-42.3964
74.9843-0.3304-2.4024.28732.01188.31360.101-0.5799-0.08130.5013-0.1017-0.64840.21280.53590.00070.5138-0.0296-0.04870.13320.0910.479344.3367-51.0388-24.1078
81.79840.28630.2652.8206-2.71293.32930.1230.2269-0.13060.0337-0.10570.0174-0.2462-0.3057-0.01730.42040.1522-0.06610.4342-0.03510.344737.6072-57.0647-29.0823
92.61470.272-1.10484.078-1.11982.56630.1368-0.09610.29710.3775-0.2162-0.5599-0.27880.18790.07940.4613-0.0129-0.11750.32760.09420.492847.746-49.3065-22.9716
108.92610.9738-3.14353.8557-1.549712.2008-0.0905-0.7430.39730.0015-0.01210.82511.0643-3.7530.10260.4181-0.47020.05331.6773-0.26680.29285.6883-87.1667-2.591
116.38161.17340.1712.8285-0.20112.75940.1266-0.1283-0.02130.084-0.1874-0.2066-0.00790.08060.06080.15840.0177-0.01720.09440.00660.065636.6908-80.2306-19.9202
129.1212-2.03423.50894.8405-1.83355.68680.0767-0.16170.65220.2107-0.1552-0.2267-0.35760.61260.07850.1536-0.12390.08050.3260.04980.243575.4103-75.6652-16.6029
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 38
2X-RAY DIFFRACTION2A39 - 82
3X-RAY DIFFRACTION3A83 - 178
4X-RAY DIFFRACTION4B1173 - 1311
5X-RAY DIFFRACTION5B1312 - 1389
6X-RAY DIFFRACTION6B1390 - 1447
7X-RAY DIFFRACTION7C5 - 55
8X-RAY DIFFRACTION8C56 - 122
9X-RAY DIFFRACTION9C123 - 178
10X-RAY DIFFRACTION10D1174 - 1261
11X-RAY DIFFRACTION11D1262 - 1356
12X-RAY DIFFRACTION12D1357 - 1451

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