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- PDB-5n47: Structure of Anticalin N7E in complex with the three-domain fragm... -

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Basic information

Entry
Database: PDB / ID: 5n47
TitleStructure of Anticalin N7E in complex with the three-domain fragment Fn7B8 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 / STRUCTURAL PROTEIN
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 / negative regulation of transforming growth factor beta production / positive regulation of cell projection organization / Extracellular matrix organization / positive regulation of substrate-dependent cell migration, cell attachment to substrate / Metal sequestration by antimicrobial proteins ...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 / negative regulation of transforming growth factor beta production / positive regulation of cell projection organization / Extracellular matrix organization / positive regulation of substrate-dependent cell migration, cell attachment to substrate / Metal sequestration by antimicrobial proteins / siderophore transport / Fibronectin matrix formation / calcium-independent cell-matrix adhesion / neural crest cell migration involved in autonomic nervous system development / response to kainic acid / response to mycotoxin / response to blue light / fibrinogen complex / cellular response to increased oxygen levels / peptide cross-linking / response to fructose / integrin activation / cellular response to X-ray / ALK mutants bind TKIs / short-term memory / cell-substrate junction assembly / cellular response to interleukin-6 / iron ion sequestering activity / enterobactin binding / proteoglycan binding / extracellular matrix structural constituent / response to herbicide / MET activates PTK2 signaling / Molecules associated with elastic fibres / peptidase activator activity / biological process involved in interaction with symbiont / Syndecan interactions / p130Cas linkage to MAPK signaling for integrins / response to iron(II) ion / response to muscle activity / endoplasmic reticulum-Golgi intermediate compartment / positive regulation of reactive oxygen species biosynthetic process / endodermal cell differentiation / 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 / ECM proteoglycans / long-term memory / 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 / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / cell-matrix adhesion / acute-phase response / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / Post-translational protein phosphorylation / wound healing / Iron uptake and transport / Signaling by high-kinase activity BRAF mutants / cellular response to nerve growth factor stimulus / MAP2K and MAPK activation / response to wounding / response to virus / specific granule lumen / integrin binding / cellular response to hydrogen peroxide / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of fibroblast proliferation / 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 / cellular response to tumor necrosis factor / Signaling by BRAF and RAF1 fusions / Signaling by ALK fusions and activated point mutants / Platelet degranulation / nervous system development / GPER1 signaling / regulation of cell shape / heparin binding / : / 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 / Kringle-like fold / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / 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: 3 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Oct 23, 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: Neutrophil gelatinase-associated lipocalin
B: Fibronectin
C: Neutrophil gelatinase-associated lipocalin
D: Fibronectin
E: Neutrophil gelatinase-associated lipocalin
F: Fibronectin


Theoretical massNumber of molelcules
Total (without water)157,6886
Polymers157,6886
Non-polymers00
Water00
1
A: Neutrophil gelatinase-associated lipocalin
B: Fibronectin


Theoretical massNumber of molelcules
Total (without water)52,5632
Polymers52,5632
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Neutrophil gelatinase-associated lipocalin
D: Fibronectin


Theoretical massNumber of molelcules
Total (without water)52,5632
Polymers52,5632
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Neutrophil gelatinase-associated lipocalin
F: Fibronectin


Theoretical massNumber of molelcules
Total (without water)52,5632
Polymers52,5632
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)135.148, 135.148, 203.939
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31E
12D
22F
13B
23D
33F
14B
24D
34F

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPASPASP5AA6 - 1776 - 177
21ASPASPASPASP5CC6 - 1776 - 177
31ASPASPASPASP5EE6 - 1776 - 177
12PROPROGLUGLU1DD1173 - 12661 - 94
22PROPROGLUGLU1FF1173 - 12661 - 94
13VALVALALAALA5BB1267 - 135795 - 185
23VALVALALAALA5DD1267 - 135795 - 185
33VALVALALAALA5FF1267 - 135795 - 185
14VALVALSERSER5BB1358 - 1449186 - 277
24VALVALSERSER5DD1358 - 1449186 - 277
34VALVALSERSER5FF1358 - 1449186 - 277

