PDB-8tv2: Structure of apo FabS1C_L1

ID or keywords:

Entry

Database: PDB / ID: 8tv2

Title

Structure of apo FabS1C_L1

Components

S1C variant of Fab_L1 heavy chain
S1C variant of Fab_L1 light chain

Keywords

SIGNALING PROTEIN/IMMUNE SYSTEM / Cell signalling / antibody / agonist / high affinity / clustering / activation / SIGNALING PROTEIN-IMMUNE SYSTEM complex / IMMUNE SYSTEM

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.65 Å

Authors

Singer, A.U. / Bruce, H.A. / Blazer, L. / Adams, J.J. / Sicheri, F. / Sidhu, S.S.

Funding support

United States, 2items

Citation

Journal: To be published
Title: Synthetic Antibodies targeting EPHA2 Induce Diverse Signaling-Competent Clusters with Differential Activation
Authors: Adams, J.J. / Bruce, H.A. / Ploder, L. / Garcia, J. / Khutoreskaya, G. / Jarvik, N. / Costa, L.E. / Gorelik, M. / Pot, I. / Sicheri, F. / Blazer, L.L. / Singer, A.U. / Sidhu, S.S.

History

Deposition	Aug 17, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 31, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8tv2.cif.gz	386.5 KB	Display	PDBx/mmCIF format
PDB format	pdb8tv2.ent.gz	281 KB	Display	PDB format
PDBx/mmJSON format	8tv2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8tv2_validation.pdf.gz	3 MB	Display	wwPDB validaton report
Full document	8tv2_full_validation.pdf.gz	3 MB	Display
Data in XML	8tv2_validation.xml.gz	31.3 KB	Display
Data in CIF	8tv2_validation.cif.gz	43.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tv/8tv2 ftp://data.pdbj.org/pub/pdb/validation_reports/tv/8tv2	HTTPS FTP

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Related structure data

Related structure data	8trvC 8tv1C 8tv5 PDB Unreleased entry C: citing same article (ref.)

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

D: S1C variant of Fab_L1 heavy chain

E: S1C variant of Fab_L1 light chain

A: S1C variant of Fab_L1 heavy chain

B: S1C variant of Fab_L1 light chain

hetero molecules

96.6 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

D: S1C variant of Fab_L1 heavy chain

E: S1C variant of Fab_L1 light chain

hetero molecules

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

2

A: S1C variant of Fab_L1 heavy chain

B: S1C variant of Fab_L1 light chain

hetero molecules

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

Unit cell

Length a, b, c (Å)	74.259, 74.259, 370.837
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	152
Space group name H-M	P3₁21
Space group name Hall	P3₁2"
Symmetry operation	#1: x,y,z #2: -y,x-y,z+1/3 #3: -x+y,-x,z+2/3 #4: x-y,-y,-z+2/3 #5: -x,-x+y,-z+1/3 #6: y,x,-z

#1: Antibody	S1C variant of Fab_L1 heavy chain Mass: 25257.072 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Fab produced by randomization of CDR regions and selected by phage display. Fabs utilize IMGT (LeClerc et al., Dev Comp Immunol. 2003 Jan;27(1):55-77) numbering. Source: (gene. exp.) Homo sapiens (human) / Plasmid: pSCSTa / Cell line (production host): Expi293 / Production host: Homo sapiens (human)
#2: Antibody	S1C variant of Fab_L1 light chain Mass: 22858.264 Da / Num. of mol.: 2 / Mutation: SPHAGLSSP replaced by QGTTS; Q165S, K167Y Source method: isolated from a genetically manipulated source Details: Fab produced by randomization of CDR regions and selected by phage display. Fabs utilize IMGT (LeClerc et al., Dev Comp Immunol. 2003 Jan;27(1):55-77) numbering. Source: (gene. exp.) Homo sapiens (human) / Plasmid: pSCSTa / Cell line (production host): Expi293 / Production host: Homo sapiens (human)
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.07 Å³/Da / Density % sol: 59.99 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 18% PEG6000, 1M Lithium Chloride, 100 mM Sodium citrate 5.0 PH range: 5 / Temp details: room temperature

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 4, 2022 / Details: mirrors
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97918 Å / Relative weight: 1
Reflection	Resolution: 2.65→92.71 Å / Num. obs: 33902 / % possible obs: 94.1 % / Redundancy: 8.9 % / B_iso Wilson estimate: 67.19 Å² / CC_1/2: 0.994 / R_merge(I) obs: 0.128 / R_pim(I) all: 0.045 / R_rim(I) all: 0.136 / Net I/σ(I): 9.3
Reflection shell	Resolution: 2.65→2.78 Å / Redundancy: 8.7 % / R_merge(I) obs: 1.136 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3816 / CC_1/2: 0.702 / R_pim(I) all: 0.405 / R_rim(I) all: 1.209 / % possible all: 82.3

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
MOSFLM		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.65→64.31 Å / SU ML: 0.3998 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.8604
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2473	2002	5.94 %
R_work	0.2043	31713	-
obs	0.207	33715	93.91 %

