Antibodies

Recombinant antibodies within the ULTRA-DD project

Within work package 2 of the ULTRA-DD project one of the aims is to generate recombinant antibodies to selected target proteins to be used as research tools. A subset of these antibodies will be declared biological probes. These antibodies are targeting proteins present in the extracellular matrix and must be shown to have an effect on live cells in an assay format or to have a diagnostic use by detection of specific proteins in biological samples. The best antibody for each target protein will be made available through disclosing the sequence here. Selected ones will also be available through distributors, either in scFv or IgG format.

Antibody generation method

A core aim of the SGC labs has always been the ability to produce high-quality proteins. Over the years, SGC labs have been able to produce thousands of expression clones and protocols for medically relevant proteins. From this gold mine we can now cherry pick the proteins of highest importance to our partner projects and use them as antigens for antibody generation. The SGC KI team is collaborating closely with the Drug Discovery and Development platform (DDD) at the Science for Life Laboratory in Stockholm. DDD contributes with state-of-the-art combinatorial libraries of human antibody candidates where high-quality binders can be obtained through phage display technology. In contrast to traditionally used methods to generate antibodies that rely on immunizations of animals, phage display is animal-free and yields recombinant antibodies, which are completely renewable and can be converted to any desired format depending on downstream application.

Antibody validation method

Selected antibody candidates are first validated for their binding against their antigen using various immune-based assays in 96-well format. Binders that pass this initial validation are then subjected to cell-based validation, testing whether they can bind their target antigens produced endogenously in a human cell. This is done via immunoprecipitation followed by mass spectrometry, or IP-MS for short. The strength of this method is in its ability to detect not only the target protein that the antibody pulls down, but also its protein complex partners, and potential cross-reactivity targets. Compared to other traditional methods like western blot where you see only a band on a gel, IP-MS also provides the identity of each protein in the immunoprecipitate.

Antibody validation criteria:

  • Binds its target antigen with an affinity of at least 20 nM
  • Can immunoprecipitate its endogenous target protein from HEK293 cell lysate (or other relevant cell line or biological sample)
  • Specific in IP-MS, or at least that any cross-reactivity is known

Additional for biological probes:

  • Functional activity towards a target in the extracellular space measured in a cell-based assay
  • or
  • Diagnostic detection of proteins in biological samples

 

