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

ID or keywords:

Entry

Database: PDB / ID: 8peq

Title

Complex of diubiquitin-derived artificial binding protein (Affilin) variant Af2 with its target oncofetal fibronectin (fragment 7B8)

Components

Affilin variant Af2
Fibronectin

Keywords

DE 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 / calcium-independent cell-matrix adhesion / negative regulation of transforming growth factor beta production / Fibronectin matrix formation / Extracellular matrix organization / 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 ...negative regulation of monocyte activation / calcium-independent cell-matrix adhesion / negative regulation of transforming growth factor beta production / Fibronectin matrix formation / Extracellular matrix organization / 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 / biological process involved in interaction with symbiont / Molecules associated with elastic fibres / proteoglycan binding / MET activates PTK2 signaling / extracellular matrix structural constituent / Syndecan interactions / p130Cas linkage to MAPK signaling for integrins / endodermal cell differentiation / GRB2:SOS provides linkage to MAPK signaling for Integrins / endoplasmic reticulum-Golgi intermediate compartment / Non-integrin membrane-ECM interactions / basement membrane / ECM proteoglycans / positive regulation of axon extension / Integrin cell surface interactions / collagen binding / Degradation of the extracellular matrix / Integrin signaling / substrate adhesion-dependent cell spreading / cell-matrix adhesion / regulation of ERK1 and ERK2 cascade / extracellular matrix / platelet alpha granule lumen / acute-phase response / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / Post-translational protein phosphorylation / regulation of protein phosphorylation / Signaling by high-kinase activity BRAF mutants / wound healing / MAP2K and MAPK activation / response to wounding / GPER1 signaling / 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 / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Signaling by BRAF and RAF1 fusions / positive regulation of fibroblast proliferation / Signaling by ALK fusions and activated point mutants / integrin binding / Platelet degranulation / nervous system development / heparin binding / heart development / regulation of cell shape / angiogenesis / Interleukin-4 and Interleukin-13 signaling / collagen-containing extracellular matrix / protease binding / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / blood microparticle / cell adhesion / apical plasma membrane / 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

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.32 Å

Authors

Parthier, C. / Katzschmann, A. / Fiedler, E. / Haupts, U. / Reimann, A.

Funding support

1items

Citation

Journal: to be published
Title: Ubiquitin-derived artificial binding proteins targeting oncofetal fibronectin reveal scaffold plasticity by beta-strand slippage
Authors: Katzschmann, A. / Fiedler, E. / Haupts, U. / Reimann, A. / Settele, F. / Gloser-Braeunig, M. / Parthier, C.

History

Deposition	Jun 14, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 26, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8peq.cif.gz	513 KB	Display	PDBx/mmCIF format
PDB format	pdb8peq.ent.gz	422.3 KB	Display	PDB format
PDBx/mmJSON format	8peq.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8peq_validation.pdf.gz	476.4 KB	Display	wwPDB validaton report
Full document	8peq_full_validation.pdf.gz	488.9 KB	Display
Data in XML	8peq_validation.xml.gz	49.4 KB	Display
Data in CIF	8peq_validation.cif.gz	70.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pe/8peq ftp://data.pdbj.org/pub/pdb/validation_reports/pe/8peq	HTTPS FTP

