9MOV: Factor Va

Cryo-EM structure of factor Va bound to activated protein C. Determined by electron microscopy at 3.0 Å resolution. Released 21 May 2025.

Method: Electron microscopy
Resolution: 3.0 Å
Organism: Homo sapiens
Chains: 4
Atoms: 13,898
Mol. weight: 202.61 kDa
Ligands: NAG, CA
Released: 21 May 2025

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

Secondary structure: helices and β-sheets

9MOV contains 37 α-helices and 137 β-strands across 4 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: 11 helices, 59 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	1
β-strand	8-15	8	2
β-strand	33-40	8	2
β-strand	41	1	3
α-helix	43-45	3
β-strand	48	1	3
α-helix	49-50	2
β-strand	62-64	3	4
β-strand	69-72	4	1
β-strand	73	1	5
β-strand	75-76	2	2
β-strand	82	1	6
β-strand	85	1	7
α-helix	106-112	7
β-strand	114	1	6
α-helix	115	1
β-strand	121	1	5
β-strand	124-125	2	1
β-strand	139-144	6	4
β-strand	145	1	7
α-helix	153-156	4
β-strand	160-165	6	4
β-strand	181-188	8	8
β-strand	205-206	2	8
β-strand	209-210	2	8
α-helix	215-216	2
β-strand	217-218	2	9
β-strand	224	1	10
β-strand	225-232	8	8
β-strand	240-243	4	9
β-strand	249	1	11
β-strand	257-259	3	9
β-strand	264-268	5	8
β-strand	269	1	11
β-strand	271	1	10
β-strand	277-282	6	9
α-helix	285-289	5
β-strand	293-297	5	9
β-strand	325	1	12
β-strand	328-332	5	13
α-helix	337-341	5
β-strand	364-368	5	13
β-strand	371	1	12
β-strand	395-397	3	14
β-strand	402-407	6	12
β-strand	417-418	2	15
β-strand	453-458	6	12
β-strand	473-475	3	14
β-strand	478-479	2	15
α-helix	483-487	5
β-strand	495-497	3	14
β-strand	514-515	2	16
β-strand	520-522	3	17
α-helix	529-538	10
α-helix	553-556	4
β-strand	559-561	3	17
β-strand	564	1	17
β-strand	572-573	2	18
β-strand	579-584	6	16
β-strand	586	1	19
β-strand	594-598	5	20
β-strand	605	1	21
β-strand	608	1	21
β-strand	612-615	4	20
β-strand	617	1	19
β-strand	621-626	6	16
β-strand	634	1	22
β-strand	635-637	3	20
β-strand	650	1	22
β-strand	651-652	2	18

Chain B: 8 helices, 49 β-strands

Element	Residues	Length	Sheet
β-strand	1552-1564	13	23
β-strand	1586-1594	9	23
α-helix	1611-1613	3
β-strand	1620-1623	4	24
β-strand	1626-1634	9	23
β-strand	1640	1	25
β-strand	1642-1643	2	26
α-helix	1664-1666	3
β-strand	1672	1	25
α-helix	1673	1
β-strand	1674	1	23
β-strand	1677-1684	8	23
β-strand	1697-1702	6	24
β-strand	1703-1704	2	26
α-helix	1708-1711	4
β-strand	1718-1723	6	24
β-strand	1740-1743	4	27
β-strand	1746-1747	2	28
β-strand	1778-1779	2	28
β-strand	1791-1792	2	29
β-strand	1797-1803	7	27
β-strand	1812-1815	4	30
β-strand	1821-1822	2	27
β-strand	1830	1	27
β-strand	1834-1836	3	30
β-strand	1841-1847	7	27
β-strand	1852-1855	4	29
β-strand	1857-1858	2	30
α-helix	1861-1863	3
β-strand	1871-1874	4	29
β-strand	1882	1	31
β-strand	1896-1897	2	32
α-helix	1906-1908	3
β-strand	1920	1	33
β-strand	1935-1944	10	32
β-strand	1949-1951	3	34
β-strand	1964-1970	7	32
β-strand	1977-1978	2	32
β-strand	1990	1	32
β-strand	2001	1	34
β-strand	2009-2019	11	32
β-strand	2026	1	33
β-strand	2027-2029	3	34
β-strand	2031	1	31
β-strand	2033-2034	2	32
α-helix	2057-2059	3
β-strand	2063	1	35
β-strand	2066	1	35
β-strand	2084	1	36
β-strand	2095-2098	4	37
β-strand	2104-2109	6	38
β-strand	2123-2128	6	37
α-helix	2149-2151	3
β-strand	2162-2169	8	38
β-strand	2172-2179	8	37
β-strand	2186	1	36
β-strand	2189-2193	5	38

