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- PDB-8peq: Complex of diubiquitin-derived artificial binding protein (Affili... -

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Basic information

Entry
Database: PDB / ID: 8peq
TitleComplex of diubiquitin-derived artificial binding protein (Affilin) variant Af2 with its target oncofetal fibronectin (fragment 7B8)
Components
  • Affilin variant Af2
  • Fibronectin
KeywordsDE NOVO PROTEIN / extra domain B / EDB / oncofetal fibronectin / ubiquitin / diubiqutin / Affilin / beta strand register shift / strand slippage / scaffold / artificial binding protein / plasticity / directed evolution
Function / homology
Function and homology information


negative regulation of monocyte activation / negative regulation of transforming growth factor beta production / Extracellular matrix organization / positive regulation of substrate-dependent cell migration, cell attachment to substrate / Fibronectin matrix formation / calcium-independent cell-matrix adhesion / neural crest cell migration involved in autonomic nervous system development / peptidase activator activity / fibrinogen complex / peptide cross-linking ...negative regulation of monocyte activation / negative regulation of transforming growth factor beta production / Extracellular matrix organization / positive regulation of substrate-dependent cell migration, cell attachment to substrate / Fibronectin matrix formation / calcium-independent cell-matrix adhesion / 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 / proteoglycan binding / biological process involved in interaction with symbiont / extracellular matrix structural constituent / Molecules associated with elastic fibres / MET activates PTK2 signaling / Syndecan interactions / p130Cas linkage to MAPK signaling for integrins / response to muscle activity / endoplasmic reticulum-Golgi intermediate compartment / endodermal cell differentiation / GRB2:SOS provides linkage to MAPK signaling for Integrins / regulation of protein phosphorylation / basement membrane / Non-integrin membrane-ECM interactions / ECM proteoglycans / Integrin cell surface interactions / positive regulation of axon extension / endothelial cell migration / regulation of ERK1 and ERK2 cascade / collagen binding / Degradation of the extracellular matrix / Integrin signaling / extracellular matrix / 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 / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / response to wounding / positive regulation of fibroblast proliferation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / 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 / Signaling by ALK fusions and activated point mutants / integrin binding / GPER1 signaling / Platelet degranulation / nervous system development / heparin binding / regulation of cell shape / heart development / protease binding / : / Interleukin-4 and Interleukin-13 signaling / angiogenesis / blood microparticle / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell adhesion / apical plasma membrane / receptor ligand activity / endoplasmic reticulum lumen / signaling receptor binding / positive regulation of cell population proliferation / positive regulation of gene expression / extracellular space / extracellular exosome / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
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 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 / Kringle-like fold / Fibronectin type III domain / EGF-like domain signature 1. / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsParthier, C. / Katzschmann, A. / Fiedler, E. / Haupts, U. / Reimann, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Commun Biol / Year: 2024
Title: Ubiquitin-derived artificial binding proteins targeting oncofetal fibronectin reveal scaffold plasticity by beta-strand slippage.
Authors: Katzschmann, A. / Haupts, U. / Reimann, A. / Settele, F. / Gloser-Braunig, M. / Fiedler, E. / Parthier, C.
History
DepositionJun 14, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fibronectin
B: Fibronectin
C: Fibronectin
J: Affilin variant Af2
L: Affilin variant Af2
M: Affilin variant Af2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,9058
Polymers141,7136
Non-polymers1922
Water9,656536
1
A: Fibronectin
L: Affilin variant Af2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4304
Polymers47,2382
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint-27 kcal/mol
Surface area21490 Å2
MethodPISA
2
B: Fibronectin
J: Affilin variant Af2


Theoretical massNumber of molelcules
Total (without water)47,2382
Polymers47,2382
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-8 kcal/mol
Surface area21560 Å2
MethodPISA
3
C: Fibronectin
M: Affilin variant Af2


Theoretical massNumber of molelcules
Total (without water)47,2382
Polymers47,2382
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-10 kcal/mol
Surface area21630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.650, 105.856, 78.993
Angle α, β, γ (deg.)90.00, 93.53, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Fibronectin / FN / Cold-insoluble globulin / CIG


Mass: 29808.859 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FN1, FN / Plasmid: pET28a / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P02751
#2: Protein Affilin variant Af2


