Cryo-EM structure of aPlexinA1-19-43 Fab in complex with PlexinA1 dimer

2026-01-21 REL PDBj INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY PDBj PDBj 2024-08-09 2026-01-21 2026-01-21 2026-01-21 Other government PRP/065/19FX Hong Kong Cryo-EM structure of aPlexinA1-19-43 Fab in complex with PlexinA1 dimer Tian H Fung CP Signalling, Fab, Complex, PROTEIN BINDING, PROTEIN BINDING-IMMUNE SYSTEM complex Tian H Fung CP Burman L Chong YE Liu C Geng Y Yang L Chow MW Zhang Y Ho KWH Zhu G Wu Z Yang XL Xu Z Nangle LA A bispecific antibody designed to act as a NRP2/PLXNA1 agonist mimics anticancer activity of SEMA3F. J.Biol.Chem. US 302 111056 111056 2025 41391772 doi:10.1016/j.jbc.2025.111056 1083-351X 0071 JBCHA3 9j4c FULLOVERLAP EMDB EMD-61131 associated EM volume

Dimer complex of Human Plexin-A1 27-710 with aPlexinA1-19-43 Fab binding Dimer complex of Human Plexin-A1 27-710 with aPlexinA1-19-43 Fab binding 0 1 2 3

Fab fragments generated from cloning the variable region of PlexinA1 antibody generated from mouse, into Fab vector. Fab fragments and PlexinA1 27-710 are expressed and purified from CHO cells.

Dimer of Human Plexin-A1 27-710 1 1 Homo sapiens aPlexinA1-19-43 Fab 1 2 3

Heavy chain and light chain of aPlexinA1-19-43 Fab expressed and purified from CHO cells

Mus musculus Plexin-A1 Homo sapiens 0.07671073399999999

Human Plexin A1 27 to 710 with His Tag

1 Cricetulus griseus LEVO EAGLPRAGGGSQPPFRTFSASDWGLTHLVVHEQTGEVYVGAVNRIYKLSGNLTLLRAHVTGPVEDNEKCYPPPSVQSCPH GLGSTDNVNKLLLLDYAANRLLACGSASQGICQFLRLDDLFKLGEPHHRKEHYLSSVQEAGSMAGVLIAGPPGQGQAKLF VGTPIDGKSEYFPTLSSRRLMANEEDADMFGFVYQDEFVSSQLKIPSDTLSKFPAFDIYYVYSFRSEQFVYYLTLQLDTQ LTSPDAAGEHFFTSKIVRLCVDDPKFYSYVEFPIGCEQAGVEYRLVQDAYLSRPGRALAHQLGLAEDEDVLFTVFAQGQK NRVKPPKESALCLFTLRAIKEKIKERIQSCYRGEGKLSLPWLLNKELGCINSPLQIDDDFCGQDFNQPLGGTVTIEGTPL FVDKDDGLTAVAAYDYRGRTVVFAGTRSGRIRKILVDLSNPGGRPALAYESVVAQEGSPILRDLVLSPNHQYLYAMTEKQ VTRVPVESCVQYTSCELCLGSRDPHCGWCVLHSICSRRDACERADEPQRFAADLLQCVQLTVQPRNVSVTMSQVPLVLQA WNVPDLSAGVNCSFEDFTESESVLEDGRIHCRSPSAREVAPITRGQGDQRVVKLYLKSKETGKKFASVDFVFYNCSVHQS CLSCVNGSFPCHWCKYRHVCTHNVADCAFLEGRVNVSEDCPQILHHHHHH Q9UIW2 Light chain of aPlexinA1-19-43 Fab Mus musculus 0.023413872999999998 1 Cricetulus griseus LEVO QIVLTQSPAILSASPGEKVTMSCSVSSSITYMHWYQQKPGTSPKRWIYDTSKLASGVPARFSGSGSGTSFSLTISNMEAE DAATYYCHQRSSYPYSFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLN SWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC Heavy chain of aPlexinA1-19-43 Fab Mus musculus 0.025302013999999998 1 Cricetulus griseus LEVO EVQLQQSGPELVKPGASVKISCKASGYKFTENYMDWVKQSHGESLEWIGDISPDNGDTSYNQKFRDKATLTVDKSSSTAY MELRSLTSEDSAVYYCAQIIYYDYVGYALDYWGQGTSVTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVT VTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDCGGSHHHHHH singleParticle particle 0.1 7.4

