7KXY: Human Factor Va

Cryo-EM structure of human Factor Va at 4.4 Angstrom resolution. Determined by electron microscopy at 4.4 Å resolution. Released 10 Mar 2021.

Method: Electron microscopy
Resolution: 4.4 Å
Organism: Homo sapiens
Chains: 2
Atoms: 9,510
Mol. weight: 156.56 kDa
Released: 10 Mar 2021

Explore 7KXY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7KXY contains 10 α-helices and 74 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.

Chain A: 4 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	1
β-strand	9-13	5	2
β-strand	35-39	5	2
β-strand	62-64	3	3
β-strand	70	1	1
β-strand	86	1	4
β-strand	139-140	2	3
β-strand	144	1	4
β-strand	162-165	4	3
β-strand	184	1	5
α-helix	215-216	2
β-strand	224-231	8	5
β-strand	242	1	6
β-strand	250	1	7
β-strand	253-254	2	7
β-strand	264-271	8	5
β-strand	281	1	6
β-strand	324	1	8
β-strand	331-334	4	9
β-strand	362-365	4	9
β-strand	394-395	2	10
β-strand	405	1	8
β-strand	418	1	11
α-helix	426-428	3
β-strand	478	1	11
β-strand	494-495	2	10
β-strand	517	1	12
β-strand	522	1	13
α-helix	550-553	4
β-strand	559	1	13
β-strand	583	1	12
β-strand	594-595	2	14
β-strand	597	1	15
β-strand	614-615	2	14
β-strand	636	1	15
α-helix	641-644	4

Chain B: 6 helices, 42 β-strands

Element	Residues	Length	Sheet
β-strand	1555-1556	2	16
β-strand	1594-1595	2	16
β-strand	1616	1	17
β-strand	1620-1622	3	17
β-strand	1628	1	18
β-strand	1631	1	16
β-strand	1648	1	19
α-helix	1672-1673	2
β-strand	1682	1	18
β-strand	1683	1	19
β-strand	1698-1703	6	17
α-helix	1708-1712	5
β-strand	1717-1722	6	17
α-helix	1734-1735	2
α-helix	1780-1782	3
β-strand	1796	1	20
β-strand	1800-1801	2	21
β-strand	1814-1816	3	22
β-strand	1822	1	23
β-strand	1823	1	24
β-strand	1829	1	24
β-strand	1843-1844	2	21
β-strand	1845	1	23
β-strand	1848	1	20
β-strand	1852	1	25
β-strand	1856-1858	3	22
α-helix	1862-1865	4
β-strand	1874	1	25
β-strand	1896-1897	2	26
β-strand	1920	1	27
α-helix	1922-1924	3
β-strand	1935-1936	2	26
β-strand	1943	1	28
β-strand	1947	1	29
β-strand	1962	1	30
β-strand	1965-1970	6	31
β-strand	1977-1978	2	31
β-strand	2010	1	28
β-strand	2012-2017	6	31
β-strand	2020	1	30
β-strand	2026	1	27
β-strand	2031	1	29
β-strand	2041	1	32
β-strand	2055	1	33
β-strand	2096	1	33
β-strand	2120	1	34
β-strand	2185	1	34
β-strand	2191	1	32

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Coagulation factor Va	A	protein	709	Homo sapiens	P12259 (AlphaFold model)
Coagulation factor Va	B	protein	651	Homo sapiens	P12259 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7KXY_1 Coagulation factor Va (chains A)
AQLRQFYVAAQGISWSYRPEPTNSSLNLSVTSFKKIVYREYEPYFKKEKPQSTISGLLGP
TLYAEVGDIIKVHFKNKADKPLSIHPQGIRYSKLSEGASYLDHTFPAEKMDDAVAPGREY
TYEWSISEDSGPTHDDPPCLTHIYYSHENLIEDFNSGLIGPLLICKKGTLTEGGTQKTFD
KQIVLLFAVFDESKSWSQSSSLMYTVNGYVNGTMPDITVCAHDHISWHLLGMSSGPELFS
IHFNGQVLEQNHHKVSAITLVSATSTTANMTVGPEGKWIISSLTPKHLQAGMQAYIDIKN
CPKKTRNLKKITREQRRHMKRWEYFIAAEEVIWDYAPVIPANMDKKYRSQHLDNFSNQIG
KHYKKVMYTQYEDESFTKHTVNPNMKEDGILGPIIRAQVRDTLKIVFKNMASRPYSIYPH
GVTFSPYEDEVNSSFTSGRNNTMIRAVQPGETYTYKWNILEFDEPTENDAQCLTRPYYSD
VDIMRDIASGLIGLLLICKSRSLDRRGIQRAADIEQQAVFAVFDENKSWYLEDNINKFCE
NPDEVKRDDPKFYESNIMSTINGYVPESITTLGFCFDDTVQWHFCSVGTQNEILTIHFTG
HSFIYGKRHEDTLTLFPMRGESVTVTMDNVGTWMLTSMNSSPRSKKLRLKFRDVKCIPDD
DEDSYEIFEPPESTVMATRKMHDRLEPEDEESDADYDYQNRLAAALGIR

Sequence of entity 2 (B), FASTA

>7KXY_2 Coagulation factor Va (chains B)
SNNGNRRNYYIAAEEISWDYSEFVQRETDIEDSDDIPEDTTYKKVVFRKYLDSTFTKRDP
RGEYEEHLGILGPIIRAEVDDVIQVRFKNLASRPYSLHAHGLSYEKSSEGKTYEDDSPEW
FKEDNAVQPNSSYTYVWHATERSGPESPGSACRAWAYYSAVNPEKDIHSGLIGPLLICQK
GILHKDSNMPMDMREFVLLFMTFDEKKSWYYEKKSRSSWRLTSSEMKKSHEFHAINGMIY
SLPGLKMYEQEWVRLHLLNIGGSQDIHVVHFHGQTLLENGNKQHQLGVWPLLPGSFKTLE
MKASKPGWWLLNTEVGENQRAGMQTPFLIMDRDCRMPMGLSTGIISDSQIKASEFLGYWE
PRLARLNNGGSYNAWSVEKLAAEFASKPWIQVDMQKEVIITGIQTQGAKHYLKSCYTTEF
YVAYSSNQINWQIFKGNSTRNVMYFNGNSDASTIKENQFDPPIVARYIRISPTRAYNRPT
LRLELQGCEVNGCSTPLGMENGKIENKQITASSFKKSWWGDYWEPFRARLNAQGRVNAWQ
AKANNNKQWLEIDLLKIKKITAIITQGCKSLSSEMYVKSYTIHYSEQGVEWKPYRLKSSM
VDKIFEGNTNTKGHVKNFFNPPIISRFIRVIPKTWNQSIALRLELFGCDIY

Primary citation

Cryo-EM structures of human coagulation factors V and Va. Ruben, E.A., Rau, M.J., Fitzpatrick, J.A.J. et al. Blood (2021) 137:3137-3144. DOI 10.1182/blood.2021010684 · 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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