9TLG: Human prothrombinase with meizothrombin

Structure of human prothrombinase with meizothrombin. Determined by electron microscopy at 3.1 Å resolution. Released 12 Aug 2026.

Method: Electron microscopy
Resolution: 3.1 Å
Organism: Homo sapiens
Chains: 6
Atoms: 16,551
Mol. weight: 267.09 kDa
Ligands: CA, NAG
Released: 12 Aug 2026

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

Secondary structure: helices and β-sheets

9TLG contains 49 α-helices and 177 β-strands across 6 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 A: 17 helices, 59 β-strands

Element	Residues	Length	Sheet
β-strand	4-15	12	1
β-strand	33-37	5	1
β-strand	40	1	1
β-strand	41	1	2
α-helix	43-45	3
β-strand	48	1	2
α-helix	49-52	4
β-strand	58	1	3
β-strand	62-65	4	3
β-strand	69-77	9	1
β-strand	82	1	4
β-strand	85-86	2	3
β-strand	98	1	5
α-helix	106-109	4
β-strand	114	1	4
β-strand	119-125	7	1
α-helix	132-133	2
β-strand	139-145	7	3
β-strand	147	1	5
α-helix	152-156	5
β-strand	159-165	7	3
β-strand	170-171	2	6
β-strand	175-176	2	6
β-strand	183-191	9	7
β-strand	202-206	5	7
α-helix	215-216	2
β-strand	217-220	4	8
β-strand	224-232	9	7
β-strand	238-243	6	9
β-strand	249	1	7
β-strand	257-261	5	9
β-strand	264-271	8	7
β-strand	276	1	8
β-strand	280-282	3	9
α-helix	285-289	5
β-strand	296-299	4	8
α-helix	305-308	4
β-strand	327-331	5	10
β-strand	334	1	11
α-helix	347-350	4
β-strand	362	1	11
β-strand	365-369	5	10
α-helix	379-381	3
α-helix	391-393	3
β-strand	397	1	12
β-strand	402-409	8	13
β-strand	415	1	14
β-strand	418	1	15
β-strand	447	1	14
β-strand	451-458	8	13
β-strand	472-473	2	12
β-strand	478	1	15
α-helix	483-487	5
β-strand	497-498	2	12
β-strand	503	1	16
β-strand	509	1	16
β-strand	514-524	11	17
α-helix	531-537	7
α-helix	552-556	5
β-strand	557-559	3	17
β-strand	561	1	18
β-strand	564	1	18
α-helix	570-571	2
β-strand	572-574	3	19
β-strand	580-588	9	17
β-strand	596-598	3	19
β-strand	603-604	2	17
β-strand	609-610	2	17
β-strand	612-613	2	19
β-strand	617	1	17
β-strand	620-625	6	17
β-strand	631-637	7	19
β-strand	648-653	6	19
α-helix	657-659	3
β-strand	665-668	4	20
α-helix	670-672	3