NCS ensembles :
ID
1
2
3
4

NCS oper:
IDCodeMatrixVector
1given(1, 1), (1, 1), (1)1
2given(2, -0.042887, 0.033892), (2, -0.026592, 0.999032), (2, -0.998726, -0.028056)0.998505, -0.035052, -0.041944
3given(3, -0.556851, 0.611658), (3, -0.263301, -0.771649), (3, 0.787775, 0.174448)0.561954, 0.57899, 0.590744
4given(1, 1), (1, 1), (1)1
5given(2, -0.779117, -0.264593), (2, -0.247617, -0.702943), (2, -0.575902, 0.660198)-0.568303, 0.666751, 0.482157
6given(1, 1), (1, 1), (1)1
7given(2, -0.008583, 0.049674), (2, 0.004047, 0.998759), (2, -0.999955, 0.003616)0.998729, -0.049641, -0.008774
8given(3, -0.572022, 0.586379), (3, -0.253826, -0.791461), (3, 0.779977, 0.172478)0.573542, 0.556023, 0.601571
9given(1, 1), (1, 1), (1)1
10given(2, -0.104462, 0.116116), (2, 0.017538, 0.993221), (2, -0.994374, 0.005319)0.987727, -0.114907, -0.105791
11given(3, -0.448544, 0.458212), (3, 0.178786, -0.795226), (3, 0.875696, 0.39706)0.767365, 0.579354, 0.274772

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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: 21727.689 Da / Num. of mol.: 3
Mutation: Q28H, L36E, A40S, I41L, Q49R, L70R, K73S, D77H, W79L, C87S, N96L, Y100K, L103H, Y106F, K125T, S127A, K134F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LCN2, HNL, NGAL / Plasmid: pNGAL98-N7E
Production host: Escherichia coli str. K-12 substr. W3110 (bacteria)
References: UniProt: P80188
#2: Protein Fibronectin / FN / Cold-insoluble globulin / CIG


Mass: 30834.922 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FN1, FN / Plasmid: pASK75-Fn7B8-His / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P02751
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: 2.95 Å3/Da / Density % sol: 58.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 17 % (w/v) PEG3350, 0.2 M NaCl, 0.1 M Na-malonate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 24, 2012
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 3→35 Å / Num. obs: 38486 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 14.67 % / Biso Wilson estimate: 63.078 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.124 / Rrim(I) all: 0.129 / Χ2: 1.022 / Net I/σ(I): 21.7 / Num. measured all: 564576 / Scaling rejects: 168
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
3-3.115.0651.0593.0835280.8881.096100
3.1-3.215.0630.7174.4231110.9370.742100
3.2-3.514.9930.4137.6773820.9770.428100
3.5-414.7970.21614.6979150.9920.22499.9
4-514.7190.08631.479350.9990.089100
5-614.490.06638.4235420.9990.068100
6-814.1430.05642.8928780.9990.05899.9
8-1013.540.03657.85105010.038100
10-3511.9970.0359.53114510.03196.5