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Related structure data

Related structure data	8pf0C C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#70 - Oct 2005 Designer Proteins similarity (1) #60 - Dec 2004 Ubiquitin similarity (5) #134 - Feb 2011 Integrin similarity (8) #83 - Nov 2006 Fibrin similarity (5) #43 - Jul 2003 Src Tyrosine Kinase similarity (4) #209 - May 2017 Tissue Transglutaminase and Celiac Disease similarity (4) #25 - Jan 2002 Thrombin similarity (1) #79 - Jul 2006 Amyloid-beta Precursor Protein similarity (1) #189 - Sep 2015 Amyloids similarity (1) #185 - May 2015 Titin similarity (1) #52 - Apr 2004 Growth Hormone similarity (1) #267 - Mar 2022 Vascular Endothelial Growth Factor (VegF similarity (2) #148 - Apr 2012 Ras Protein similarity (1) #37 - Jan 2003 Serum Albumin similarity (1) #237 - Sep 2019 Nanodiscs and HDL similarity (1) #56 - Aug 2004 Caspases similarity (1) #126 - Jun 2010 Epidermal Growth Factor similarity (1) #141 - Sep 2011 O-GlcNAc Transferase similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#70 - Oct 2005
Designer Proteins
similarity (1)
#60 - Dec 2004
Ubiquitin
similarity (5)
#134 - Feb 2011
Integrin
similarity (8)
#83 - Nov 2006
Fibrin
similarity (5)
#43 - Jul 2003
Src Tyrosine Kinase
similarity (4)
#209 - May 2017
Tissue Transglutaminase and Celiac Disease
similarity (4)
#25 - Jan 2002
Thrombin
similarity (1)
#79 - Jul 2006
Amyloid-beta Precursor Protein
similarity (1)
#189 - Sep 2015
Amyloids
similarity (1)
#185 - May 2015
Titin
similarity (1)
#52 - Apr 2004
Growth Hormone
similarity (1)
#267 - Mar 2022
Vascular Endothelial Growth Factor (VegF
similarity (2)
#148 - Apr 2012
Ras Protein
similarity (1)
#37 - Jan 2003
Serum Albumin
similarity (1)
#237 - Sep 2019
Nanodiscs and HDL
similarity (1)
#56 - Aug 2004
Caspases
similarity (1)
#126 - Jun 2010
Epidermal Growth Factor
similarity (1)
#141 - Sep 2011
O-GlcNAc Transferase
similarity (1)

Deposited unit

A: Fibronectin

B: Fibronectin

C: Fibronectin

J: Affilin variant Af2

L: Affilin variant Af2

M: Affilin variant Af2

hetero molecules

142 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Fibronectin

L: Affilin variant Af2

hetero molecules

defined by author&software
Evidence: gel filtration
47.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Fibronectin

J: Affilin variant Af2

defined by author&software
47.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Fibronectin

M: Affilin variant Af2

defined by author&software
47.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

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 number	5
Space group name H-M	C121

#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 interest	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

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

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

BESSY

/ Beamline: 14.1 / Wavelength: 0.9184 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 19, 2014

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9184 Å / Relative weight: 1

Reflection

Resolution: 2.3→45 Å / Num. obs: 59628 / % possible obs: 96.8 % / Redundancy: 3.5 % / CC_1/2: 0.998 / R_merge(I) obs: 0.058 / R_rim(I) all: 0.068 / Net I/σ(I): 16.46

Reflection shell

Resolution (Å)	R_merge(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	Diffraction-ID
2.3-2.4	0.399	5777	0.839	0.474	1
2.4-2.5	0.336	6193	0.897	0.395	1
2.5-2.6	0.247	5272	0.938	0.29	1
2.6-2.7	0.188	4532	0.96	0.223	1
2.7-3.08	0.113	12345	0.986	0.133	1
3.08-3.46	0.055	7526	0.996	0.066	1
3.46-3.84	0.042	4811	0.997	0.05	1
3.84-4.22	0.033	3248	0.998	0.039	1
4.22-4.6	0.028	2230	0.998	0.034	1
4.6-10	0.026	6940	0.999	0.03	1
10-20	0.023	664	0.998	0.028	1
20-30	0.03	68	0.998	0.037	1

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
XSCALE		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method 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

	R_factor	Num. reflection	% reflection
R_free	0.251	2983	5 %
R_work	0.1982	-	-
obs	0.2008	59625	99.07 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.32→44.8 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9940	0	10	536	10486

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	10146
X-RAY DIFFRACTION	f_angle_d	1.017	13885
X-RAY DIFFRACTION	f_dihedral_angle_d	13.329	3764
X-RAY DIFFRACTION	f_chiral_restr	0.063	1659
X-RAY DIFFRACTION	f_plane_restr	0.008	1809