SGC Binder Name Target HGNC Name NCBI Entrez Gene ID UniProt ID Antigen (amino acid coverage) Target Annotation IP-MS Comment Validated IgG Product Available Full scFv Sequence (VH-linker-VL)
O-AARS-51 (binds both) AARS 16 P49588 1-455 (c1) of 968, AddGene no. 153046 Alanyl-tRNA synthetase Antibodies for AARS with separate epitopes scFv, IgG link FASTA
O-AARS-32 (binds c2 only) AARS 16 P49588 1-968 (c2) of 968, Full-length, AddGene no. 153047 Alanyl-tRNA synthetase Antibodies for AARS with separate epitopes scFv, IgG link FASTA
O-AASSA-25 AASS 10157 Q9UDR5 455-926 of 926 Aminoadipate-semialdehyde synthase   scFv   FASTA
Q-ACACAA-10 ACACA 31 Q13085 1572 - 2338 of 2346 Acetyl-CoA carboxylase 1   scFv   FASTA
Z-AIMP1-1 AIMP1 9255 Q12904 147-312 of 312 Aminoacyl tRNA synthase complex-interacting multifunctional protein 1 Immunoprecipitates the complete Multisynthetase complex scFv   FASTA
Q-ALAS2A-11 ALAS2 212 P22557 143 - 587 of 587 5-aminolevulinate synthase, erythroid-specific, mitochondria   scFv   FASTA
C-BRD1-3 BRD1 23774 O95696 925-1049 of 1058, PWWP domain Bromodomain-containing protein 1   scFv, IgG link FASTA
A-BRDA4-3 BRD4 23476 O60885 333-460 of 1362, Bromodomain 2 Bromodomain-containing protein 4 isoform long   scFv, IgG link FASTA
G-BRD4-4 BRD4 23476 O60885 44-168 of 1362, Bromodomain 1 Bromodomain-containing protein 4 isoform long   scFv, IgG link FASTA
C-BRPF3-8 BRPF3 27154 Q9ULD4 1056-1195 of 1205, PWWP domain Bromodomain and PHD finger-containing protein 3   scFv, IgG link FASTA
Z-CARS-8 CARS 833 P49589 1-748 of 748, Full-length Cysteinyl-tRNA synthetase   scFv   FASTA
J-CDAN1A-5 CDAN1 146059 Q8IWY9 840-1202 of 1227 Codanin-1   scFv, IgG link FASTA
O-DARS-1 DARS 1615 P14868 1-501 of 501, Full-length, AddGene no. 153048 Aspartyl-tRNA synthetase   scFv, IgG link FASTA
J-DHTKD1A-1 DHTKD1 55526 Q96HY7 45-919 of 919 Dehydrogenase E1 and transketolase domain containing protein 1   scFv, IgG link FASTA
T-FAM83BA-6 FAM83B 222584 Q5T0W9 117-294 of 1011 Protein FAM83B   scFv   FASTA
Z-FARSB-5 FARSB 10056 Q9NSD9 1-589 of 589, Full-length Phenylalanyl-tRNA synthetase, beta subunit   scFv   FASTA
O-FHL1-1 FHL1 2273 Q13642 1-280, Full-length isoform 1 Four and a half LIM domains protein 1   scFv, IgG link FASTA
Z-FUS-5 FUS 2521 P35637 266-526 of 526 RNA-binding protein FUS   scFv   FASTA
J-GALTA-3 GALT 2592 P07902 1-379 of 379, Full-length Galactose-1-phosphate uridylyltransferase   scFv, IgG link FASTA
L-GARS-2 GARS 2617 P41250 55-739 of 739, AddGene no. 153049 Glycyl-tRNA synthetase   scFv   FASTA
J-HARS-4 HARS 3035 P12081 1-509 of 509, Full-length, AddGene no. 153050 Histidyl-tRNA synthetase   scFv, IgG link FASTA
Q-IL18-6 IL18 3606 Q14116 37-193 of 193, Full-length excl. signal peptide Interleukin-18   scFv   FASTA
T-IL2-12 IL2 3558 P60568 21-153 of 153, Full-length excl. signal peptide Interleukin-2 Bio-probe, not yet validated in IP-MS scFv   FASTA
Q-IL6-9 IL6 3569 P05231 28-212 of 212, Full-length excl. signal peptide Interleukin-6   scFv   FASTA
O-IL8-15 IL8 3576 P10145 28-99 of 99, Full-length excl. signal peptide Interleukin-8   scFv, IgG link FASTA
J-IRF5-5 IRF5 3663 Q13568, Q64GB1 232-434 of 498 Interferon regulatory factor 5 Detected IRF5 in plasma serum scFv   FASTA
