9CTH: Activated Factor V heavy chain

Preliminary map of the Prothrombin-prothrombinase complex on nano discs. Determined by electron microscopy at 6.47 Å resolution. Released 7 Aug 2024.

Method: Electron microscopy
Resolution: 6.47 Å
Organism: Homo sapiens
Chains: 5
Atoms: 18,147
Mol. weight: 266.03 kDa
Ligands: NAG
Released: 7 Aug 2024

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

Secondary structure: helices and β-sheets

9CTH contains 67 α-helices and 179 β-strands across 5 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: 15 helices, 64 β-strands

Element	Residues	Length	Sheet
β-strand	3-13	11	1
β-strand	35-41	7	1
α-helix	43-45	3
β-strand	48	1	1
α-helix	49-50	2
β-strand	62-65	4	2
β-strand	69-75	7	1
β-strand	82	1	3
β-strand	85-86	2	2
α-helix	93-95	3
α-helix	106-108	3
β-strand	114	1	3
α-helix	115	1
β-strand	119-125	7	1
β-strand	139-145	7	2
α-helix	152-156	5
β-strand	157	1	1
β-strand	159-165	7	2
β-strand	170	1	4
β-strand	176	1	4
β-strand	181-188	8	5
β-strand	205-206	2	5
β-strand	209-210	2	5
α-helix	214-216	3
β-strand	217-220	4	6
β-strand	224-231	8	5
β-strand	238-242	5	7
β-strand	248-250	3	8
β-strand	253-255	3	8
β-strand	257-261	5	7
β-strand	264-271	8	5
β-strand	276-280	5	6
β-strand	281-282	2	7
α-helix	285-289	5
β-strand	294-299	6	6
α-helix	302-304	3
β-strand	323-324	2	9
β-strand	325	1	10
β-strand	328-330	3	11
β-strand	366-368	3	11
β-strand	371	1	10
α-helix	392-394	3
β-strand	396-398	3	12
β-strand	402-408	7	9
β-strand	409	1	13
β-strand	410	1	11
β-strand	415	1	14
β-strand	417-418	2	12
β-strand	435	1	15
β-strand	444	1	15
β-strand	447	1	14
β-strand	449	1	13
β-strand	452-458	7	9
β-strand	472-479	8	12
α-helix	483-487	5
β-strand	492-498	7	12
β-strand	513	1	16
β-strand	522-524	3	17
α-helix	531	1
α-helix	532-537	6
β-strand	557-559	3	17
β-strand	561	1	18
β-strand	564	1	18
α-helix	566-568	3
α-helix	570-572	3
β-strand	573-575	3	19
β-strand	579-581	3	16
β-strand	584-586	3	20
β-strand	595-598	4	21
β-strand	602-603	2	16
β-strand	605	1	22
β-strand	608	1	22
β-strand	612-614	3	21
β-strand	619-621	3	20
β-strand	624-626	3	16
β-strand	633	1	23
β-strand	635-637	3	21
β-strand	651	1	23
β-strand	652-654	3	19

Chain B: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	6-9	4
α-helix	13-18	6
α-helix	24-31	8
α-helix	34-46	13
β-strand	60-63	4	41
β-strand	68-71	4	41
α-helix	72-73	2
β-strand	77	1	42
β-strand	83	1	42
α-helix	84-87	4
α-helix	92-95	4
β-strand	99-103	5	43
β-strand	106-110	5	43
β-strand	115-117	3	44
β-strand	124-126	3	44

Chain C: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	20-21	2	45
α-helix	22-23	2
β-strand	30-35	6	46
β-strand	40-46	7	46
β-strand	51-54	4	46
α-helix	56-60	5
β-strand	64-68	5	46
β-strand	72	1	47
β-strand	81-90	10	46
β-strand	95	1	48
β-strand	100	1	48
β-strand	104-108	5	46
α-helix	111-112	2
α-helix	125-131	7
β-strand	135-140	6	45
β-strand	143	1	49
α-helix	150	1
β-strand	151	1	49
β-strand	154	1	47
β-strand	156-161	6	45
β-strand	162	1	50
α-helix	165-171	7
β-strand	181-183	3	50
β-strand	199-201	3	45
β-strand	208-211	4	45
β-strand	213	1	50
β-strand	226-228	3	50
α-helix	232-234	3
α-helix	235-242	8

