8EOK: C3bB proconvertase

Structure of the C3bB proconvertase in complex with lufaxin and factor Xa. Determined by electron microscopy at 3.53 Å resolution. Released 30 Aug 2023.

Method: Electron microscopy
Resolution: 3.53 Å
Organisms: Homo sapiens, Lutzomyia longipalpis
Chains: 6
Atoms: 22,233
Mol. weight: 339.15 kDa
Ligands: MG, NAG
Released: 30 Aug 2023

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

Secondary structure: helices and β-sheets

8EOK contains 69 α-helices and 197 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: 4 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-8	6	45
β-strand	15-23	9	45
β-strand	36-39	4	46
β-strand	44-47	4	46
β-strand	54-64	11	45
β-strand	77-79	3	46
β-strand	91-93	3	46
β-strand	101-110	10	45
α-helix	117-120	4
β-strand	128	1	47
α-helix	133	1
β-strand	134	1	47
α-helix	135	1
β-strand	137	1	48
β-strand	144	1	48
β-strand	151-153	3	49
β-strand	161-164	4	49
β-strand	167-169	3	49
β-strand	170-171	2	50
β-strand	180-187	8	50
α-helix	189-191	3
β-strand	197-201	5	51
β-strand	208-210	3	50
β-strand	212-217	6	50
β-strand	228-230	3	51
β-strand	241-247	7	51
β-strand	252-261	10	50

Chain C: 10 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	54
β-strand	20-21	2	55
α-helix	22-23	2
β-strand	30-34	5	56
β-strand	40-46	7	56
β-strand	51-54	4	56
α-helix	56-59	4
β-strand	65-68	4	56
β-strand	72	1	57
β-strand	81-90	10	56
β-strand	95	1	58
β-strand	100	1	58
β-strand	104-108	5	56
α-helix	111-112	2
β-strand	115	1	59
β-strand	118	1	59
α-helix	122-124A	4
α-helix	125-127	3
α-helix	128-131A	5
β-strand	135-140	6	55
β-strand	143	1	60
α-helix	150	1
β-strand	151	1	60
α-helix	152	1
β-strand	154	1	57
β-strand	156-162	7	55
α-helix	165-171	7
β-strand	180-183	4	55
β-strand	189	1	54
β-strand	198-203	6	55
β-strand	206-215	10	55
β-strand	226-230	5	55
α-helix	235-241	7

Chain D: 18 helices, 47 β-strands

Element	Residues	Length	Sheet
β-strand	19-20	2	29
β-strand	23-27	5	30
β-strand	32-36	5	30
β-strand	41-44	4	29
β-strand	48-50	3	30
β-strand	51	1	31
β-strand	57	1	31
α-helix	58-59	2
β-strand	71-75	5	29
β-strand	78	1	32
α-helix	79-81	3
β-strand	88-90	3	33
β-strand	96	1	32
β-strand	101-105	5	33
β-strand	111-113	3	34
β-strand	117-119	3	33
β-strand	120	1	35
β-strand	126	1	35
β-strand	132-134	3	34
β-strand	149-152	4	36
β-strand	161-166	6	36
β-strand	171	1	37
β-strand	177-179	3	36
β-strand	180	1	38
β-strand	186	1	38
β-strand	194	1	37
α-helix	202-213	12
β-strand	215-216	2	39
β-strand	234-235	2	39
β-strand	243-251	9	40
α-helix	264-276	13
β-strand	282-289	8	40
β-strand	293-297	5	40
α-helix	307-314	8
α-helix	330-341	12
β-strand	355-362	8	40
α-helix	374-383	10
β-strand	398-405	8	40
α-helix	411-417	7
β-strand	427-430	4	40
α-helix	433-446	14
α-helix	464-467	4
β-strand	471-477	7	41
β-strand	483-489	7	41
β-strand	495-498	4	41
α-helix	509-511	3
β-strand	527-530	4	41
β-strand	553-556	4	41
β-strand	575	1	42
α-helix	576-580	5
α-helix	590-597	8
β-strand	602-611	10	43
β-strand	614-623	10	43
α-helix	628-632	5
α-helix	635-637	3
α-helix	647-650	4
β-strand	655-658	4	43
β-strand	660	1	44
β-strand	666	1	44
β-strand	677-682	6	43
β-strand	685-695	11	43
α-helix	700-702	3
β-strand	715-719	5	43
α-helix	724-730	7
β-strand	738	1	42