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.32-2.36	0.3727	134	0.2938	2525	X-RAY DIFFRACTION	94
2.36-2.4	0.353	143	0.2749	2713	X-RAY DIFFRACTION	100
2.4-2.44	0.295	140	0.2707	2655	X-RAY DIFFRACTION	99
2.44-2.49	0.2864	143	0.2394	2724	X-RAY DIFFRACTION	100
2.49-2.54	0.3226	143	0.2414	2707	X-RAY DIFFRACTION	100
2.54-2.59	0.2985	142	0.2393	2698	X-RAY DIFFRACTION	100
2.59-2.65	0.3102	142	0.2433	2703	X-RAY DIFFRACTION	100
2.65-2.72	0.3261	143	0.2422	2713	X-RAY DIFFRACTION	99
2.72-2.79	0.2947	141	0.2487	2679	X-RAY DIFFRACTION	100
2.79-2.87	0.3414	144	0.2516	2735	X-RAY DIFFRACTION	100
2.87-2.97	0.2925	140	0.2466	2670	X-RAY DIFFRACTION	99
2.97-3.07	0.3037	143	0.2331	2714	X-RAY DIFFRACTION	100
3.07-3.2	0.2834	143	0.2141	2722	X-RAY DIFFRACTION	100
3.2-3.34	0.2336	144	0.2023	2725	X-RAY DIFFRACTION	100
3.34-3.52	0.248	142	0.1914	2711	X-RAY DIFFRACTION	100
3.52-3.74	0.2513	143	0.1771	2708	X-RAY DIFFRACTION	99
3.74-4.03	0.203	141	0.1661	2690	X-RAY DIFFRACTION	99
4.03-4.43	0.1954	144	0.1433	2724	X-RAY DIFFRACTION	99
4.43-5.07	0.1742	139	0.1426	2635	X-RAY DIFFRACTION	97
5.07-6.38	0.2277	143	0.1762	2722	X-RAY DIFFRACTION	99
6.39-44.8	0.2177	146	0.1883	2769	X-RAY DIFFRACTION	98

