PDB-8ts5: Structure of the apo FabS1C_C1

ID or keywords:

Entry

Database: PDB / ID: 8ts5

Title

Structure of the apo FabS1C_C1

Components

(S1C variant of Fab C1 ...) x 2

Keywords

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

Function / homology

ACETATE ION / DI(HYDROXYETHYL)ETHER

Function and homology information

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

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

Funding support

United States, 2items

Citation

Journal: Protein Sci. / Year: 2024
Title: Engineered antigen-binding fragments for enhanced crystallization of antibody:antigen complexes.
Authors: Bruce, H.A. / Singer, A.U. / Filippova, E.V. / Blazer, L.L. / Adams, J.J. / Enderle, L. / Ben-David, M. / Radley, E.H. / Mao, D.Y.L. / Pau, V. / Orlicky, S. / Sicheri, F. / Kurinov, I. / ...

History

Deposition	Aug 10, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 22, 2023	Provider: repository / Type: Initial release
Revision 1.1	Jan 10, 2024	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.title ..._citation.journal_volume / _citation.title / _citation.year / _citation_author.name

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8ts5.cif.gz	349.1 KB	Display	PDBx/mmCIF format
PDB format	pdb8ts5.ent.gz	283.1 KB	Display	PDB format
PDBx/mmJSON format	8ts5.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	8ts5_validation.pdf.gz	507 KB	Display	wwPDB validaton report
Full document	8ts5_full_validation.pdf.gz	520.8 KB	Display
Data in XML	8ts5_validation.xml.gz	39.4 KB	Display
Data in CIF	8ts5_validation.cif.gz	55.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ts/8ts5 ftp://data.pdbj.org/pub/pdb/validation_reports/ts/8ts5	HTTPS FTP

-
Related structure data

Related structure data	8t58C 8t6iC 8t7fC 8t7gC 8t7iC 8t8iC 8t9yC 8trsSC 8trtC 8trv S: Starting model for refinement C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

-
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

A: S1C variant of Fab C1 heavy chain

G: S1C variant of Fab C1 light chain

B: S1C variant of Fab C1 heavy chain

C: S1C variant of Fab C1 light chain

hetero molecules

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

1

A: S1C variant of Fab C1 heavy chain

G: S1C variant of Fab C1 light chain

B: S1C variant of Fab C1 heavy chain

hetero molecules

defined by author&software
73.6 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: S1C variant of Fab C1 light chain

hetero molecules

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

Unit cell

Length a, b, c (Å)	44.688, 73.792, 174.202
Angle α, β, γ (deg.)	90.00, 96.37, 90.00
Int Tables number	4
Space group name H-M	P12₁1
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

-
Antibody , 2 types, 4 molecules ABGC

#1: Antibody	S1C variant of Fab C1 heavy chain Mass: 23814.611 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 C1 light chain Mass: 23432.895 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)

#1: Antibody

S1C variant of Fab C1 heavy chain

Mass: 23814.611 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 C1 light chain

Mass: 23432.895 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)

-
Non-polymers , 7 types, 512 molecules

#3: Chemical	ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER Mass: 209.240 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₉NO₅ / Comment: pH buffer*YM
#4: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#5: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C₂H₆O₂
#6: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₃O₂
#7: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#8: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#9: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 476 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Has ligand of interest	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.02 Å³/Da / Density % sol: 59.28 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.1 M ammonium acetate, 0.1 M Bis-Tris, pH 5.5, 17% PEG10000 Temp details: room temperature

-
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: Apr 8, 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: 1.98→86.56 Å / Num. obs: 76017 / % possible obs: 96.9 % / Redundancy: 3.4 % / B_iso Wilson estimate: 31.62 Å² / CC_1/2: 0.993 / R_merge(I) obs: 0.095 / R_pim(I) all: 0.061 / R_rim(I) all: 0.114 / Net I/σ(I): 10.4
Reflection shell	Resolution: 1.98→2.02 Å / Redundancy: 3.5 % / R_merge(I) obs: 0.648 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3866 / CC_1/2: 0.629 / R_pim(I) all: 0.408 / R_rim(I) all: 0.768 / % possible all: 82.6

-
Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 8TRS

8trs

Resolution: 2.1→86.56 Å / SU ML: 0.296 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.972
Stereochemistry target values: GEOSTD + MONOMER LIBRARY + CDL V1.2

	R_factor	Num. reflection	% reflection
R_free	0.264	3096	4.82 %
R_work	0.22	-	-
obs	0.222	64268	97.5 %

Solvent computation

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

Displacement parameters

B_iso mean: 37.5 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→86.56 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6376	0	164	476	7016