Chain C: 9 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	6-8	3
α-helix	10-11	2
α-helix	13	1
α-helix	14-18	5
α-helix	24-31	8
α-helix	34-44	11
α-helix	53-54	2
β-strand	69-71	3	39
β-strand	76-78	3	39
α-helix	80-81	2
β-strand	84-85	2	40
β-strand	91-92	2	40
α-helix	101-104	4
β-strand	108-111	4	41
β-strand	116-119	4	41
β-strand	124-126	3	42
β-strand	133-135	3	42

Chain D: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	171	1	43
β-strand	174-175	2	44
α-helix	176-177	2
β-strand	184-188	5	45
β-strand	194-200	7	45
β-strand	201	1	46
β-strand	206-209	4	45
α-helix	212-215	4
β-strand	220-222	3	45
β-strand	240	1	47
β-strand	244-245	2	45
β-strand	258-260	3	45
β-strand	263	1	47
α-helix	275	1
β-strand	276	1	46
β-strand	277	1	44
α-helix	278-280	3
α-helix	281-283	3
α-helix	284-288	5
β-strand	296-299	4	44
β-strand	319-321	3	44
β-strand	325	1	44
α-helix	328-334	7
α-helix	338-340	3
β-strand	343-346	4	44
β-strand	354	1	43
β-strand	363-366	4	44
β-strand	373-380	8	44
β-strand	391-395	5	44
α-helix	400-403	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Coagulation factor Va heavy chain	A	protein	709	Homo sapiens	P12259 (AlphaFold model)
Coagulation factor Va light chain	B	protein	651	Homo sapiens	P12259 (AlphaFold model)
Vitamin K-dependent protein C	C	protein	146	Homo sapiens	P04070 (AlphaFold model)
Vitamin K-dependent protein C heavy chain	D	protein	240	Homo sapiens	P04070 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9MOV_1 Coagulation factor Va heavy chain (chains A)
AQLRQFYVAAQGISWSYRPEPTNSSLNLSVTSFKKIVYREYEPYFKKEKPQSTISGLLGP
TLYAEVGDIIKVHFKNKADKPLSIHPQGIRYSKLSEGASYLDHTFPAEKMDDAVAPGREY
TYEWSISEDSGPTHDDPPCLTHIYYSHENLIEDFNSGLIGPLLICKKGTLTEGGTQKTFD
KQIVLLFAVFDESKSWSQSSSLMYTVNGYVNGTMPDITVCAHDHISWHLLGMSSGPELFS
IHFNGQVLEQNHHKVSAITLVSATSTTANMTVGPEGKWIISSLTPKHLQAGMQAYIDIKN
CPKKTRNLKKITREQRRHMKRWEYFIAAEEVIWDYAPVIPANMDKKYRSQHLDNFSNQIG
KHYKKVMYTQYEDESFTKHTVNPNMKEDGILGPIIRAQVRDTLKIVFKNMASRPYSIYPH
GVTFSPYEDEVNSSFTSGRNNTMIRAVQPGETYTYKWNILEFDEPTENDAQCLTRPYYSD
VDIMRDIASGLIGLLLICKSRSLDRRGIQRAADIEQQAVFAVFDENKSWYLEDNINKFCE
NPDEVKRDDPKFYESNIMSTINGYVPESITTLGFCFDDTVQWHFCSVGTQNEILTIHFTG
HSFIYGKRHEDTLTLFPMRGESVTVTMDNVGTWMLTSMNSSPRSKKLRLKFRDVKCIPDD
DEDSYEIFEPPESTVMATRKMHDRLEPEDEESDADYDYQNRLAAALGIR