Solvent computation

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

Displacement parameters

B_iso mean: 78.09 Å²

Refinement step

Cycle: LAST / Resolution: 2.65→64.31 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6502	0	10	31	6543

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0094	6672
X-RAY DIFFRACTION	f_angle_d	1.1969	9117
X-RAY DIFFRACTION	f_chiral_restr	0.0678	1041
X-RAY DIFFRACTION	f_plane_restr	0.0106	1157
X-RAY DIFFRACTION	f_dihedral_angle_d	17.4614	2269

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 (%)
2.65-2.71	0.5847	97	0.4878	1498	X-RAY DIFFRACTION	65.05
2.71-2.79	0.4059	145	0.3857	2375	X-RAY DIFFRACTION	99.6
2.79-2.87	0.3766	150	0.3001	2354	X-RAY DIFFRACTION	99.33
2.87-2.96	0.3412	145	0.271	2379	X-RAY DIFFRACTION	99.64
2.96-3.07	0.2742	155	0.2527	2378	X-RAY DIFFRACTION	99.92
3.07-3.19	0.2895	146	0.2592	2347	X-RAY DIFFRACTION	99.92
3.19-3.34	0.3122	151	0.2628	2374	X-RAY DIFFRACTION	99.72
3.34-3.51	0.3088	121	0.2487	1917	X-RAY DIFFRACTION	80.14
3.51-3.73	0.2649	123	0.2145	2002	X-RAY DIFFRACTION	83.11
3.73-4.02	0.2699	132	0.1934	2092	X-RAY DIFFRACTION	86.67
4.02-4.42	0.1988	153	0.1708	2415	X-RAY DIFFRACTION	100
4.42-5.06	0.168	157	0.1503	2440	X-RAY DIFFRACTION	99.88
5.07-6.38	0.1947	154	0.1774	2493	X-RAY DIFFRACTION	100
6.38-64.31	0.2407	173	0.1732	2649	X-RAY DIFFRACTION	99.96

