cryo-EM structure of Vitamin K-dependent gamma-carboxylase complexed with factor IX(Gla). Determined by electron microscopy at 2.41 Å resolution. Released 22 Oct 2025.
Explore 9L25 in 3D Show helices and sheets RCSB PDB PDBe
9L25 contains 41 α-helices and 18 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
| Element | Residues | Length | Sheet |
|---|---|---|---|
| α-helix | 33-38 | 6 | |
| α-helix | 42-45 | 4 | |
| α-helix | 48-55 | 8 | |
| β-strand | 58-59 | 2 | 1 |
| α-helix | 62-81 | 20 | |
| α-helix | 88-91 | 4 | |
| α-helix | 109-111 | 3 | |
| α-helix | 112-131 | 20 | |
| α-helix | 135-152 | 18 | |
| α-helix | 154-156 | 3 | |
| α-helix | 159-172 | 14 | |
| α-helix | 182-185 | 4 | |
| β-strand | 195-196 | 2 | 1 |
| α-helix | 197-217 | 21 | |
| α-helix | 221-224 | 4 | |
| α-helix | 232-234 | 3 | |
| α-helix | 236-243 | 8 | |
| α-helix | 247-249 | 3 | |
| α-helix | 250-257 | 8 | |
| α-helix | 258-271 | 14 | |
| α-helix | 276-293 | 18 | |
| α-helix | 299-306 | 8 | |
| α-helix | 307-310 | 4 | |
| α-helix | 315-321 | 7 | |
| α-helix | 325-327 | 3 | |
| α-helix | 332-333 | 2 | |
| α-helix | 336-339 | 4 | |
| α-helix | 355-357 | 3 | |
| α-helix | 358-376 | 19 | |
| α-helix | 377-379 | 3 | |
| α-helix | 385-387 | 3 | |
| β-strand | 406-416 | 11 | 2 |
| β-strand | 423-426 | 4 | 2 |
| α-helix | 436-438 | 3 | |
| α-helix | 441-454 | 14 | |
| α-helix | 455-458 | 4 | |
| β-strand | 464-473 | 10 | 2 |
| β-strand | 478 | 1 | 3 |
| β-strand | 479-480 | 2 | 2 |
| β-strand | 482 | 1 | 4 |
| β-strand | 502 | 1 | 4 |
| α-helix | 503-505 | 3 | |
| α-helix | 507-512 | 6 | |
| α-helix | 513-521 | 9 | |
| β-strand | 527-534 | 8 | 3 |
| β-strand | 539-543 | 5 | 5 |
| β-strand | 551-557 | 7 | 3 |
| β-strand | 560-564 | 5 | 5 |
| β-strand | 569-573 | 5 | 5 |
| β-strand | 578-581 | 4 | 3 |
| β-strand | 586-591 | 6 | 5 |
| β-strand | 597-604 | 8 | 3 |
| α-helix | 606-626 | 21 | |
| α-helix | 654-674 | 21 | |
| α-helix | 677-707 | 31 | |
| α-helix | 713-723 | 11 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | -16--15 | 2 | 2 |
| α-helix | -13--10 | 4 | |
| α-helix | -4--3 | 2 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Vitamin K-dependent gamma-carboxylase | A | protein | 698 | Homo sapiens | P38435 (AlphaFold model) |
| Coagulation factor IX | B | protein | 28 | Homo sapiens | P00740 (AlphaFold model) |
>9L25_1 Vitamin K-dependent gamma-carboxylase (chains A) SRIGKLLGFEWTDLSSWRRLVTLLNRPTDPASLAVFRFLFGFLMVLDIPQERGLSSLDRK YLDGLDVCRFPLLDALRPLPLDWMYLVYTIMFLGALGMMLGLCYRISCVLFLLPYWYVFL LDKTSWNNHSYLYGLLAFQLTFMDANHYWSVDGLLNAHRRNAHVPLWNYAVLRGQIFIVY FIAGVKKLDADWVEGYSMEYLSRHWLFSPFKLLLSEELTSLLVVHWGGLLLDLSAGFLLF FDVSRSIGLFFVSYFHCMNSQLFSIGMFSYVMLASSPLFCSPEWPRKLVSYCPRRLQQLL PLKAAPQPSVSCVYKRSRGKSGQKPGLRHQLGAAFTLLYLLEQLFLPYSHFLTQGYNNWT NGLYGYSWDMMVHSRSHQHVKITYRDGRTGELGYLNPGVFTQSRRWKDHADMLKQYATCL SRLLPKYNVTEPQIYFDIWVSINDRFQQRIFDPRVDIVQAAWSPFQRTSWVQPLLMDLSP WRAKLQEIKSSLDNHTEVVFIADFPGLHLENFVSEDLGNTSIQLLQGEVTVELVAEQKNQ TLREGEKMQLPAGEYHKVYTTSPSPSCYMYVYVNTTELALEQDLAYLQELKEKVENGSET GPLPPELQPLLEGEVKGGPEPTPLVQTFLRRQQRLQEIERRRNTPFHERFFRFLLRKLYV FRRSFLMTCISLRNLILGRPSLEQLAQEVTYANLRPFE
>9L25_2 Coagulation factor IX (chains B) TVFLDHENANKILNRPKRYNSGKLEEFV
| ID | Name | Formula | Copies |
|---|---|---|---|
| NAG | 2-acetamido-2-deoxy-beta-D-glucopyranose | C8 H15 N O6 | 1 |
| A1AVC | vitamin K1 hydroquinone | C31 H48 O2 | 1 |
| CLR | Cholesterol | C27 H46 O | 1 |
| PEE | 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine | C41 H78 N O8 P | 3 |
| Y01 | Cholesterol hemisuccinate | C31 H50 O4 | 1 |
| CO2 | Carbon dioxide | C O2 | 1 |
| BCT | Bicarbonate ion | C H O3 | 1 |
Structural insight into bicarbonate-mediated carboxylation by human vitamin K-dependent carboxylase. Wu, K., Wang, Z., Yao, D. et al. Nat Commun (2025) 16:10480-10480. DOI 10.1038/s41467-025-65488-3 · PubMed
Other PDB entries of the same protein (UniProt P38435 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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