Mass: 17428.832 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET-20b(+) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 536 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.48 Å3/Da / Density % sol: 50.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.3 / Details: 500 mM lithium sulfate, 15% PEG 8000 (w/v)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.3→45 Å / Num. obs: 59628 / % possible obs: 96.8 % / Redundancy: 3.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.058 / Rrim(I) all: 0.068 / Net I/σ(I): 16.46
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.3-2.40.39957770.8390.4741
2.4-2.50.33661930.8970.3951
2.5-2.60.24752720.9380.291
2.6-2.70.18845320.960.2231
2.7-3.080.113123450.9860.1331
3.08-3.460.05575260.9960.0661
3.46-3.840.04248110.9970.051
3.84-4.220.03332480.9980.0391
4.22-4.60.02822300.9980.0341
4.6-100.02669400.9990.031
10-200.0236640.9980.0281
20-300.03680.9980.0371

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.32→44.8 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.251 2983 5 %
Rwork0.1982 --
obs0.2008 59625 99.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.32→44.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9940 0 10 536 10486
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810146
X-RAY DIFFRACTIONf_angle_d1.01713885
X-RAY DIFFRACTIONf_dihedral_angle_d13.3293764
X-RAY DIFFRACTIONf_chiral_restr0.0631659
X-RAY DIFFRACTIONf_plane_restr0.0081809
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.32-2.360.37271340.29382525X-RAY DIFFRACTION94
2.36-2.40.3531430.27492713X-RAY DIFFRACTION100
2.4-2.440.2951400.27072655X-RAY DIFFRACTION99
2.44-2.490.28641430.23942724X-RAY DIFFRACTION100
2.49-2.540.32261430.24142707X-RAY DIFFRACTION100
2.54-2.590.29851420.23932698X-RAY DIFFRACTION100
2.59-2.650.31021420.24332703X-RAY DIFFRACTION100
2.65-2.720.32611430.24222713X-RAY DIFFRACTION99
2.72-2.790.29471410.24872679X-RAY DIFFRACTION100
2.79-2.870.34141440.25162735X-RAY DIFFRACTION100
2.87-2.970.29251400.24662670X-RAY DIFFRACTION99
2.97-3.070.30371430.23312714X-RAY DIFFRACTION100
3.07-3.20.28341430.21412722X-RAY DIFFRACTION100
3.2-3.340.23361440.20232725X-RAY DIFFRACTION100
3.34-3.520.2481420.19142711X-RAY DIFFRACTION100
3.52-3.740.25131430.17712708X-RAY DIFFRACTION99
3.74-4.030.2031410.16612690X-RAY DIFFRACTION99
4.03-4.430.19541440.14332724X-RAY DIFFRACTION99
4.43-5.070.17421390.14262635X-RAY DIFFRACTION97
5.07-6.380.22771430.17622722X-RAY DIFFRACTION99
6.39-44.80.21771460.18832769X-RAY DIFFRACTION98
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)
13.2981.63210.25642.3874-0.32394.31590.11940.0302-0.08660.0751-0.2102-0.12450.04340.50110.03480.22490.01450.00090.27280.00490.2493-22.516715.944224.6484
23.21330.40971.06660.84810.15590.7713-0.1121-0.03230.3049-0.04510.05560.1163-0.1972-0.0280.06190.2780.0048-0.05010.3076-0.02580.293-57.106911.115911.2396
33.8961-0.7994-0.16232.3397-0.33542.44950.04930.06750.09020.036-0.0050.2581-0.2755-0.3145-0.04380.22880.05030.00780.33080.01550.2481-94.393823.822111.0022
42.9397-0.6790.87294.16490.40142.0943-0.2389-0.2389-0.4947-0.5083-0.3253-0.19491.27510.26440.16120.5332-0.00260.10710.26970.01330.304-58.4793-41.4796-5.4509