Chain D: 27 helices, 31 β-strands

Element	Residues	Length	Sheet
α-helix	4-8	5
α-helix	10-11	2
α-helix	13-17	5
α-helix	24-31	8
α-helix	35-45	11
α-helix	54-62	9
α-helix	84-85	2
β-strand	86	1	51
α-helix	87-88	2
α-helix	105-107	3
β-strand	110	1	52
β-strand	113	1	52
β-strand	115	1	53
β-strand	125-127	3	53
β-strand	128	1	51
β-strand	135-137	3	53
β-strand	141	1	54
α-helix	142	1
β-strand	148	1	54
α-helix	172-175	4
β-strand	185	1	55
α-helix	189-190	2
β-strand	191	1	56
α-helix	192-193	2
α-helix	197-205	9
β-strand	220	1	57
β-strand	230	1	57
β-strand	231-232	2	58
β-strand	233	1	56
β-strand	240-241	2	58
β-strand	243	1	55
α-helix	258-260	3
α-helix	283-286	4
α-helix	308-314	7
β-strand	335-339	5	59
β-strand	350-354	5	59
β-strand	357-359	3	59
β-strand	380-383	4	59
β-strand	401-403	3	59
β-strand	424-425	2	59
β-strand	432	1	60
β-strand	435	1	60
α-helix	444-450	7
β-strand	456-458	3	61
α-helix	464-468	5
α-helix	475-477	3
α-helix	490-496	7
β-strand	506	1	62
β-strand	529-531	3	61
α-helix	539	1
β-strand	540-541	2	61
β-strand	543-545	3	62
α-helix	549-552	4
α-helix	557-559	3
β-strand	560-562	3	62
α-helix	563-565	3
α-helix	569-572	4
α-helix	575-578	4

Chain E: 10 helices, 55 β-strands

Element	Residues	Length	Sheet
β-strand	1555-1556	2	24
β-strand	1558-1564	7	25
α-helix	1569-1571	3
β-strand	1586-1592	7	25
β-strand	1595	1	24
β-strand	1603	1	24
α-helix	1604-1606	3
α-helix	1608-1610	3
β-strand	1620-1622	3	26
β-strand	1627-1633	7	24
β-strand	1643-1644	2	26
β-strand	1648	1	24
α-helix	1664-1666	3
α-helix	1672-1673	2
β-strand	1677-1683	7	24
β-strand	1697-1703	7	26
α-helix	1708-1712	5
β-strand	1718-1723	6	26
β-strand	1728	1	27
β-strand	1735	1	27
β-strand	1739-1744	6	28
β-strand	1746	1	29
β-strand	1779	1	29
β-strand	1785	1	30
β-strand	1791-1793	3	31
β-strand	1794	1	32
β-strand	1797-1803	7	28
β-strand	1813	1	33
β-strand	1814-1816	3	31
β-strand	1821-1823	3	28
β-strand	1835	1	33
β-strand	1841	1	28
β-strand	1844-1847	4	28
β-strand	1848	1	32
β-strand	1852-1858	7	31
α-helix	1861-1864	4
β-strand	1869	1	30
β-strand	1870-1875	6	31
β-strand	1895-1897	3	34
α-helix	1906-1910	5
β-strand	1935-1951	17	34
β-strand	1953-1955	3	35
β-strand	1958-1960	3	35
β-strand	1961-1964	4	36
β-strand	1965	1	37
β-strand	1968-1970	3	34
β-strand	1977-1978	2	34
β-strand	1990	1	37
β-strand	2000-2014	15	34
β-strand	2019-2021	3	36
β-strand	2027-2033	7	34
β-strand	2040-2041	2	38
α-helix	2051-2053	3
β-strand	2054-2056	3	38
β-strand	2059	1	39
β-strand	2060-2061	2	40
β-strand	2067-2068	2	40
β-strand	2086	1	39
β-strand	2095-2110	16	38
β-strand	2124-2130	7	38
β-strand	2137-2139	3	38
α-helix	2147-2148	2
β-strand	2150-2151	2	38
β-strand	2162-2179	18	38
β-strand	2188-2193	6	38

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Activated Factor V (FVa) heavy chain	A	protein	709	Homo sapiens	P12259 (AlphaFold model)
Activated Factor V (FVa) light chain	E	protein	651	Homo sapiens	P12259 (AlphaFold model)
Activated Factor X light chain	B	protein	142	Homo sapiens	P00742 (AlphaFold model)
Activated Factor X heavy chain	C	protein	235	Homo sapiens	P00742 (AlphaFold model)
Prothrombin	D	protein	579	Homo sapiens	P00734 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9CTH_1 Activated Factor V (FVa) heavy chain (chains A)
AQLRQFYVAAQGISWSYRPEPTNSSLNLSVTSFKKIVYREYEPYFKKEKPQSTISGLLGP
TLYAEVGDIIKVHFKNKADKPLSIHPQGIRYSKLSEGASYLDHTFPAEKMDDAVAPGREY
TYEWSISEDSGPTHDDPPCLTHIYYSHENLIEDFNSGLIGPLLICKKGTLTEGGTQKTFD
KQIVLLFAVFDESKSWSQSSSLMYTVNGYVNGTMPDITVCAHDHISWHLLGMSSGPELFS
IHFNGQVLEQNHHKVSAITLVSATSTTANMTVGPEGKWIISSLTPKHLQAGMQAYIDIKN
CPKKTRNLKKITREQRRHMKRWEYFIAAEEVIWDYAPVIPANMDKKYRSQHLDNFSNQIG
KHYKKVMYTQYEDESFTKHTVNPNMKEDGILGPIIRAQVRDTLKIVFKNMASRPYSIYPH
GVTFSPYEDEVNSSFTSGRNNTMIRAVQPGETYTYKWNILEFDEPTENDAQCLTRPYYSD
VDIMRDIASGLIGLLLICKSRSLDRRGIQRAADIEQQAVFAVFDENKSWYLEDNINKFCE
NPDEVKRDDPKFYESNIMSTINGYVPESITTLGFCFDDTVQWHFCSVGTQNEILTIHFTG
HSFIYGKRHEDTLTLFPMRGESVTVTMDNVGTWMLTSMNSSPRSKKLRLKFRDVKCIPDD
DEDSYEIFEPPESTVMATRKMHDRLEPEDEESDADYDYQNRLAAALGIR