Sequence of entity 2 (B), FASTA

>9MOV_2 Coagulation factor Va light chain (chains B)
SNNGNRRNYYIAAEEISWDYSEFVQRETDIEDSDDIPEDTTYKKVVFRKYLDSTFTKRDP
RGEYEEHLGILGPIIRAEVDDVIQVRFKNLASRPYSLHAHGLSYEKSSEGKTYEDDSPEW
FKEDNAVQPNSSYTYVWHATERSGPESPGSACRAWAYYSAVNPEKDIHSGLIGPLLICQK
GILHKDSNMPMDMREFVLLFMTFDEKKSWYYEKKSRSSWRLTSSEMKKSHEFHAINGMIY
SLPGLKMYEQEWVRLHLLNIGGSQDIHVVHFHGQTLLENGNKQHQLGVWPLLPGSFKTLE
MKASKPGWWLLNTEVGENQRAGMQTPFLIMDRDCRMPMGLSTGIISDSQIKASEFLGYWE
PRLARLNNGGSYNAWSVEKLAAEFASKPWIQVDMQKEVIITGIQTQGAKHYLKSCYTTEF
YVAYSSNQINWQIFKGNSTRNVMYFNGNSDASTIKENQFDPPIVARYIRISPTRAYNRPT
LRLELQGCEVNGCSTPLGMENGKIENKQITASSFKKSWWGDYWEPFRARLNAQGRVNAWQ
AKANNNKQWLEIDLLKIKKITAIITQGCKSLSSEMYVKSYTIHYSEQGVEWKPYRLKSSM
VDKIFEGNTNTKGHVKNFFNPPIISRFIRVIPKTWNQSIALRLELFGCDIY

Sequence of entity 3 (C), FASTA

>9MOV_3 Vitamin K-dependent protein C (chains C)
ANSFLEELRHSSLERECIEEICDFEEAKEIFQNVDDTLAFWSKHVDGDQCLVLPLEHPCA
SLCCGHGTCIDGIGSFSCDCRSGWEGRFCQREVSFLNCSLDNGGCTHYCLEEVGWRRCSC
APGYKLGDDLLQCHPAVKFPCGRPWK

Sequence of entity 4 (D), FASTA

>9MOV_4 Vitamin K-dependent protein C heavy chain (chains D)
LIDGKMTRRGDSPWQVVLLDSKKKLACGAVLIHPSWVLTAAHCMDESKKLLVRLGEYDLR
RWEKWELDLDIKEVFVHPNYSKSTTDNDIALLHLAQPATLSQTIVPICLPDSGLAERELN
QAGQETLVTGWGYHSSREKEAKRNRTFVLNFIKIPVVPHNECSEVMSNMVSENMLCAGIL
GDRQDACEGDAGGPMVASFHGTWFLVGLVSWGEGCGLLHNYGVYTKVSRYLDWIHGHIRD

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	9
CA	Calcium ion	Ca	7

Primary citation

Cryo-EM structure of coagulation factor Va bound to activated protein C. Mohammed, B.M., Basore, K., Di Cera, E. Blood (2025) 145:3166-3177. DOI 10.1182/blood.2025028476 · 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
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
9TLG 3.1 Å, Structure of human prothrombinase with meizothrombin

Browse structure collections

About this viewer

MolViewer shows 9MOV directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.