Chain B: 13 helices, 56 β-strands

Element	Residues	Length	Sheet
β-strand	1551-1564	14	21
α-helix	1565-1568	4
α-helix	1577-1580	4
β-strand	1586-1594	9	21
α-helix	1611-1613	3
β-strand	1620-1623	4	22
β-strand	1627-1634	8	21
β-strand	1640	1	23
β-strand	1643	1	24
β-strand	1648	1	21
β-strand	1672	1	23
α-helix	1673	1
β-strand	1677-1683	7	21
α-helix	1690-1691	2
β-strand	1697-1702	6	22
β-strand	1703	1	24
α-helix	1708-1712	5
β-strand	1718-1723	6	22
β-strand	1739-1744	6	25
β-strand	1745-1748	4	26
α-helix	1769-1775	7
β-strand	1777-1780	4	26
β-strand	1783	1	26
β-strand	1791-1792	2	27
β-strand	1797-1803	7	25
β-strand	1812-1814	3	28
β-strand	1815-1816	2	27
β-strand	1820-1823	4	25
β-strand	1829-1831	3	25
β-strand	1834-1836	3	28
β-strand	1841-1847	7	25
β-strand	1852-1857	6	27
α-helix	1862-1865	4
β-strand	1869-1874	6	27
α-helix	1875-1876	2
β-strand	1882	1	29
α-helix	1892-1894	3
β-strand	1895-1897	3	29
α-helix	1906-1908	3
β-strand	1920-1921	2	30
β-strand	1935-1947	13	29
β-strand	1949	1	31
β-strand	1950-1951	2	32
β-strand	1953-1954	2	33
β-strand	1959-1960	2	33
β-strand	1964-1970	7	29
β-strand	1976-1978	3	29
β-strand	1990-1991	2	29
β-strand	2001	1	31
β-strand	2008-2019	12	29
β-strand	2025-2026	2	30
β-strand	2027-2028	2	32
β-strand	2031-2034	4	29
β-strand	2041	1	34
α-helix	2051-2053	3
β-strand	2054-2056	3	34
β-strand	2061	1	35
β-strand	2067	1	35
α-helix	2070-2072	3
β-strand	2084	1	36
β-strand	2095-2110	16	34
β-strand	2113-2114	2	37
β-strand	2119-2120	2	37
β-strand	2122-2130	9	34
β-strand	2137-2138	2	34
β-strand	2150-2151	2	34
β-strand	2160-2180	21	34
β-strand	2186	1	36
β-strand	2189-2194	6	34

Chain H: 7 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	38
β-strand	20-21	2	39
β-strand	30-32	3	20
β-strand	35	1	40
β-strand	43-46	4	20
β-strand	51-54	4	20
β-strand	64	1	40
β-strand	66-68	3	20
β-strand	72	1	41
β-strand	81-83	3	20
β-strand	85-91	7	20
β-strand	104-108	5	20
α-helix	111-112	2
β-strand	122	1	39
α-helix	125-130	6
α-helix	131A-132	3
β-strand	135	1	42
β-strand	137-140	4	39
β-strand	143	1	43
β-strand	151	1	43
β-strand	154	1	41
β-strand	156-158	3	39
α-helix	160	1
β-strand	161	1	42
β-strand	162	1	39
α-helix	165-170	6
β-strand	180-183	4	39
β-strand	189	1	38
β-strand	198-202	5	39
β-strand	207-215	9	39
β-strand	226-230	5	39
α-helix	231-234	4
α-helix	235-242	8

Chain L: 0 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	102-103	2	44
β-strand	106-107	2	44
β-strand	115-117	3	45
β-strand	124-126	3	45

Chain P: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	170-171	2
α-helix	173-175	3
β-strand	184-185	2	46
β-strand	188-190	3	46
α-helix	197-204	8
β-strand	220	1	47
β-strand	230	1	47
β-strand	232	1	48
β-strand	240	1	48
α-helix	249-251	3
β-strand	270	1	39
α-helix	309-315	7

Chain Q: 7 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	49
β-strand	20-21	2	50
β-strand	30-35	6	51
β-strand	40-46	7	51
β-strand	51-54	4	51
β-strand	60	1	52
β-strand	60G	1	52
α-helix	61-63	3
β-strand	64-68	5	51
β-strand	72	1	53
β-strand	81-83	3	51
β-strand	85-90	6	51
β-strand	95	1	54
β-strand	100	1	54
β-strand	104-108	5	51
β-strand	122	1	50
α-helix	126-129C	7
β-strand	135-140	6	50
α-helix	147A-147B	2
β-strand	154	1	53
β-strand	156-161	6	50
β-strand	162	1	55
α-helix	165-171	7
α-helix	175-176	2
β-strand	180-183	4	55
α-helix	184A-185	2
β-strand	189	1	49
β-strand	198-202	5	50
β-strand	207-212	6	50
β-strand	213-215	3	55
β-strand	226-229	4	55
α-helix	231-245	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Coagulation factor V heavy chain	A	protein	709	Homo sapiens	P12259 (AlphaFold model)
Coagulation factor V light chain	B	protein	651	Homo sapiens	P12259 (AlphaFold model)
Activated factor Xa heavy chain	H	protein	254	Homo sapiens	P00742 (AlphaFold model)
Coagulation factor X	L	protein	110	Homo sapiens	P00742 (AlphaFold model)
Prothrombin	P	protein	320	Homo sapiens	P00734 (AlphaFold model)
Prothrombin	Q	protein	259	Homo sapiens	P00734 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9TLG_1 Coagulation factor V heavy chain (chains A)
AQLRQFYVAAQGISWSYRPEPTNSSLNLSVTSFKKIVYREYEPYFKKEKPQSTISGLLGP
TLYAEVGDIIKVHFKNKADKPLSIHPQGIRYSKLSEGASYLDHTFPAEKMDDAVAPGREY
TYEWSISEDSGPTHDDPPCLTHIYYSHENLIEDFNSGLIGPLLICKKGTLTEGGTQKTFD
KQIVLLFAVFDESKSWSQSSSLMYTVNGYVNGTMPDITVCAHDHISWHLLGMSSGPELFS
IHFNGQVLEQNHHKVSAITLVSATSTTANMTVGPEGKWIISSLTPKHLQAGMQAYIDIKN
CPKKTRNLKKITREQRRHMKRWEYFIAAEEVIWDYAPVIPANMDKKYRSQHLDNFSNQIG
KHYKKVMYTQYEDESFTKHTVNPNMKEDGILGPIIRAQVRDTLKIVFKNMASRPYSIYPH
GVTFSPYEDEVNSSFTSGRNNTMIRAVQPGETYTYKWNILEFDEPTENDAQCLTRPYYSD
VDIMRDIASGLIGLLLICKSRSLDRRGIQRAADIEQQAVFAVFDENKSWYLEDNINKFCE
NPDEVKRDDPKFYESNIMSTINGYVPESITTLGFCFDDTVQWHFCSVGTQNEILTIHFTG
HSFIYGKRHEDTLTLFPMRGESVTVTMDNVGTWMLTSMNSSPRSKKLRLKFRDVKCIPDD
DEDSYEIFEPPESTVMATRKMHDRLEPEDEESDADYDYQNRLAAALGIR

Sequence of entity 2 (B), FASTA

>9TLG_2 Coagulation factor V light chain (chains B)
SNNGNRRNYYIAAEEISWDYSEFVQRETDIEDSDDIPEDTTYKKVVFRKYLDSTFTKRDP
RGEYEEHLGILGPIIRAEVDDVIQVRFKNLASRPYSLHAHGLSYEKSSEGKTYEDDSPEW
FKEDNAVQPNSSYTYVWHATERSGPESPGSACRAWAYYSAVNPEKDIHSGLIGPLLICQK
GILHKDSNMPMDMREFVLLFMTFDEKKSWYYEKKSRSSWRLTSSEMKKSHEFHAINGMIY
SLPGLKMYEQEWVRLHLLNIGGSQDIHVVHFHGQTLLENGNKQHQLGVWPLLPGSFKTLE
MKASKPGWWLLNTEVGENQRAGMQTPFLIMDRDCRMPMGLSTGIISDSQIKASEFLGYWE
PRLARLNNGGSYNAWSVEKLAAEFASKPWIQVDMQKEVIITGIQTQGAKHYLKSCYTTEF
YVAYSSNQINWQIFKGNSTRNVMYFNGNSDASTIKENQFDPPIVARYIRISPTRAYNRPT
LRLELQGCEVNGCSTPLGMENGKIENKQITASSFKKSWWGDYWEPFRARLNAQGRVNAWQ
AKANNNKQWLEIDLLKIKKITAIITQGCKSLSSEMYVKSYTIHYSEQGVEWKPYRLKSSM
VDKIFEGNTNTKGHVKNFFNPPIISRFIRVIPKTWNQSIALRLELFGCDIY