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	6689
X-RAY DIFFRACTION	f_angle_d	0.968	9058
X-RAY DIFFRACTION	f_dihedral_angle_d	16.747	2346
X-RAY DIFFRACTION	f_chiral_restr	0.053	1017
X-RAY DIFFRACTION	f_plane_restr	0.008	1141

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 (%)
2.1-2.13	0.3062	142	0.2691	2832	X-RAY DIFFRACTION	99
2.13-2.17	0.2853	150	0.2515	2781	X-RAY DIFFRACTION	99
2.17-2.21	0.3281	133	0.2531	2806	X-RAY DIFFRACTION	99
2.21-2.25	0.259	127	0.245	2848	X-RAY DIFFRACTION	99
2.25-2.29	0.3187	174	0.2517	2721	X-RAY DIFFRACTION	99
2.29-2.34	0.2902	134	0.2498	2873	X-RAY DIFFRACTION	99
2.34-2.39	0.3242	126	0.2547	2791	X-RAY DIFFRACTION	99
2.39-2.44	0.302	164	0.2564	2732	X-RAY DIFFRACTION	99
2.44-2.5	0.3355	137	0.2561	2822	X-RAY DIFFRACTION	97
2.5-2.57	0.3312	148	0.256	2774	X-RAY DIFFRACTION	99
2.57-2.65	0.3343	143	0.2463	2827	X-RAY DIFFRACTION	99
2.65-2.73	0.2856	147	0.2331	2771	X-RAY DIFFRACTION	99
2.73-2.83	0.2798	141	0.2218	2799	X-RAY DIFFRACTION	98
2.83-2.94	0.2891	129	0.2231	2778	X-RAY DIFFRACTION	97
2.94-3.08	0.2553	158	0.2224	2754	X-RAY DIFFRACTION	97
3.08-3.24	0.2626	128	0.2275	2758	X-RAY DIFFRACTION	96
3.24-3.44	0.2486	141	0.2082	2736	X-RAY DIFFRACTION	95
3.44-3.71	0.2772	115	0.2077	2700	X-RAY DIFFRACTION	94
3.71-4.08	0.2451	135	0.2088	2736	X-RAY DIFFRACTION	95
4.08-4.67	0.1931	135	0.1883	2715	X-RAY DIFFRACTION	96
4.67-5.88	0.2417	147	0.1978	2780	X-RAY DIFFRACTION	96
5.88-86.56	0.2378	142	0.211	2838	X-RAY DIFFRACTION	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	1.6716	-0.0597	-1.2111	2.7811	0.8461	4.8596	0.0198	-0.2094	-0.1151	0.4823	-0.0447	0.0241	0.0422	-0.1952	0.0198	0.2351	-0.0211	-0.0217	0.2432	0.0336	0.206	-13.9713	5.3802	-60.1317
2	4.1709	2.0464	-0.7486	2.7308	-0.2035	1.4633	-0.0457	-0.0243	-0.0839	-0.0823	-0.0058	-0.2789	0.0287	0.1206	0.0538	0.1654	0.0082	-0.023	0.1334	0.0126	0.1856	10.1936	14.5804	-82.1519
3	4.8761	0.0937	0.6603	1.5575	0.2966	3.4786	0.3148	0.1631	0.3577	-0.1989	-0.0024	0.1862	-0.6849	-0.1025	-0.2657	0.5025	0.0285	0.0599	0.2446	-0.0123	0.2397	-10.3089	32.0496	-60.1563
4	1.9067	1.4353	-0.7903	2.6648	-1.0927	2.5985	0.2415	-0.2799	0.2606	0.4111	-0.0886	0.1324	-0.456	0.2387	-0.148	0.4774	-0.0403	0.0883	0.3076	-0.0646	0.2411	-9.3969	26.3382	-52.9809
5	2.8052	-0.6261	0.824	7.6549	-0.1869	6.9561	0.088	-0.4536	-0.1103	0.1213	-0.0341	0.7392	0.6555	-0.5293	-0.1378	0.265	-0.0306	0.0299	0.3201	-0.0599	0.2579	-20.0372	19.5541	-57.2072
6	6.5518	5.4435	-6.0762	5.3834	-5.9101	6.5375	0.3119	-0.0895	0.2898	0.6773	0.0029	0.2551	-0.582	0.0777	-0.2595	0.4633	-0.0683	-0.0229	0.2745	-0.0578	0.2594	4.1045	35.9457	-69.1556
7	1.907	-1.0162	-0.0833	0.9811	-1.1117	2.8498	0.0334	0.1353	-0.2718	-0.0269	-0.0475	-0.2193	0.1439	0.0596	0.1118	0.2551	0.0119	0.0251	0.1817	0.0433	0.2431	9.7228	19.575	-93.7411
8	1.2971	-0.371	0.6707	3.9782	4.8301	8.893	-0.1084	-0.0387	0.0749	0.6614	0.0608	0.049	0.4384	-0.0728	0.051	0.2117	-0.0298	0.0248	0.1497	0.04	0.1803	2.6499	29.7464	-84.7821
9	0.5025	-1.1762	1.7411	2.5959	-3.9405	6.2403	0.0355	-0.0207	0.0038	0.024	0.1903	0.2261	-0.4087	0.0426	-0.3885	0.2219	0.0266	0.0013	0.1874	0.005	0.2949	-3.0125	26.9713	-91.584
10	3.7071	1.1269	1.8005	4.8007	1.4572	9.7744	0.4753	-0.6488	-0.0996	0.9824	-0.5531	-0.0137	0.07	-0.2711	-0.0285	0.4571	-0.0429	-0.01	0.2948	-0.0105	0.2833	6.9863	29.0113	-70.3025
11	2.6467	0.9984	1.1865	3.8924	1.0528	7.9287	0.0869	0.2664	-0.2303	-0.3416	-0.0494	-0.0362	0.8515	-0.5936	-0.1137	0.2942	0.0063	-0.0082	0.1422	-0.0127	0.1925	1.7911	21.0797	-96.96
12	1.9598	-0.0357	0.5242	6.9976	4.2964	4.7966	0.0159	-0.0389	-0.145	-0.3745	0.0992	0.0963	-0.5397	0.0033	-0.0894	0.1423	0.0015	-0.0093	0.1667	0.0505	0.1826	5.6055	33.3986	-93.746
13	1.2976	-0.0814	-1.2725	1.8351	-0.1298	6.7209	-0.0244	0.1785	0.0738	-0.2358	0.1376	-0.1306	-0.0629	-0.1917	-0.0327	0.2536	-0.0485	0.0259	0.305	-0.0145	0.2308	-18.3806	10.3809	-27.2306
14	3.0506	-0.0074	-0.1162	1.894	-0.1603	2.6782	0.0137	-0.079	-0.158	-0.2282	-0.0665	-0.4368	0.2473	0.1558	0.0102	0.3505	-0.0019	0.0608	0.1908	0.0142	0.2635	-1.1962	-1.071	-5.1457
15	0.6638	-0.0424	0.8533	1.6591	-1.001	2.675	-0.0819	0.2336	-0.2972	-0.4356	0.1937	0.2406	1.0427	-0.3482	-0.0917	0.7531	-0.1697	0.0152	0.398	-0.0486	0.3279	-19.012	-12.3088	-30.9318
16	2.1449	-0.7199	-0.7506	5.1842	0.0021	4.8263	-0.0945	-0.0816	-0.0676	-0.1873	-0.0159	-0.0878	0.0598	-0.0256	0.1081	0.1975	-0.003	0.0312	0.1762	0.0131	0.2295	-5.7867	-14.912	3.1958