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	3.298	1.6321	0.2564	2.3874	-0.3239	4.3159	0.1194	0.0302	-0.0866	0.0751	-0.2102	-0.1245	0.0434	0.5011	0.0348	0.2249	0.0145	0.0009	0.2728	0.0049	0.2493	-22.5167	15.9442	24.6484
2	3.2133	0.4097	1.0666	0.8481	0.1559	0.7713	-0.1121	-0.0323	0.3049	-0.0451	0.0556	0.1163	-0.1972	-0.028	0.0619	0.278	0.0048	-0.0501	0.3076	-0.0258	0.293	-57.1069	11.1159	11.2396
3	3.8961	-0.7994	-0.1623	2.3397	-0.3354	2.4495	0.0493	0.0675	0.0902	0.036	-0.005	0.2581	-0.2755	-0.3145	-0.0438	0.2288	0.0503	0.0078	0.3308	0.0155	0.2481	-94.3938	23.8221	11.0022
4	2.9397	-0.679	0.8729	4.1649	0.4014	2.0943	-0.2389	-0.2389	-0.4947	-0.5083	-0.3253	-0.1949	1.2751	0.2644	0.1612	0.5332	-0.0026	0.1071	0.2697	0.0133	0.304	-58.4793	-41.4796	-5.4509
5	1.2097	0.4297	-0.8642	3.2561	-0.9946	3.5078	-0.2467	0.1318	-0.0031	-0.1743	0.2136	0.3494	0.143	-0.5786	0.0315	0.2324	0.0009	0.0136	0.3211	0.0198	0.2848	-62.9638	-33.0918	-4.3587
6	1.6035	0.9863	-0.9307	3.055	-0.587	2.0221	-0.1261	-0.0413	-0.0452	-0.1882	-0.023	-0.2299	0.0463	0.2772	0.1404	0.2442	-0.0066	-0.0062	0.2629	0.0404	0.2907	-43.6471	-4.3383	-15.1214
7	1.3311	-0.1556	-0.9141	3.2255	0.0917	1.6423	-0.2461	0.0534	0.1517	-0.924	0.5555	-0.5732	-0.7277	0.7249	0.0586	0.5787	-0.339	0.2364	0.6061	-0.1838	0.3854	-15.6023	22.0915	-13.0161
8	1.6118	0.1938	0.9772	3.5158	1.4754	2.5364	0.0363	-0.1051	-0.2297	-0.0087	0.0826	-0.1585	0.2826	0.2827	-0.118	0.3441	0.1318	-0.0382	0.3655	-0.0342	0.4016	-52.628	-11.2053	10.6034
9	4.7505	-0.2324	0.815	3.0445	-1.2958	3.0318	0.0693	0.0961	-0.6777	-0.3044	0.1432	0.8751	0.1155	-0.1772	-0.1318	0.4349	0.0042	-0.0525	0.2942	-0.0006	0.6363	-78.4439	-2.6993	14.3849
10	3.0182	-1.281	-0.3948	1.4695	-0.4582	1.2489	0.1847	0.0145	0.4747	0.1223	-0.0772	-0.1245	-0.6573	0.1633	-0.072	0.4249	-0.0303	-0.034	0.2205	-0.0327	0.3625	-50.0093	10.4969	40.1386
11	3.2827	0.3144	-1.439	2.4627	-0.2263	2.8035	-0.1379	0.2597	-0.0592	-0.0813	0.0918	-0.2216	0.0444	0.3181	0.047	0.3199	-0.0514	0.0475	0.2291	-0.0182	0.3072	-46.9095	3.2052	36.6212
12	2.0906	-1.3792	1.9419	3.26	-0.0697	2.046	0.0021	0.0339	0.0914	-0.0717	-0.0851	-0.3827	0.1367	0.1063	0.1027	0.2797	0.0028	0.0498	0.2175	0.0362	0.3432	-46.3674	-20.8643	39.7389
13	3.0991	-1.6072	-0.3713	2.6575	0.0789	3.0913	0.1403	0.1745	-0.0248	-0.0646	-0.1172	0.2032	-0.2529	-0.3006	-0.0463	0.3131	0.0098	0.0262	0.3008	0.0069	0.3019	-65.7419	-0.1278	-14.8355
14	2.6008	-0.1954	-1.1366	3.7519	1.7317	1.5629	-0.2035	-0.2381	0.317	0.0158	-0.028	0.0671	0.02	-0.0081	0.2389	0.3334	-0.0605	-0.0871	0.378	0.0247	0.4879	-47.1638	19.5986	-11.2524
15	2.7793	-1.2334	-2.1521	2.9349	0.0653	6.0241	0.1094	0.088	0.119	0.0256	0.0145	0.0852	-0.4645	-0.187	-0.0488	0.2289	0.0305	0.0203	0.2427	-0.0138	0.2664	-86.8514	22.9665	50.0007
16	2.1874	0.6771	0.2534	1.1783	0.806	3.2154	-0.0811	0.2025	-0.4306	-0.2655	0.0183	0.2644	-0.1069	-0.2498	-0.0164	0.2335	-0.0134	0.012	0.2081	0.0062	0.3545	-71.5136	-3.9659	33.1153
17	0.2953	0.5972	0.3158	3.9093	0.3441	1.6021	0.0893	0.0479	-0.0625	0.2893	-0.0855	0.1381	0.289	-0.1071	0.0009	0.2221	0.0173	0.0215	0.2396	-0.0019	0.247	-64.9041	-17.8357	37.3864
18	1.9789	-0.0428	0.9677	3.6588	0.4101	2.699	0.1586	-0.0053	-0.2653	-0.23	-0.263	-0.0274	0.5641	-0.1772	0.0891	0.5178	0.008	-0.0107	0.322	-0.0329	0.2536	-63.9373	-44.8317	38.5709

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 1173 through 1264 )
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 1265 through 1355 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 1356 through 1447 )
4	X-RAY DIFFRACTION	4	chain 'C' and (resid 1173 through 1204 )
5	X-RAY DIFFRACTION	5	chain 'C' and (resid 1205 through 1272 )
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 1273 through 1355 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 1356 through 1447 )
8	X-RAY DIFFRACTION	8	chain 'J' and (resid 1 through 76 )
9	X-RAY DIFFRACTION	9	chain 'J' and (resid 77 through 153 )
10	X-RAY DIFFRACTION	10	chain 'L' and (resid 1 through 34 )
11	X-RAY DIFFRACTION	11	chain 'L' and (resid 35 through 76 )
12	X-RAY DIFFRACTION	12	chain 'L' and (resid 77 through 151 )
13	X-RAY DIFFRACTION	13	chain 'M' and (resid 1 through 73 )
14	X-RAY DIFFRACTION	14	chain 'M' and (resid 74 through 150 )
15	X-RAY DIFFRACTION	15	chain 'A' and (resid 1174 through 1264 )
16	X-RAY DIFFRACTION	16	chain 'A' and (resid 1265 through 1294 )
17	X-RAY DIFFRACTION	17	chain 'A' and (resid 1295 through 1377 )
18	X-RAY DIFFRACTION	18	chain 'A' and (resid 1378 through 1447 )

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+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi