PDB-8fzu: The von Willebrand factor A domain of human capillary morphogenes...

ID or keywords:

Entry

Database: PDB / ID: 8fzu

Title

The von Willebrand factor A domain of human capillary morphogenesis gene II, flexibly fused to the 1TEL crystallization chaperone, Thr-Val linker variant, Expressed with SUMO tag

Components

Transcription factor ETV6,Anthrax toxin receptor 2

Keywords

PEPTIDE BINDING PROTEIN / TELSAM fusion / polymer forming crystallization chaperone

Function / homology

Function and homology information

Signaling by membrane-tethered fusions of PDGFRA or PDGFRB / mesenchymal cell apoptotic process / vitellogenesis / collagen fibril organization / hematopoietic stem cell proliferation / uterus development / Uptake and function of anthrax toxins / single fertilization / neurogenesis / Signaling by FLT3 fusion proteins ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Gajjar, P.L. / Litchfield, C.M. / Callahan, M. / Redd, N. / Doukov, T. / Lebedev, A. / Moody, J.D.

Funding support

United States, 1items

Citation

Journal: Acta Crystallogr D Struct Biol / Year: 2023
Title: Increasing the bulk of the 1TEL-target linker and retaining the 10×His tag in a 1TEL-CMG2-vWa construct improves crystal order and diffraction limits.
Authors: Gajjar, P.L. / Pedroza Romo, M.J. / Litchfield, C.M. / Callahan, M. / Redd, N. / Nawarathnage, S. / Soleimani, S. / Averett, J. / Wilson, E. / Lewis, A. / Stewart, C. / Tseng, Y.J. / Doukov, ...

History

Deposition	Jan 30, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 19, 2023	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 2023	Group: Data collection / Database references Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8fzu.cif.gz	361.5 KB	Display	PDBx/mmCIF format
PDB format	pdb8fzu.ent.gz	259.1 KB	Display	PDB format
PDBx/mmJSON format	8fzu.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8fzu_validation.pdf.gz	449.3 KB	Display	wwPDB validaton report
Full document	8fzu_full_validation.pdf.gz	454.3 KB	Display
Data in XML	8fzu_validation.xml.gz	36.6 KB	Display
Data in CIF	8fzu_validation.cif.gz	55.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fz/8fzu ftp://data.pdbj.org/pub/pdb/validation_reports/fz/8fzu	HTTPS FTP

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Related structure data

Related structure data	8ft6C 8ft8C 8fz4C 8fzvC 8e1f 8fz3 8fz6 8fz8 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	#134 - Feb 2011 Integrin similarity (5) #267 - Mar 2022 Vascular Endothelial Growth Factor (VegF similarity (1) #28 - Apr 2002 Anthrax Toxin similarity (1) #148 - Apr 2012 Ras Protein similarity (1) #44 - Aug 2003 Calmodulin similarity (1) #55 - Jul 2004 DNA Ligase similarity (3) #195 - Mar 2016 RAF Protein Kinases similarity (2) #166 - Oct 2013 Proteasome similarity (3) #196 - Apr 2016 Lead Poisoning similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#134 - Feb 2011
Integrin
similarity (5)
#267 - Mar 2022
Vascular Endothelial Growth Factor (VegF
similarity (1)
#28 - Apr 2002
Anthrax Toxin
similarity (1)
#148 - Apr 2012
Ras Protein
similarity (1)
#44 - Aug 2003
Calmodulin
similarity (1)
#55 - Jul 2004
DNA Ligase
similarity (3)
#195 - Mar 2016
RAF Protein Kinases
similarity (2)
#166 - Oct 2013
Proteasome
similarity (3)
#196 - Apr 2016
Lead Poisoning
similarity (1)

Deposited unit

A: Transcription factor ETV6,Anthrax toxin receptor 2

B: Transcription factor ETV6,Anthrax toxin receptor 2

C: Transcription factor ETV6,Anthrax toxin receptor 2

hetero molecules

86.3 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Transcription factor ETV6,Anthrax toxin receptor 2

defined by author
Evidence: electron microscopy, Kim CA, Phillips ML, Kim W, Gingery M, Tran HH, Robinson MA, Faham S, Bowie JU. Polymerization of the SAM domain of TEL in leukemogenesis and transcriptional repression. ...Evidence: electron microscopy, Kim CA, Phillips ML, Kim W, Gingery M, Tran HH, Robinson MA, Faham S, Bowie JU. Polymerization of the SAM domain of TEL in leukemogenesis and transcriptional repression. The EMBO journal. 2001 Aug 1;20(15):4173-82.
28.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Transcription factor ETV6,Anthrax toxin receptor 2

hetero molecules

defined by author
28.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Transcription factor ETV6,Anthrax toxin receptor 2

hetero molecules

defined by author
28.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	164.096, 164.096, 54.401
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	170
Space group name H-M	P6₅
Space group name Hall	P6₅
Symmetry operation	#1: x,y,z #2: x-y,x,z+5/6 #3: y,-x+y,z+1/6 #4: -y,x-y,z+2/3 #5: -x+y,-x,z+1/3 #6: -x,-y,z+1/2