Chain G: 7 helices, 48 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	1
β-strand	11-13	3	2
β-strand	16-24	9	1
β-strand	32-38	7	2
β-strand	48-53	6	2
α-helix	56-58	3
β-strand	61-68	8	1
β-strand	82-89	8	2
β-strand	94-102	9	2
β-strand	107-112	6	3
β-strand	116-117	2	4
β-strand	122-130	9	3
β-strand	136	1	3
β-strand	140-146	7	4
β-strand	152-159	8	4
β-strand	166-172	7	3
β-strand	180-188	9	4
β-strand	196-202	7	4
β-strand	210-216	7	5
β-strand	222	1	6
β-strand	229-237	9	5
β-strand	242	1	5
β-strand	244-255	12	7
β-strand	258-272	15	7
β-strand	276-280	5	5
α-helix	282-288	7
α-helix	294-297	4
β-strand	301-309	9	7
β-strand	316-324	9	7
β-strand	327	1	6
β-strand	333-334	2	8
β-strand	341	1	9
β-strand	348-354	7	8
β-strand	355	1	10
β-strand	361	1	10
β-strand	367-368	2	11
β-strand	376-377	2	11
β-strand	384-389	6	8
β-strand	399-404	6	11
β-strand	416-420	5	11
β-strand	422	1	9
β-strand	448-454	7	12
β-strand	467-474	8	13
β-strand	477-485	9	13
β-strand	492-498	7	12
α-helix	501-503	3
β-strand	506-516	11	13
β-strand	522-532	11	13
β-strand	542-545	4	14
β-strand	558-565	8	14
β-strand	570-577	8	15
α-helix	580-583	4
α-helix	591-600	10
α-helix	613-618	6
β-strand	622-626	5	1

Chain H: 29 helices, 52 β-strands

Element	Residues	Length	Sheet
β-strand	742	1	16
β-strand	748-749	2	15
β-strand	753-755	3	15
α-helix	758-760	3
β-strand	765-772	8	14
β-strand	779-787	9	15
β-strand	793-795	3	15
β-strand	799-802	4	15
β-strand	807-812	6	17
β-strand	816-818	3	16
β-strand	823-831	9	17
β-strand	838-844	7	16
β-strand	850-851	2	18
β-strand	862-866	5	16
β-strand	870-878	9	17
β-strand	879-880	2	18
β-strand	884-894	11	16
β-strand	900-910	11	16
β-strand	914-925	12	19
β-strand	936-937	2	20
α-helix	941-943	3
β-strand	948	1	19
α-helix	949	1
β-strand	955-962	8	19
α-helix	989-1008	20
α-helix	1012-1014	3
α-helix	1020-1036	17
β-strand	1038	1	21
β-strand	1044	1	21
α-helix	1051-1052	2
α-helix	1054-1066	13
α-helix	1075-1088	14
α-helix	1101-1102	2
α-helix	1117-1133	17
α-helix	1143-1155	13
α-helix	1164-1176	13
α-helix	1183-1191	9
β-strand	1193	1	22
β-strand	1197	1	22
α-helix	1204-1206	3
α-helix	1207-1221	15
α-helix	1227-1234	8
α-helix	1249-1263	15
β-strand	1271-1277	7	20
β-strand	1284-1286	3	20
β-strand	1289	1	20
β-strand	1298-1302	5	19
β-strand	1309-1315	7	20
β-strand	1318-1328	11	19
β-strand	1339	1	23
β-strand	1342-1346	5	24
β-strand	1362-1368	7	24
β-strand	1370	1	23
β-strand	1379-1384	6	25
α-helix	1385-1386	2
β-strand	1389-1391	3	24
α-helix	1393-1401	9
β-strand	1405-1406	2	25
α-helix	1410-1413	4
β-strand	1421-1426	6	25
β-strand	1435-1443	9	24
α-helix	1450-1452	3
β-strand	1454-1459	6	25
β-strand	1466-1469	4	25
α-helix	1476-1478	3
α-helix	1479-1481	3
β-strand	1482	1	26
β-strand	1491	1	26
α-helix	1507-1513	7
β-strand	1521-1531	11	27
β-strand	1537-1548	12	27
β-strand	1559-1564	6	27
α-helix	1566-1568	3
α-helix	1569-1572	4
β-strand	1579-1584	6	27
β-strand	1590	1	28
β-strand	1597	1	28
β-strand	1598-1599	2	27
β-strand	1605-1609	5	27
α-helix	1612-1614	3
α-helix	1621-1636	16