51.20970.4297-0.86423.2561-0.99463.5078-0.24670.1318-0.0031-0.17430.21360.34940.143-0.57860.03150.23240.00090.01360.32110.01980.2848-62.9638-33.0918-4.3587
61.60350.9863-0.93073.055-0.5872.0221-0.1261-0.0413-0.0452-0.1882-0.023-0.22990.04630.27720.14040.2442-0.0066-0.00620.26290.04040.2907-43.6471-4.3383-15.1214
71.3311-0.1556-0.91413.22550.09171.6423-0.24610.05340.1517-0.9240.5555-0.5732-0.72770.72490.05860.5787-0.3390.23640.6061-0.18380.3854-15.602322.0915-13.0161
81.61180.19380.97723.51581.47542.53640.0363-0.1051-0.2297-0.00870.0826-0.15850.28260.2827-0.1180.34410.1318-0.03820.3655-0.03420.4016-52.628-11.205310.6034
94.7505-0.23240.8153.0445-1.29583.03180.06930.0961-0.6777-0.30440.14320.87510.1155-0.1772-0.13180.43490.0042-0.05250.2942-0.00060.6363-78.4439-2.699314.3849
103.0182-1.281-0.39481.4695-0.45821.24890.18470.01450.47470.1223-0.0772-0.1245-0.65730.1633-0.0720.4249-0.0303-0.0340.2205-0.03270.3625-50.009310.496940.1386
113.28270.3144-1.4392.4627-0.22632.8035-0.13790.2597-0.0592-0.08130.0918-0.22160.04440.31810.0470.3199-0.05140.04750.2291-0.01820.3072-46.90953.205236.6212
122.0906-1.37921.94193.26-0.06972.0460.00210.03390.0914-0.0717-0.0851-0.38270.13670.10630.10270.27970.00280.04980.21750.03620.3432-46.3674-20.864339.7389
133.0991-1.6072-0.37132.65750.07893.09130.14030.1745-0.0248-0.0646-0.11720.2032-0.2529-0.3006-0.04630.31310.00980.02620.30080.00690.3019-65.7419-0.1278-14.8355
142.6008-0.1954-1.13663.75191.73171.5629-0.2035-0.23810.3170.0158-0.0280.06710.02-0.00810.23890.3334-0.0605-0.08710.3780.02470.4879-47.163819.5986-11.2524
152.7793-1.2334-2.15212.93490.06536.02410.10940.0880.1190.02560.01450.0852-0.4645-0.187-0.04880.22890.03050.02030.2427-0.01380.2664-86.851422.966550.0007
162.18740.67710.25341.17830.8063.2154-0.08110.2025-0.4306-0.26550.01830.2644-0.1069-0.2498-0.01640.2335-0.01340.0120.20810.00620.3545-71.5136-3.965933.1153
170.29530.59720.31583.90930.34411.60210.08930.0479-0.06250.2893-0.08550.13810.289-0.10710.00090.22210.01730.02150.2396-0.00190.247-64.9041-17.835737.3864
181.9789-0.04280.96773.65880.41012.6990.1586-0.0053-0.2653-0.23-0.263-0.02740.5641-0.17720.08910.51780.008-0.01070.322-0.03290.2536-63.9373-44.831738.5709
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 1173 through 1264 )
2X-RAY DIFFRACTION2chain 'B' and (resid 1265 through 1355 )
3X-RAY DIFFRACTION3chain 'B' and (resid 1356 through 1447 )
4X-RAY DIFFRACTION4chain 'C' and (resid 1173 through 1204 )
5X-RAY DIFFRACTION5chain 'C' and (resid 1205 through 1272 )
6X-RAY DIFFRACTION6chain 'C' and (resid 1273 through 1355 )
7X-RAY DIFFRACTION7chain 'C' and (resid 1356 through 1447 )
8X-RAY DIFFRACTION8chain 'J' and (resid 1 through 76 )
9X-RAY DIFFRACTION9chain 'J' and (resid 77 through 153 )
10X-RAY DIFFRACTION10chain 'L' and (resid 1 through 34 )
11X-RAY DIFFRACTION11chain 'L' and (resid 35 through 76 )
12X-RAY DIFFRACTION12chain 'L' and (resid 77 through 151 )
13X-RAY DIFFRACTION13chain 'M' and (resid 1 through 73 )
14X-RAY DIFFRACTION14chain 'M' and (resid 74 through 150 )
15X-RAY DIFFRACTION15chain 'A' and (resid 1174 through 1264 )
16X-RAY DIFFRACTION16chain 'A' and (resid 1265 through 1294 )
17X-RAY DIFFRACTION17chain 'A' and (resid 1295 through 1377 )
18X-RAY DIFFRACTION18chain 'A' and (resid 1378 through 1447 )

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