#1: Protein	Transcription factor ETV6,Anthrax toxin receptor 2 / ETS translocation variant 6 / ETS-related protein Tel1 / Tel / Capillary morphogenesis gene 2 protein / CMG-2 Mass: 28705.766 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ETV6, TEL, TEL1, ANTXR2, CMG2 / Production host: Escherichia coli (E. coli) / References: UniProt: P41212, UniProt: P58335
#2: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 827 / 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: 2.46 Å³/Da / Density % sol: 49.9 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1M HEPES 2.0M ammonium sulfate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 21, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 1.9→71.06 Å / Num. obs: 66252 / % possible obs: 90.48 % / Redundancy: 10.1 % / B_iso Wilson estimate: 24.16 Å² / CC_1/2: 0.998 / CC star: 1 / R_merge(I) obs: 0.1787 / R_pim(I) all: 0.05901 / Net I/σ(I): 4.67
Reflection shell	Resolution: 1.9→1.968 Å / R_merge(I) obs: 2.574 / Num. unique obs: 2186 / CC_1/2: 0.607 / R_rim(I) all: 2.709

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
Blu-Ice		data collection
autoPROC		data reduction
autoPROC		data scaling
PHASER		phasing
Coot	0.9.6 EL	model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.9→71.06 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.7026
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2664	3116	5.2 %
R_work	0.2377	56842	-
obs	0.2392	59958	90.48 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 29.15 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→71.06 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5823	0	6	827	6656

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0039	6015
X-RAY DIFFRACTION	f_angle_d	0.6601	8193
X-RAY DIFFRACTION	f_chiral_restr	0.0427	936
X-RAY DIFFRACTION	f_plane_restr	0.0045	1062
X-RAY DIFFRACTION	f_dihedral_angle_d	10.6663	2157

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 (%)
1.9-1.93	0.3599	57	0.3119	964	X-RAY DIFFRACTION	33.94
1.93-1.96	0.327	51	0.3052	914	X-RAY DIFFRACTION	32.69
1.96-2	0.3082	49	0.3192	952	X-RAY DIFFRACTION	33.73
2-2.03	0.3366	152	0.331	2587	X-RAY DIFFRACTION	90.76
2.03-2.07	0.326	166	0.3278	2781	X-RAY DIFFRACTION	99.93
2.07-2.11	0.3407	167	0.3108	2849	X-RAY DIFFRACTION	99.97
2.11-2.16	0.3608	149	0.3015	2852	X-RAY DIFFRACTION	100
2.16-2.21	0.3442	152	0.2901	2820	X-RAY DIFFRACTION	100
2.21-2.26	0.3592	156	0.2893	2854	X-RAY DIFFRACTION	99.83
2.26-2.33	0.3194	137	0.2705	2818	X-RAY DIFFRACTION	99.93
2.33-2.39	0.2952	141	0.2837	2871	X-RAY DIFFRACTION	99.93
2.39-2.47	0.2978	149	0.2795	2867	X-RAY DIFFRACTION	99.93
2.47-2.56	0.3079	121	0.2613	2872	X-RAY DIFFRACTION	99.97
2.56-2.66	0.2877	181	0.2587	2815	X-RAY DIFFRACTION	99.93
2.66-2.78	0.2803	180	0.2472	2840	X-RAY DIFFRACTION	100
2.78-2.93	0.3013	131	0.2537	2878	X-RAY DIFFRACTION	99.83
2.93-3.11	0.2901	145	0.2435	2853	X-RAY DIFFRACTION	100
3.11-3.35	0.2033	124	0.2145	2899	X-RAY DIFFRACTION	99.97
3.35-3.69	0.2249	175	0.1992	2851	X-RAY DIFFRACTION	99.97
3.69-4.22	0.2242	176	0.1825	2868	X-RAY DIFFRACTION	99.93
4.23-5.32	0.2143	153	0.1804	2906	X-RAY DIFFRACTION	99.93
5.32-71.06	0.2219	204	0.2078	2931	X-RAY DIFFRACTION	99.52