Sequence of entity 3 (H), FASTA

>9TLG_3 Activated factor Xa heavy chain (chains H)
IVGGQECKDGECPWQALLINEENEGFCGGTILSEFYILTAAHCLYQAKRFKVRVGDRNTE
QEEGGEAVHEVEVVIKHNRFTKETYDFDIAVLRLKTPITFRMNVAPACLPERDWANETLM
KQDTGIVSGFGRTHEKGRQSTRLKMLEVPYVDRHSCMLSSDFRITQNMFCAGYDTKQEDA
CQGDAGGPHVTRFKDTYFVTGIVSWGEGCARKGKYGIYTKVTRFLKWIKRSMKTRGLPKA
KSHAPEVITSSPLK

Sequence of entity 4 (L), FASTA

>9TLG_4 Coagulation factor X (chains L)
MRKLCRAFNGDCDQFCKRVQSSVVCSCARGYTLADNGKACIPTGPYPCGKQTLERRKRSV
AQATSSSGEAPDSITWKPYDAADLDPTENPFDLLDFNQTQPERGDNNLTR

Sequence of entity 5 (P), FASTA

>9TLG_5 Prothrombin (chains P)
ANTFLEEVRKGNLERECVEETCSYEEAFEALESSTATDVFWAKYTACETARTPRDKLAAC
LEGNCAEGLGTNYRGHVNITRSGIECQLWRSRYPHKPEINSTTHPGADLQENFCRNPDSS
TTGPWCYTTDPTVRRQECSIPVCGQDQVTVAMTPRSEGSSVNLSPPLEQCVPDRGQQYQG
RLAVTTHGLPCLAWASAQAKALSKHQDFNSAVQLVENFCRNPDGDEEGVWCYVAGKPGDF
GYCDLNYCEEAVEEETGDGLDEDSDRAIEGRTATSEYQTFFNPRTFGSGEADCGLRPLFE
KKSLEDKTERELLESYIDGR

Sequence of entity 6 (Q), FASTA

>9TLG_6 Prothrombin (chains Q)
IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPWDKNFTENDLL
VRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDIALMKLKKPVAFSDYIHPVCL
PDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVLQVVNLPIVERPVCKDSTRIR
ITDNMFCAGYKPDEGKRGDACEGDAGGPFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFY
THVFRLKKWIQKVIDQFGE

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

Water and common crystallization additives (NA) are not listed.

Primary citation

Prothrombinase processivity is conferred by substrate allostery. Ustok, F.I., Faille, A., Warren, A.J. et al. EMBO J (2026) 45:3954-3977. DOI 10.1038/s44318-026-00782-4 · PubMed

Other PDB entries of the same protein (UniProt P12259 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9I24 1.2 Å, Coagulation factor Xa complex with a2-loop peptide
3P6Z 1.7 Å, Structural basis of thrombin mediated factor V activation: essential role of the…
3S9C 1.8 Å, Russell's viper venom serine proteinase, RVV-V in complex with the fragment (residues…
1CZT 1.87 Å, Crystal structure of the C2 domain of human coagulation factor V
1CZS 1.9 Å, Crystal structure of the C2 domain of human coagulation factor V: complex with…
1CZV 2.4 Å, Crystal structure of the C2 domain of human coagulation factor V: dimeric crystal form
3P70 2.55 Å, Structural basis of thrombin-mediated factor V activation: essential role of the…
9T00 2.8 Å, Crystal structure of prethrombin-2 with a peptide corresponding to the C-terminus of the…
36JB 2.9 Å, Coagulation factor V DTQQ, membrane-bound, on Ptd-choline : Ptd-serine 75:25 vesicles
9MOV 3.0 Å, Cryo-EM structure of factor Va bound to activated protein C
8TN9 3.05 Å, Structural architecture of the acidic region of the B domain of coagulation factor V
9TLE 3.1 Å, Structure of human prothrombinase with prothrombin

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