9P0X: Nanodisc-embedded human TF/FVIIa/XK1

Nanodisc-embedded human TF/FVIIa/XK1 in complex with 10H10 Fab (nanodisc-subtracted). Determined by electron microscopy at 3.7 Å resolution. Released 27 Aug 2025.

Method: Electron microscopy
Resolution: 3.7 Å
Organisms: Homo sapiens, Escherichia coli, Mus musculus
Chains: 7
Atoms: 9,725
Mol. weight: 184.27 kDa
Ligands: MG, CA, BGC, FUC
Released: 27 Aug 2025

Explore 9P0X in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9P0X contains 38 α-helices and 123 β-strands across 7 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.

Chain H: 4 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	27
β-strand	10-12	3	28
α-helix	13	1
β-strand	18-25	8	27
α-helix	29-31	3
β-strand	34-39	6	28
β-strand	46-47	2	28
β-strand	49-51	3	28
β-strand	58-60	3	28
α-helix	62-64	3
β-strand	68-73	6	27
β-strand	78-83	6	27
α-helix	88-90	3
β-strand	92-99	8	28
β-strand	107-110	4	28
β-strand	114-118	5	28
β-strand	124	1	29
β-strand	129-130	2	30
β-strand	142-145	4	31
β-strand	147-148	2	30
β-strand	149-152	4	32
β-strand	153	1	29
β-strand	158-161	4	33
β-strand	170-172	3	31
β-strand	176-177	2	32
β-strand	182-184	3	32
β-strand	186-191	6	31
β-strand	200-201	2	34
β-strand	202-206	5	33
β-strand	211-213	3	33
β-strand	216-217	2	34

Chain K: 2 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	25-27	3
β-strand	35	1	17
β-strand	39-45	7	26
β-strand	50-56	7	26
α-helix	69-76	8

Chain L: 8 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	35
β-strand	10-13	4	36
β-strand	15	1	37
β-strand	17	1	37
β-strand	19-25	7	35
β-strand	30-31	2	38
β-strand	36-37	2	38
β-strand	39-44	6	36
β-strand	51-55	5	36
β-strand	59-60	2	36
α-helix	61	1
β-strand	69-71	3	35
β-strand	76-81	6	35
α-helix	86-88	3
β-strand	91-96	6	36
α-helix	102	1
β-strand	104	1	36
β-strand	109-112	4	36
β-strand	122-124	3	39
α-helix	125-127	3
α-helix	128-133	6
β-strand	135	1	40
β-strand	138-141	4	39
β-strand	145	1	41
β-strand	150-156	7	42
β-strand	159-160	2	42
β-strand	165-166	2	39
α-helix	170-173	4
β-strand	179	1	41
β-strand	182-185	4	39
β-strand	188	1	40
α-helix	189-192	4
β-strand	197-204	8	42
α-helix	210	1
β-strand	211-216	6	42

Chain S: 8 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	154	1	8
β-strand	157-158	2	9
α-helix	159-160	2
β-strand	167	1	10
β-strand	168-172	5	11
β-strand	175-178	4	11
β-strand	181	1	10
β-strand	182	1	12
β-strand	187-190	4	12
α-helix	192-194	3
α-helix	201-203	3
β-strand	204-208	5	11
β-strand	212	1	13
β-strand	221-224	4	11
β-strand	225-231	7	12
β-strand	244-248	5	12
β-strand	255	1	14
β-strand	258	1	14
α-helix	266-271B	6
β-strand	279-283	5	9
β-strand	286	1	15
β-strand	293	1	15
β-strand	296	1	13
β-strand	298-302	5	9
β-strand	304	1	16
α-helix	307-313	7
β-strand	329-330	2	16
β-strand	338	1	8
β-strand	347-351	5	9
β-strand	356-362	7	9
β-strand	364	1	17
β-strand	375-376	2	16
β-strand	377-378	2	9
α-helix	380-383	4
α-helix	384-391	8
α-helix	394-395	2
β-strand	400-403	4	12