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	2.14056932283	0.829919073104	-0.0651051650611	2.30559392954	-0.304394929106	1.80732844715	0.0225630586611	0.0308391943893	-0.179368745062	-0.0150501329278	-0.0827235093148	-0.15289049369	0.11143563903	0.2746885158	0.033366328845	0.190731772507	0.0521276052836	0.00331842669103	0.213052955633	0.0243805647016	0.137987750366	100.89941885	37.3245274368	-15.3336064269
2	2.4501246191	0.129829706761	-0.126959093578	4.30767692874	-0.0452741418716	1.52128286289	-0.0276361245113	0.0545762215992	-0.170840960428	-0.0907910340203	0.0607289074277	0.0446533063144	0.166125391966	0.0110050140698	-0.0313173005148	0.178202987497	0.0366247489614	-0.0239643050797	0.178329833514	-0.00768846726503	0.17671359365	111.693713622	24.7787646038	13.0989063931
3	4.74309686878	1.85421846307	1.18580426313	2.80131367962	0.335154345089	2.72508840108	-0.0776914927229	0.950684889882	0.19780303096	0.0124938885313	0.19079554325	0.594865131104	-0.133446702729	-0.883740817368	-0.214447700615	0.300010972564	-0.0276583590334	0.0424653069405	0.325961461759	0.0214740552612	0.181818382904	141.362492595	20.4348439384	66.552205863
4	1.64006273369	1.65879854269	0.0596398910109	3.53878475091	1.46838613213	1.2337985567	0.0863151035586	-0.234137946167	-0.0992849421564	0.318077929965	-0.111094903017	-0.123106047552	0.335368288062	-0.00548661201276	0.0391904543141	0.196410405802	0.027183877841	0.0459074635958	0.224831044426	0.0546093384849	0.150941801241	143.141413971	10.6943778498	74.3200619113
5	1.80656041852	0.164500639612	0.194599158108	2.60072853005	-0.425290201504	2.46353792163	0.0693292910968	0.15391819487	0.00265143584527	-0.111490166549	-0.132765611052	-0.248076010933	0.222559910062	0.112381385485	0.0422393397306	0.10493663441	0.00857009652775	0.0219985291463	0.171763205828	0.0117295712144	0.133894883353	151.856754152	9.64128394592	68.055986753
6	1.37743372002	0.833329049975	0.265915172756	1.27561764899	-0.0286041294769	1.61748329464	-0.0108820488782	-0.0417548480989	-0.0215535610706	-0.0267989598921	0.0325259464189	0.0807122060334	-0.0107752998166	-0.163774894307	-0.0382603467823	0.0989290934807	0.054986234235	0.0181419486784	0.152490726274	0.00744337452317	0.13625633798	133.307951836	13.9738706174	41.2052582151
7	0.824337310502	-0.424021034527	0.586005890105	0.667057335828	-0.413860362538	2.22492663132	0.0961475385673	-0.123199550588	0.306116725973	0.0651262053078	-0.120085920451	0.255955202982	-0.0494966021267	-0.457056399882	0.0454886549059	0.177352068627	0.11272251352	0.0202757215398	0.351172057783	0.0203850937745	0.272449434473	122.045245202	18.9225014593	44.5585734526
8	1.90220306247	-1.05827242855	0.274098680181	3.12650577324	-0.635559266749	1.73265040201	-0.0194704533277	0.283500863406	0.144008670942	-0.130941190149	0.0491263350727	-0.212712053929	0.0713256962194	0.187185796631	-0.0140302108293	0.198411260922	-0.000409889000327	0.0100336517495	0.195365743562	0.014277358278	0.128357618535	100.656380384	58.695690074	-25.9682526528
9	0.659818011615	0.376550142795	0.43355197357	0.763798143158	0.15033443399	1.17677585986	-0.016788307586	-0.0633345936693	0.168522500268	-0.0512800100449	-0.064208444469	-0.0159027251571	-0.149511727615	0.0328362750218	0.101117515506	0.200909678897	-0.00241271844552	0.0104683031763	0.224905990655	-0.018840240577	0.234565851506	109.725571564	63.5302362866	-0.0108501054304
10	3.09206486779	-0.424717728058	0.139142567059	1.62694352397	0.446983889876	2.58831847478	0.0299127152571	0.0596882276638	-0.189026908883	0.0017008103847	0.0520367000286	-0.0264620114596	0.137534146518	0.192475158262	-0.07642674024	0.184565247743	-0.0133860221397	-0.00264227360153	0.208680560271	0.00926365847025	0.206261764134	116.989646628	60.0397050335	2.61351188704

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 3 through 78 )	A	A	3 - 78	1 - 76
2	2	chain 'A' and (resid 79 through 255 )	A	A	79 - 255	77 - 253
3	3	chain 'B' and (resid 3 through 17 )	B	B	3 - 17	1 - 15
4	4	chain 'B' and (resid 18 through 45 )	B	B	18 - 45	16 - 43
5	5	chain 'B' and (resid 46 through 78 )	B	B	46 - 78	44 - 76
6	6	chain 'B' and (resid 79 through 208 )	B	B	79 - 208	77 - 206
7	7	chain 'B' and (resid 209 through 255 )	B	B	209 - 255	207 - 253
8	8	chain 'C' and (resid 2 through 64 )	C	C	2 - 64	1 - 63
9	9	chain 'C' and (resid 65 through 113 )	C	C	65 - 113	64 - 112
10	10	chain 'C' and (resid 114 through 256 )	C	C	114 - 256	113 - 255

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