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 130 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 131 through 238 )
3	X-RAY DIFFRACTION	3	chain 'G' and (resid 1 through 18 )
4	X-RAY DIFFRACTION	4	chain 'G' and (resid 19 through 106 )
5	X-RAY DIFFRACTION	5	chain 'G' and (resid 107 through 120 )
6	X-RAY DIFFRACTION	6	chain 'G' and (resid 121 through 131 )
7	X-RAY DIFFRACTION	7	chain 'G' and (resid 132 through 146 )
8	X-RAY DIFFRACTION	8	chain 'G' and (resid 147 through 168 )
9	X-RAY DIFFRACTION	9	chain 'G' and (resid 169 through 181 )
10	X-RAY DIFFRACTION	10	chain 'G' and (resid 182 through 192 )
11	X-RAY DIFFRACTION	11	chain 'G' and (resid 193 through 206 )
12	X-RAY DIFFRACTION	12	chain 'G' and (resid 207 through 232 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 1 through 130 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 131 through 238 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 1 through 131 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 132 through 232 )

-
News

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

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
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

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and 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

-
Antibody , 2 types, 4 molecules ABGC

-
Non-polymers , 7 types, 512 molecules

-
Details

-
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

-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

-Antibody , 2 types, 4 molecules ABGC

-Non-polymers , 7 types, 512 molecules

-Details

-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

-
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

-
Antibody , 2 types, 4 molecules ABGC

-
Non-polymers , 7 types, 512 molecules

-
Details

-
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