Chain T: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	13-17	5	18
β-strand	20-24	5	18
β-strand	32-39	8	19
β-strand	46-52	7	19
β-strand	56-58	3	18
α-helix	60-63	4
β-strand	71	1	20
β-strand	72-79	8	19
β-strand	95-96	2	19
β-strand	100	1	20
α-helix	102-105	4
α-helix	106	1
β-strand	107	1	18
α-helix	108-109	2
β-strand	113-119	7	21
β-strand	122-127	6	21
β-strand	131-136	6	22
β-strand	139-142	4	22
α-helix	143-147	5
α-helix	148-150	3
β-strand	152	1	23
β-strand	153-157	5	24
β-strand	166-170	5	24
β-strand	177-178	2	21
β-strand	186-187	2	25
β-strand	188	1	24
β-strand	192	1	23
β-strand	201	1	23
α-helix	202-207	6
β-strand	208-209	2	25

Chain V: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	13-17	5
α-helix	24-31	8
α-helix	34-44	11
β-strand	60-64	5	1
β-strand	67-71	5	1
β-strand	76-77	2	2
β-strand	83-84	2	2
α-helix	85-87	3
β-strand	101-103	3	3
β-strand	111-113	3	3
β-strand	118-120	3	4
β-strand	127-129	3	4

Chain X: 5 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	10-11	2
α-helix	14-17	4
α-helix	24-31	8
α-helix	34-44	11
β-strand	61	1	5
β-strand	70	1	5
β-strand	77	1	6
β-strand	83	1	6
α-helix	92-95	4
β-strand	99-101	3	7
β-strand	108-110	3	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Factor VII light chain	V	protein	142	Homo sapiens	P08709 (AlphaFold model)
Factor X light chain	X	protein	131	Homo sapiens	P00742 (AlphaFold model)
Coagulation factor VII Heavy Chain	S	protein	254	Homo sapiens	P08709 (AlphaFold model)
Tissue factor,Maltose/maltodextrin-binding periplasmic protein	T	protein	611	Homo sapiens, Escherichia coli	P0AEX9 (AlphaFold model), P13726 (AlphaFold model)
Tissue factor pathway inhibitor	K	protein	68	Homo sapiens	P10646
Human 10H10 antibody Fab heavy chain	H	protein	221	Mus musculus
Human 10H10 antibody Fab light chain	L	protein	220	Mus musculus

Sequence of entity 1 (V), FASTA

>9P0X_1 Factor VII light chain (chains V)
ANAFLEELRPGSLERECKEEQCSFEEAREIFKDAERTKLFWISYSDGDQCASSPCQNGGS
CKDQLQSYICFCLPAFEGRNCETHKDDQLICVNENGGCEQYCSDHTGTKRSCRCHEGYSL
LADGVSCTPTVEYPCGKIPILE

Sequence of entity 2 (X), FASTA

>9P0X_2 Factor X light chain (chains X)
ANSFLEEMKKGHLERECMEETCSYEEAREVFEDSDKTNEFWNKYKDGDQCETSPCQNQGK
CKDGLGEYTCTCLEGFEGKNCELFTRKLCSLDNGDCDQFCHEEQNSVVCSCARGYTLADN
GKACIPTGPYP

Sequence of entity 3 (S), FASTA

>9P0X_3 Coagulation factor VII Heavy Chain (chains S)
IVGGKVCPKGECPWQVLLLVNGAQLCGGTLINTIWVVSAAHCFDKIKNWRNLIAVLGEHD
LSEHDGDEQSRRVAQVIIPSTYVPGTTNHDIALLRLHQPVVLTDHVVPLCLPERTFSERT
LAFVRFSLVSGWGQLLDRGATALELMVLNVPRLMTQDCLQQSRKVGDSPNITEYMFCAGY
SDGSKDSCKGDSGGPHATHYRGTWYLTGIVSWGQGCATVGHFGVYTRVSQYIEWLQKLMR
SEPRPGVLLRAPFP

