8FDG: Coagulation factor V short

Cryo-EM structure of coagulation factor V short. Determined by electron microscopy at 3.2 Å resolution. Released 15 Mar 2023.

Method: Electron microscopy
Resolution: 3.2 Å
Organism: Homo sapiens
Chains: 1
Atoms: 12,163
Mol. weight: 172.75 kDa
Released: 15 Mar 2023

Explore 8FDG in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8FDG contains 18 α-helices and 102 β-strands across 1 chain. 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: 18 helices, 102 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
β-strand	48	1	3
α-helix	49-50	2
α-helix	59-61	3
β-strand	62-65	4	4
β-strand	69-72	4	1
β-strand	75-76	2	2
β-strand	82	1	5
β-strand	85	1	6
α-helix	106-108	3
β-strand	114	1	5
β-strand	119	1	2
β-strand	122-125	4	1
β-strand	140-144	5	4
β-strand	145	1	6
α-helix	150-154	5
β-strand	157	1	2
β-strand	160-165	6	4
β-strand	181-185	5	7
β-strand	187-191	5	8
β-strand	202-206	5	8
β-strand	209	1	8
β-strand	217-219	3	9
β-strand	224-229	6	7
β-strand	232	1	8
β-strand	238-243	6	9
β-strand	248-250	3	7
β-strand	253-255	3	7
β-strand	257-261	5	9
β-strand	266-271	6	7
β-strand	276-282	7	9
α-helix	285-289	5
β-strand	293-298	6	9
β-strand	324-333	10	10
β-strand	363-370	8	10
β-strand	395-397	3	11
β-strand	401-410	10	10
β-strand	415	1	12
β-strand	418-419	2	11
β-strand	447	1	12
β-strand	452-459	8	10
α-helix	461-463	3
α-helix	464-466	3
β-strand	472-478	7	11
α-helix	483-488	6
β-strand	493-498	6	11
β-strand	511-515	5	13
β-strand	519-524	6	13
α-helix	531-538	8
α-helix	550-553	4
α-helix	554-556	3
β-strand	557-561	5	13
β-strand	564	1	13
β-strand	572-575	4	14
β-strand	579-586	8	13
β-strand	594-596	3	15
β-strand	597	1	14
β-strand	605	1	16
β-strand	608	1	16
β-strand	613-615	3	15
β-strand	620-626	7	13
β-strand	631-636	6	14
β-strand	648-654	7	14
α-helix	655-657	3
β-strand	725	1	17
β-strand	728	1	17
α-helix	761-763	3
β-strand	849-861	13	18
β-strand	883-891	9	18
β-strand	892	1	19
β-strand	900	1	19
β-strand	917-920	4	20
β-strand	924-931	8	18
β-strand	937	1	21
β-strand	940	1	22
β-strand	945	1	18
β-strand	969	1	21
β-strand	973-980	8	18
α-helix	983-985	3
β-strand	994-997	4	20
β-strand	1000	1	22
β-strand	1017-1020	4	20
β-strand	1036-1041	6	23
β-strand	1045	1	24
α-helix	1058-1061	4
β-strand	1074	1	24
β-strand	1088-1089	2	25
β-strand	1094-1101	8	23
β-strand	1109-1111	3	26
β-strand	1112-1113	2	25
β-strand	1119-1120	2	23
β-strand	1126-1127	2	23
β-strand	1131-1133	3	26
β-strand	1137-1144	8	23
β-strand	1149-1154	6	25
β-strand	1166-1171	6	25