L-KARS-5 KARS 3735 Q15046 1-597 of 597, Full-length, AddGene no. 153051 Lysyl-tRNA synthetase   scFv, IgG link FASTA
Q-JMJD2DA-4 KDM4D 55693 Q6B0I6 1-342 of 523 Lysine-specific demethylase 4D   scFv   FASTA
O-LARS-15 LARS 51520 Q9P2J5 260-509 of 1176, AddGene no. 153052 Leucyl-tRNA synthetase Immunoprecipitates the complete Multisynthetase complex scFv   FASTA
O-MARS-11 MARS 4141 P56192 1-225 of 900, AddGene no. 153053 Methionyl-tRNA synthetase Immunoprecipitates LARS as well scFv, IgG link FASTA
Z-MATR3-4 MATR3 9782 P43243 390-578 of 847 Matrin-3   scFv   FASTA
L-NARS-2 NARS 4677 O43776 1-548 of 548, Full-length, AddGene no. 153054 Asparaginyl-tRNA synthetase   scFv, IgG link FASTA
Z-OPTN-10 OPTN 10133 Q96CV9 1-510 of 577 Optineurin   scFv   FASTA
Q-PHIPA-23 PHIP 55023 Q8WWQ0 1302 - 1434 of 1821, Bromodomain 2 PH-interacting protein   scFv   FASTA
A-PRMT3-3 PRMT3 10196 O60678 211-531 of 531, HMT Protein arginine methyltransferase 3 isoform 1   scFv, IgG link FASTA
Z-QARS-1 QARS 5859 P47897 1-775 of 775, Full-length Glutamine-tRNA ligase Immunoprecipitates the complete Multisynthetase complex scFv   FASTA
L-RARS-5 RARS 5917 P54136 70-660 of 660, AddGene no. 153055 Arginyl-tRNA synthetase Immunoprecipitates the complete Multisynthetase complex scFv, IgG link FASTA
L-Sacsin-74 SACS 26278 Q9NZJ4 1-339 of 4579, Ubl+sr1 domains Sacsin, DnaJ homolog subfamily C member 29.   scFv   FASTA
L-SARS-7 SARS 6301 P49591 1-514 of 514, Full-length, AddGene no. 153056 Seryl-tRNA synthetase   scFv, IgG link FASTA
G-SMARCA4-2 SMARCA4 6597 P51532 1451-1580 of 1647, Bromodomain SWI/SNF-related matrix-associated actin-dependent regulator of chromatin a4 isoform B Immunoprecipitates the complete SWI/SNF complex scFv, IgG link FASTA
G-SP140-8 SP140 11262 Q13342 688-862 of 867, Bromodomain Nuclear body protein SP140   scFv, IgG link FASTA
J-SPRTNC-1 SPRTN 83932 Q9H040 1-216 of 489 SprT-like N-terminal domain   scFv, IgG link FASTA
L-TARS-11 TARS 6897 P26639 320-723 of 723, AddGene no. 153057 Threonyl-tRNA synthetase   scFv, IgG link FASTA
O-TREM2-2 TREM2 54209 Q9NZC2 19-131 of 230 Triggering receptor expressed on myeloid cells 2   scFv   FASTA
T-TRIM33-4 TRIM33 51592 Q9UPN9 882-1127 of 1127 E3 ubiquitin-protein ligase TRIM33   scFv   FASTA
Z-UBQLN2-7 UBQLN2 29978 Q9UHD9 1-624 of 624 aa, Full-length Ubiquilin-2   scFv   FASTA
Z-VCP-10 VCP 7415 P55072 1-806 of 806, Full-length Transitional endoplasmic reticulum ATPase   scFv   FASTA
L-WARS-26 WARS 7453 P23381 1-471 of 471, Full-length, AddGene no. 153058 Tryptophanyl-tRNA synthetase   scFv, IgG link FASTA
A-WDR5-1 WDR5 11091 P61964 1-334 of 334, Full-length WD repeat domain 5 [Homo sapiens]   scFv, IgG link FASTA
Q-WNK3B-4 WNK3 65267 Q9BYP7 123-500 of 1800 Serine/threonine-protein kinase WNK3   scFv   FASTA
L-YARS-18 YARS 8565 P54577 1-528 of 528, Full-length, AddGene no. 153059 Tyrosyl-tRNA synthetase, cytoplasmic   scFv   FASTA
L-YARS2-9 YARS2 51067 Q9Y2Z4 31-477 of 477, AddGene no. 153060 Tyrosyl-tRNA synthetase 2, mitochondrial   scFv   FASTA

 

The table can be downloaded as an XLSX / CSV.
The single all-sequence FASTA for all entries can be downloaded here.