Sequence of entity 2 (E), FASTA

>9CTH_2 Activated Factor V (FVa) light chain (chains E)
SNNGNRRNYYIAAEEISWDYSEFVQRETDIEDSDDIPEDTTYKKVVFRKYLDSTFTKRDP
RGEYEEHLGILGPIIRAEVDDVIQVRFKNLASRPYSLHAHGLSYEKSSEGKTYEDDSPEW
FKEDNAVQPNSSYTYVWHATERSGPESPGSACRAWAYYSAVNPEKDIHSGLIGPLLICQK
GILHKDSNMPMDMREFVLLFMTFDEKKSWYYEKKSRSSWRLTSSEMKKSHEFHAINGMIY
SLPGLKMYEQEWVRLHLLNIGGSQDIHVVHFHGQTLLENGNKQHQLGVWPLLPGSFKTLE
MKASKPGWWLLNTEVGENQRAGMQTPFLIMDRDCRMPMGLSTGIISDSQIKASEFLGYWE
PRLARLNNGGSYNAWSVEKLAAEFASKPWIQVDMQKEVIITGIQTQGAKHYLKSCYTTEF
YVAYSSNQINWQIFKGNSTRNVMYFNGNSDASTIKENQFDPPIVARYIRISPTRAYNRPT
LRLELQGCEVNGCSTPLGMENGKIENKQITASSFKKSWWGDYWEPFRARLNAQGRVNAWQ
AKANNNKQWLEIDLLKIKKITAIITQGCKSLSSEMYVKSYTIHYSEQGVEWKPYRLKSSM
VDKIFEGNTNTKGHVKNFFNPPIISRFIRVIPKTWNQSIALRLELFGCDIY

Sequence of entity 3 (B), FASTA

>9CTH_3 Activated Factor X light chain (chains B)
ANSFLEEMKKGHLERECMEETCSYEEAREVFEDSDKTNEFWNKYKDGDQCETSPCQNQGK
CKDGLGEYTCTCLEGFEGKNCELFTRKLCSLDNGDCDQFCHEEQNSVVCSCARGYTLADN
GKACIPTGPYPCGKQTLERRKR

Sequence of entity 4 (C), FASTA

>9CTH_4 Activated Factor X heavy chain (chains C)
IVGGQECKDGECPWQALLINEENEGFCGGTILSEFYILTAAHCLYQAKRFKVRVGDRNTE
QEEGGEAVHEVEVVIKHNRFTKETYDFDIAVLRLKTPITFRMNVAPACLPERDWAESTLM
TQKTGIVSGFGRTHEKGRQSTRLKMLEVPYVDRNSCKLSSSFIITQNMFCAGYDTKQEDA
CQGDAGGPHVTRFKDTYFVTGIVSWGEGCARKGKYGIYTKVTAFLKWIDRSMKTR

Sequence of entity 5 (D), FASTA

>9CTH_5 Prothrombin (chains D)
ANTFLEEVRKGNLERECVEETCSYEEAFEALESSTATDVFWAKYTACETARTPRDKLAAC
LEGNCAEGLGTNYRGHVNITRSGIECQLWRSRYPHKPEINSTTHPGADLQENFCRNPDSS
TTGPWCYTTDPTVRRQECSIPVCGQDQVTVAMTPRSEGSSVNLSPPLEQCVPDRGQQYQG
RLAVTTHGLPCLAWASAQAKALSKHQDFNSAVQLVENFCRNPDGDEEGVWCYVAGKPGDF
GYCDLNYCEEAVEEETGDGLDEDSDRAIEGRTATSEYQTFFNPRTFGSGEADCGLRPLFE
KKSLEDKTERELLESYIDGRIVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLT
AAHCLLYPPWDKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDI
ALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETWTANVGKGQPSVL
QVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDAGGPFVMKSPFNNRWY
QMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQFGE

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	6

Primary citation

The Prothrombin-Prothrombinase Interaction. Stojanovski, B.M., Mohammed, B.M., Di Cera, E. Subcell Biochem (2024) 104:409-423. DOI 10.1182/blood-2010-09-311035 · 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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