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	7.38788876117	-2.20219702368	0.128771002618	3.04545229444	0.357663643739	3.50400336406	-0.379492497644	-0.419944152258	1.59704019825	0.641542576356	0.553197369161	-0.194988482787	-0.699280122758	-0.053050441745	-0.167599945086	0.752579794737	0.0327701862058	0.233734166354	0.458646920712	-0.112430389279	0.94065835013	9.23849844327	9.46349525444	19.0707440268
2	5.63049124447	-2.86244037063	-2.14269911109	3.48515239955	0.997473230044	3.17260063009	-0.0620553755116	0.133428670997	0.23375392614	0.0213948810208	0.135789680329	-0.169984535014	0.16173654704	-0.0905977189539	-0.0797887120705	0.366194362599	-0.0891862417153	0.123913607162	0.302678188688	0.0339858576192	0.487771797727	17.7490802892	-10.0504376726	7.84478762338
3	6.8615475565	1.69031071717	2.84940296586	2.71099270759	-0.201285279226	3.83764113981	0.00418053306945	0.156978552989	-0.0126781223709	-0.203510957758	0.212662249941	-0.207266617822	0.115651363225	-0.0584921590708	-0.220217418588	0.31063546359	-0.0300387031138	0.147692808752	0.36286218816	-0.0645149746303	0.563642109325	20.9248213921	-14.8217787479	0.314804091605
4	7.32904494734	-0.522042608674	1.10269769347	0.0729999661917	-0.348748911322	2.34178667276	0.331117090814	0.984501187709	-0.394559196317	-0.252831945855	-0.502691311364	-0.133050060128	0.518954431685	0.226195231536	0.11028308284	0.785926927687	-0.135132856868	0.260646843035	0.610440322402	-0.0958739649952	0.765263912618	28.866692042	-15.6106580683	-6.79219253384
5	4.86667237344	-0.332669172005	1.17984066763	4.7630980435	-0.481591980917	2.43308449842	-0.384580163642	-0.484872444463	-0.683150403503	1.00223725122	0.111748875897	0.904474098177	0.194361588673	-0.656737293056	0.273484824783	0.755165941262	0.0941975423356	0.456893254739	0.525907494935	0.0553389303637	1.08352196122	-5.50816109413	-9.10417312227	20.1366592359
6	3.26237149387	-3.08986503201	-1.6382240235	8.2494300068	3.83082114128	3.28073721542	-0.517842839939	-0.295370863909	-0.794817325636	1.26246995218	-0.0215779754501	1.15737877783	0.462037901276	-0.380336083226	0.53118354349	0.665586424427	0.120498940214	0.352114388342	0.588650605073	0.0513792768841	0.895448261028	1.91512900936	-14.8272569805	18.7763897954
7	0.0486978190923	-0.509536029758	0.156946361276	5.44000367315	-1.47082869814	2.64976472257	-0.301361581186	0.36839284309	-1.262034834	-0.266052069383	0.0411360986422	-1.16210828577	0.361772975396	0.677464484768	0.159019982784	0.439482606782	0.00474257570275	0.216723416804	0.473828587699	-0.151749864973	0.847828314307	30.1301492013	-25.6876152422	0.486735569573
8	6.85920785412	3.16996405043	1.48424833876	6.43188227395	-1.19306910663	3.19543281895	-0.143702643922	0.243069997072	-0.649000672358	0.516029346554	0.0574332604127	-0.385442968071	0.159364895792	0.138766372815	0.0772135439974	0.499528407552	-0.0249844388069	0.15371595116	0.342179620331	-0.127243173413	0.631396157364	22.1113889679	-30.937663256	7.66003988804
9	4.22072063782	-1.16654215449	0.824167928138	3.01680138313	-0.392685202629	1.51661379853	-0.569150591954	-0.609177576725	-0.44875325815	0.527804175019	0.591233058154	-0.0848000149756	0.090529070659	-0.059829526621	-0.0176718560383	0.719814424301	0.219896945473	0.269569983992	0.576395515364	0.000531645876074	0.711436975838	-18.2125785614	11.5477107185	35.879155962
10	3.66635271596	-1.3867308388	0.491077065424	3.03485029336	1.82558825646	5.73578375515	-0.139930243716	-0.0697789322575	-0.264593756993	-0.146476924589	0.548176463329	-0.293925298289	-0.635007231448	0.0643621262445	-0.409026386178	0.810640852663	0.188531089942	0.277240645371	0.460069825293	0.0143856050014	0.712580944136	-23.1778641434	16.9321223512	27.8300623583
11	1.57774889653	-0.562268356945	0.516596166899	2.67094913476	-0.657104058434	1.14509132423	-0.330020858612	-0.41851539808	-0.138997468195	0.222008461	-0.0596940373077	0.456035729738	0.481848469875	-0.0801229344792	0.147022102406	1.58674998828	0.969508745072	0.557621150701	0.690534259653	0.651362821721	0.864130655612	-43.7912497486	11.7758201789	57.1459674369
12	5.38247507633	1.50929226559	-3.30903495583	2.25077846461	1.25757441239	5.6078366545	-0.847084274108	-0.645199028994	0.501543554868	0.576482263587	1.06362703559	-0.351761943036	-0.227777856423	0.536855171556	-0.183143699124	1.35889556794	0.34933357411	0.437782706542	0.636093499566	0.139237466012	1.0368577991	-32.0782547123	37.8691044302	34.6955469929
13	5.13153533195	-1.60260433947	3.76263387453	5.3172560503	0.383079543572	4.76312299849	-0.123472468536	0.369945329318	0.177239584187	0.0459220097123	0.370402148046	-0.0415530651402	-0.494208625963	0.142358685882	-0.241910343339	0.88720509049	0.242921452646	0.353977425151	0.533008672476	0.113725722355	0.643092175672	-30.6257039755	29.6808321856	28.9642223184
14	0.251921113729	-0.355976051688	0.0127965928989	2.27926976141	0.254101398827	0.0609400840311	0.293283374206	-0.247654825672	-0.0856196953745	0.529837155489	0.227067741938	-0.150808416459	-0.184794649793	0.422783776494	-0.204243435083	1.59161939946	1.15965803788	0.636455401838	0.719215177342	0.434967164985	0.847061142857	-44.5416296749	24.6315424353	58.1908924188
15	1.12233546676	0.348337668594	-0.0122953122336	0.614476294379	-0.579225372096	2.54435383313	0.104830193758	-0.305130992381	0.238742724639	0.389590917222	0.325486750645	-0.296933620127	0.111856305626	0.505151161403	-0.404035001212	1.60224399895	0.67856106845	0.514471850436	1.01240025228	0.288499661984	0.815006334636	-45.1542944268	28.3362805244	64.5280521072

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 'D' and (resid 1 through 117 )	D	A	1 - 117	1 - 109
2	2	chain 'D' and (resid 118 through 169 )	D	A	118 - 169	110 - 161
3	3	chain 'D' and (resid 170 through 227 )	D	A	170 - 227	162 - 219
4	4	chain 'D' and (resid 228 through 240 )	D	A	228 - 240	220 - 232
5	5	chain 'E' and (resid 2 through 106 )	E	B	2 - 106	1 - 89
6	6	chain 'E' and (resid 107 through 131 )	E	B	107 - 131	90 - 111
7	7	chain 'E' and (resid 132 through 146 )	E	B	132 - 146	112 - 126
8	8	chain 'E' and (resid 147 through 232 )	E	B	147 - 232	127 - 210
9	9	chain 'A' and (resid 1 through 99 )	A	C	1 - 99	1 - 91
10	10	chain 'A' and (resid 100 through 135 )	A	C	100 - 135	92 - 127
11	11	chain 'A' and (resid 136 through 238 )	A	C	136 - 238	128 - 225
12	12	chain 'B' and (resid 2 through 25 )	B	D	2 - 25	1 - 24
13	13	chain 'B' and (resid 26 through 116 )	B	D	26 - 116	25 - 96
14	14	chain 'B' and (resid 117 through 155 )	B	D	117 - 155	97 - 135
15	15	chain 'B' and (resid 156 through 231 )	B	D	156 - 231	136 - 209

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