β-strand	1178-1179	2	27
α-helix	1189-1191	3
β-strand	1192-1193	2	27
α-helix	1204-1206	3
β-strand	1217-1218	2	28
β-strand	1232-1247	16	27
β-strand	1250-1252	3	29
β-strand	1255-1257	3	29
β-strand	1258-1267	10	27
β-strand	1274-1275	2	27
β-strand	1297-1318	22	27
β-strand	1322-1323	2	28
β-strand	1325-1331	7	27
β-strand	1392-1406	15	30
β-strand	1419-1427	9	30
β-strand	1434-1435	2	30
β-strand	1437	1	31
β-strand	1444	1	31
β-strand	1458-1477	20	30
β-strand	1486-1490	5	30
α-helix	1502-1504	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Coagulation factor V	A	protein	1505	Homo sapiens	P12259 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8FDG_1 Coagulation factor V (chains A)
AQLRQFYVAAQGISWSYRPEPTNSSLNLSVTSFKKIVYREYEPYFKKEKPQSTISGLLGP
TLYAEVGDIIKVHFKNKADKPLSIHPQGIRYSKLSEGASYLDHTFPAEKMDDAVAPGREY
TYEWSISEDSGPTHDDPPCLTHIYYSHENLIEDFNSGLIGPLLICKKGTLTEGGTQKTFD
KQIVLLFAVFDESKSWSQSSSLMYTVNGYVNGTMPDITVCAHDHISWHLLGMSSGPELFS
IHFNGQVLEQNHHKVSAITLVSATSTTANMTVGPEGKWIISSLTPKHLQAGMQAYIDIKN
CPKKTRNLKKITREQRRHMKRWEYFIAAEEVIWDYAPVIPANMDKKYRSQHLDNFSNQIG
KHYKKVMYTQYEDESFTKHTVNPNMKEDGILGPIIRAQVRDTLKIVFKNMASRPYSIYPH
GVTFSPYEDEVNSSFTSGRNNTMIRAVQPGETYTYKWNILEFDEPTENDAQCLTRPYYSD
VDIMRDIASGLIGLLLICKSRSLDRRGIQRAADIEQQAVFAVFDENKSWYLEDNINKFCE
NPDEVKRDDPKFYESNIMSTINGYVPESITTLGFCFDDTVQWHFCSVGTQNEILTIHFTG
HSFIYGKRHEDTLTLFPMRGESVTVTMDNVGTWMLTSMNSSPRSKKLRLKFRDVKCIPDD
DEDSYEIFEPPESTVMATRKMHDRLEPEDEESDADYDYQNRLAAALGIRSFRNSSLNQEE
EEFNLTALALENGTEFVSSNTDIIVGSNYSSPSNILGQMPSPSSPTLNDTFLSKEFNPLV
IVGLSKDGTDYIEIIPKEEVQSSEDDYAEIDYVPYDDPYKTDVRTNINSSRDPDNIAAWY
LRSNNGNRRNYYIAAEEISWDYSEFVQRETDIEDSDDIPEDTTYKKVVFRKYLDSTFTKR
DPRGEYEEHLGILGPIIRAEVDDVIQVRFKNLASRPYSLHAHGLSYEKSSEGKTYEDDSP
EWFKEDNAVQPNSSYTYVWHATERSGPESPGSACRAWAYYSAVNPEKDIHSGLIGPLLIC
QKGILHKDSNMPVDMREFVLLFMTFDEKKSWYYEKKSRSSWRLTSSEMKKSHEFHAINGM
IYSLPGLKMYEQEWVRLHLLNIGGSQDIHVVHFHGQTLLENGNKQHQLGVWPLLPGSFKT
LEMKASKPGWWLLNTEVGENQRAGMQTPFLIMDRDCRMPMGLSTGIISDSQIKASEFLGY
WEPRLARLNNGGSYNAWSVEKLAAEFASKPWIQVDMQKEVIITGIQTQGAKHYLKSCYTT
EFYVAYSSNQINWQIFKGNSTRNVMYFNGNSDASTIKENQFDPPIVARYIRISPTRAYNR
PTLRLELQGCEVNGCSTPLGMENGKIENKQITASSFKKSWWGDYWEPFRARLNAQGRVNA
WQAKANNNKQWLEIDLLKIKKITAIITQGCKSLSSEMYVKSYTIHYSEQGVEWKPYRLKS
SMVDKIFEGNTNTKGHVKNFFNPPIISRFIRVIPKTWNQSIALRLELFGCDIYEDQVDPR
LIDGK

Primary citation

Cryo-EM structure of coagulation factor V short. Mohammed, B.M., Pelc, L.A., Rau, M.J. et al. Blood (2023) 141:3215-3225. DOI 10.1182/blood.2022019486 · 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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