1x PBS 7.4

Quantifoil R2/2 GOLD 300 CARBON HOLEY GLOW DISCHARGE 30 ETHANE 100 291.15 FEI VITROBOT MARK IV

To prepare cryo-grids, 3 ul samples were applied to glow discharged Quantifoil Au grids (R2/2, 300 mesh), which were subsequently blotted with filter paper (Ted Pella) for 3 seconds at 18oC and 100% humidity. The grids were immediately plunge frozen in liquid ethane using a FEI Vitrobot IV (ThermoFisher).

This sample is a 1:1 mixture of aPlexinA1-19-43 Fab in complex with PlexinA1 dimer. The sample was mono disperse.

FEI TITAN KRIOS OTHER OTHER OTHER 300 1.2 2.5 FEI FALCON III (4k x 4k) 1989 50.0

A total of 2,084 movies were acquired and imported into Cryo-SPARC using the following parameters: Raw pixel size 1.026 A, Accelerating Voltage 300 kV, Spherical Aberration 2.7 mm, and Total exposure dose 50 e/A^2. Motion correction and CTF estimation were performed using Full-frame Motion Correction and Patch CTF. After that, 1,989 micrographs were selected from the 2,084 micrographs based on average intensity (-10055.05 to 2041.77)

1 3741859

After Inspect Particle Picks (NCC score > 0.620, 10421 < local power score < 17132) and Extract From Micrographs (Extraction box size 320 pix), a total of 3,741,859 particles were extracted

cryoSPARC 4.1.2 PHASE FLIPPING AND AMPLITUDE CORRECTION 1 3.33 FSC 0.143 CUT-OFF cryoSPARC 4.1.2 253734 MAXIMUM LIKELIHOOD cryoSPARC 4.1.2 MAXIMUM LIKELIHOOD cryoSPARC 4.1.2 6 cryoSPARC 4.1.2 emd_61131.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 280 280 280 0 0 0 280 280 280 287.28 287.28 287.28 90.0 90.0 90.0 X Y Z -1.4498564 2.5345814 0.00083649304 0.055359047 1.026 1.026 1.026 0.173 AUTHOR ::::EMDATABANK.org::::EMD-61131:::: Cryo-EM structure of aPlexinA1-19-43 Fab in complex with PlexinA1 dimer. Sharpened main map. 5L59 A 27-710 PDB experimental model

Inital model was based on PDB entry 5L59, and truncated to the appropriate lenght of 27-710

H AlphaFold in silico model

Intial model of Fab was generated in silico using alphafold servers.

L AlphaFold in silico model

Intial model of Fab was generated in silico using alphafold servers.

AB INITIO MODEL

Initial local fitting was done using Chimera X, followed by manual fitting using Coot. Finally it was refined using Phenix real space refinement

REAL emd_61131_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 280 280 280 0 0 0 280 280 280 287.28 287.28 287.28 90.0 90.0 90.0 X Y Z -0.28897825 0.9950381 0.000836493 0.03625845 1.026 1.026 1.026 AUTHOR ::::EMDATABANK.org::::EMD-61131:::: Cryo-EM structure of aPlexinA1-19-43 Fab in complex with PlexinA1 dimer. Raw Map emd_61131_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 280 280 280 0 0 0 280 280 280 287.28 287.28 287.28 90.0 90.0 90.0 X Y Z -0.42394122 1.1073488 0.000873391 0.048091285 1.026 1.026 1.026 AUTHOR ::::EMDATABANK.org::::EMD-61131:::: Cryo-EM structure of aPlexinA1-19-43 Fab in complex with PlexinA1 dimer. Half Map B emd_61131_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 280 280 280 0 0 0 280 280 280 287.28 287.28 287.28 90.0 90.0 90.0 X Y Z -0.38612282 1.1191527 0.00086855737 0.048152365 1.026 1.026 1.026 AUTHOR ::::EMDATABANK.org::::EMD-61131:::: Cryo-EM structure of aPlexinA1-19-43 Fab in complex with PlexinA1 dimer. Half Map A