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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: 3→35 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.902 / SU B: 37.802 / SU ML: 0.304 / SU R Cruickshank DPI: 0.3714 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.384
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.241 1926 5 %RANDOM
Rwork0.208 ---
obs0.2096 36560 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 240.24 Å2 / Biso mean: 97.772 Å2 / Biso min: 37.46 Å2
Baniso -1Baniso -2Baniso -3
1-2.44 Å2-0 Å20 Å2
2--2.44 Å20 Å2
3----4.88 Å2
Refinement stepCycle: final / Resolution: 3→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9943 0 0 0 9943
Num. residues----1268
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01910194
X-RAY DIFFRACTIONr_bond_other_d0.0010.029510
X-RAY DIFFRACTIONr_angle_refined_deg1.3081.96613932
X-RAY DIFFRACTIONr_angle_other_deg0.886321995
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.34251262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.80924.462446
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.894151630
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4891552
X-RAY DIFFRACTIONr_chiral_restr0.0780.21607
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02111469
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022235
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1012MEDIUM POSITIONAL0.270.5
12C1012MEDIUM POSITIONAL0.20.5
13E1012MEDIUM POSITIONAL0.230.5
11A1777LOOSE POSITIONAL0.735
12C1777LOOSE POSITIONAL0.565
13E1777LOOSE POSITIONAL0.635
11A1012MEDIUM THERMAL5.252
12C1012MEDIUM THERMAL3.852
13E1012MEDIUM THERMAL6.12
11A1777LOOSE THERMAL5.2810
12C1777LOOSE THERMAL4.3510
13E1777LOOSE THERMAL6.1910
21D1374TIGHT THERMAL2.010.5
31B532MEDIUM POSITIONAL0.180.5
32D532MEDIUM POSITIONAL0.190.5
33F532MEDIUM POSITIONAL0.240.5
31B792LOOSE POSITIONAL0.475
32D792LOOSE POSITIONAL0.475
33F792LOOSE POSITIONAL0.455
31B532MEDIUM THERMAL2.682
32D532MEDIUM THERMAL2.952
33F532MEDIUM THERMAL2.442
31B792LOOSE THERMAL3.3110
32D792LOOSE THERMAL4.510
33F792LOOSE THERMAL3.1410
41B537MEDIUM POSITIONAL0.180.5
42D537MEDIUM POSITIONAL0.20.5
43F537MEDIUM POSITIONAL0.230.5
41B854LOOSE POSITIONAL0.495
42D854LOOSE POSITIONAL0.465
43F854LOOSE POSITIONAL0.515
41B537MEDIUM THERMAL4.062
42D537MEDIUM THERMAL3.52
43F537MEDIUM THERMAL6.712
41B854LOOSE THERMAL4.2810
42D854LOOSE THERMAL4.0910
43F854LOOSE THERMAL7.4610
LS refinement shellResolution: 3→3.077 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 124 -
Rwork0.305 2660 -
all-2784 -
obs--99.96 %
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)
12.4578-0.18721.51175.5002-0.25444.4584-0.00220.1476-0.1031-0.0768-0.0610.0129-0.0901-0.05520.06320.2518-0.01590.09730.028-0.070.2801-38.82672.280811.5613
27.017-0.172-0.3361.95530.74044.0009-0.1344-0.29660.07490.19250.0631-0.6715-0.09290.52630.07120.40370.00970.06620.0903-0.00740.4495-24.91118.086230.3306
35.83780.0032-3.07132.9843-0.225910.478-0.0775-0.3424-0.44320.29520.09050.04930.5915-0.4668-0.0130.39170.00180.10170.26770.0610.495-54.17160.697549.5234
44.19030.4634-1.19287.9790.18053.0104-0.0114-0.10630.0666-0.1218-0.0444-0.6079-0.08970.15370.05580.1879-0.00690.06790.00880.00760.3885-20.1914-30.729321.4024
54.03540.47611.270.4482-1.29386.5480.1318-0.49630.29360.63470.1950.2375-1.6373-0.5939-0.32682.27070.33060.23181.1546-0.09020.7971-37.5424-31.521772.0856
63.1071-0.77280.17512.23480.19786.9668-0.1787-0.61630.2160.71640.17070.3804-0.2201-0.73390.0080.4479-0.02190.10160.2545-0.08590.4387-39.2421-25.177734.6611
78.09370.5644.02873.65910.08316.30340.3885-0.4094-0.50280.3166-0.05530.270.4957-0.5687-0.33330.3152-0.07810.07320.3003-0.05910.3819-58.2366-34.83294.2546
84.89090.813-0.10263.4732-0.57.20440.0503-0.7722-0.48370.4843-0.2108-0.15881.05690.43190.16040.54450.0864-0.00490.7240.10040.438310.5846-50.502117.9284
90.80190.18160.53361.51812.30053.58880.026-0.24561.177-0.0085-0.1824-0.1898-0.1592-0.39260.15641.70040.09090.07142.131-0.14762.1335-5.3651-14.856853.9957
100.526-0.007-1.07694.71330.42336.25720.0347-0.64240.3271.1807-0.1435-0.1950.30910.5570.10880.93440.002-0.0781.9612-0.01810.657416.0985-43.186740.5607
116.6521-1.5334-0.94650.79190.91592.4689-0.0842-0.7926-0.37540.02620.334-0.5949-0.44471.3599-0.24990.9607-0.0054-0.24533.11790.63121.55849.23-45.068125.2031
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 182
2X-RAY DIFFRACTION2B1267 - 1357
3X-RAY DIFFRACTION3B1358 - 1449
4X-RAY DIFFRACTION4C2 - 177
5X-RAY DIFFRACTION5D1173 - 1266
6X-RAY DIFFRACTION6D1267 - 1357
7X-RAY DIFFRACTION7D1358 - 1452
8X-RAY DIFFRACTION8E6 - 177
9X-RAY DIFFRACTION9F1173 - 1266
10X-RAY DIFFRACTION10F1267 - 1357
11X-RAY DIFFRACTION11F1358 - 1449

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