Sequence of entity 4 (T), FASTA

>9P0X_4 Tissue factor,Maltose/maltodextrin-binding periplasmic protein (chains T)
TVAAYNLTWKSTNFKTILEWEPKPVNQVYTVQISTKSGDWKSKCFYTTDTECDLTDEIVK
DVKQTYLARVFSYPAGNVESTGSAGEPLYENSPEFTPYLETNLGQPTIQSFEQVGTKVNV
TVEDERTLVRRNNTFLSLRDVFGKDLIYTLYYWKSSSSGKKTAKTNTNEFLIDVDKGENY
CFSVQAVIPSRTVNRKSTDSPVECMGQEKGEFREIFYIIGAVVFVVIILVIILAISLHKG
SGSGMKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGD
GPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSL
IYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGK
YDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNI
DTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNK
DKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQ
TVDEALKDAQT

Sequence of entity 5 (K), FASTA

>9P0X_5 Tissue factor pathway inhibitor (chains K)
TDTELPPLKLMHSFCAFKADDGPCKAIMKRFFFNIFTRQCEEFIYGGCEGNQNRFESLEE
CKKMCTRD

Sequence of entity 6 (H), FASTA

>9P0X_6 Human 10H10 antibody Fab heavy chain (chains H)
QVHLQQSGAELMKPGASVKISCKASGYTFITYWIEWVKQRPGHGLEWIGDILPGSGSTNY
NENFKGKATFTADSSSNTAYMQLSSLTSEDSAVYYCARSGYYGNSGFAYWGQGTLVTVSA
AKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSD
LYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRD

Sequence of entity 7 (L), FASTA

>9P0X_7 Human 10H10 antibody Fab light chain (chains L)
DIVMTQSPSSLTVTAGEKVTMSCKSSQSLLSSGNQKNYLTWYQQIPGQPPKLLIYWASTR
ESGVPDRFTGSGSGTDFTLTINSVQAEDLAVYYCQNDYTYPLTFGAGTKLELKRADAAPT
VSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSATDQDSKDSTYS
MSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	4
CA	Calcium ion	Ca	12
BGC	beta-D-glucopyranose	C6 H12 O6	1
FUC	alpha-L-fucopyranose	C6 H12 O5	1

Primary citation

Cryo-EM structure of the tissue factor/factor VIIa complex with a factor X mimetic reveals a novel allosteric mechanism. Sedzro, J.C., Photenhauer, A.L., Birkle, F. et al. Blood (2025) 146:2833-2842. DOI 10.1182/blood.2025029430 · PubMed

Other PDB entries of the same protein (UniProt P08709 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6R2W 1.25 Å, Crystal structure of the super-active FVIIa variant VYT in complex with tissue factor
5PAG 1.36 Å, Crystal Structure of Factor VIIa in complex with (2R)-2-hydroxy-N-[[3-[5-hydroxy-4-(1H-py…
5PAX 1.36 Å, Crystal Structure of Factor VIIa in complex with 1-(2,6-difluorophenyl)-3-[[3-[5-hydroxy-…
4YLQ 1.4 Å, Crystal Structure of a FVIIa-Trypsin Chimera (FT) in Complex with Soluble Tissue Factor
5PAO 1.4 Å, Crystal Structure of Factor VIIa in complex with (2S)-2,3-dihydroxy-N-[[3-[5-hydroxy-4-(1…
5PAV 1.4 Å, Crystal Structure of Factor VIIa in complex with N-(6-aminopyridin-3-yl)-5-hydroxy-1-phen…
5L0S 1.45 Å, human POGLUT1 in complex with Factor VII EGF1 and UDP
5PAE 1.45 Å, Crystal Structure of Factor VIIa in complex with (2S)-2-hydroxy-N-[[3-[5-hydroxy-4-(1H-py…
5PB2 1.45 Å, Crystal Structure of Factor VIIa in complex with 2-phenyl-4-(1H-pyrrolo[3,2-c]pyridin-2-y…
5PAS 1.48 Å, Crystal Structure of Factor VIIa in complex with (2S)-2-hydroxy-N-[[3-[5-hydroxy-4-(1H-py…
5PAC 1.5 Å, human factor VIIa in complex with 5-hydroxy-N-(4-oxo-3H-quinazolin-6-yl)-1-[3-[(phenylcar…
5PAF 1.5 Å, Crystal Structure of Factor VIIa in complex with N-(2-amino-1H-benzimidazol-5-yl)-2-[3-[(…

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