Chain L: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
α-helix	92-95	4
β-strand	100-103	4	52
β-strand	106-109	4	52
β-strand	115-117	3	53
β-strand	124-126	3	53

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Complement C3 beta chain	G	protein	645	Homo sapiens	P01024 (AlphaFold model)
Complement C3b alpha' chain	H	protein	915	Homo sapiens	P01024 (AlphaFold model)
Complement factor B	D	protein	763	Homo sapiens	P00751 (AlphaFold model)
Lufaxin	A	protein	284	Lutzomyia longipalpis	Q5WPU8 (AlphaFold model)
Factor X light chain	L	protein	134	Homo sapiens	P00742 (AlphaFold model)
Activated factor Xa heavy chain	C	protein	254	Homo sapiens	P00742 (AlphaFold model)

Sequence of entity 1 (G), FASTA

>8EOK_1 Complement C3 beta chain (chains G)
SPMYSIITPNILRLESEETMVLEAHDAQGDVPVTVTVHDFPGKKLVLSSEKTVLTPATNH
MGNVTFTIPANREFKSEKGRNKFVTVQATFGTQVVEKVVLVSLQSGYLFIQTDKTIYTPG
STVLYRIFTVNHKLLPVGRTVMVNIENPEGIPVKQDSLSSQNQLGVLPLSWDIPELVNMG
QWKIRAYYENSPQQVFSTEFEVKEYVLPSFEVIVEPTEKFYYIYNEKGLEVTITARFLYG
KKVEGTAFVIFGIQDGEQRISLPESLKRIPIEDGSGEVVLSRKVLLDGVQNPRAEDLVGK
SLYVSATVILHSGSDMVQAERSGIPIVTSPYQIHFTKTPKYFKPGMPFDLMVFVTNPDGS
PAYRVPVAVQGEDTVQSLTQGDGVAKLSINTHPSQKPLSITVRTKKQELSEAEQATRTMQ
ALPYSTVGNSNNYLHLSVLRTELRPGETLNVNFLLRMDRAHEAKIRYYTYLIMNKGRLLK
AGRQVREPGQDLVVLPLSITTDFIPSFRLVAYYTLIGASGQREVVADSVWVDVKDSCVGS
LVVKSGQSEDRQPVPGQQMTLKIEGDHGARVVLVAVDKGVFVLNKKNKLTQSKIWDVVEK
ADIGCTPGSGKDYAGVFSDAGLTFTSSSGQQTAQRAELQCPQPAA

Sequence of entity 2 (H), FASTA

>8EOK_2 Complement C3b alpha' chain (chains H)
SNLDEDIIAEENIVSRSEFPESWLWNVEDLKEPPKNGISTKLMNIFLKDSITTWEILAVS
MSDKKGICVADPFEVTVMQDFFIDLRLPYSVVRNEQVEIRAVLYNYRQNQELKVRVELLH
NPAFCSLATTKRRHQQTVTIPPKSSLSVPYVIVPLKTGLQEVEVKAAVYHHFISDGVRKS
LKVVPEGIRMNKTVAVRTLDPERLGREGVQKEDIPPADLSDQVPDTESETRILLQGTPVA
QMTEDAVDAERLKHLIVTPSGCGEQNMIGMTPTVIAVHYLDETEQWEKFGLEKRQGALEL
IKKGYTQQLAFRQPSSAFAAFVKRAPSTWLTAYVVKVFSLAVNLIAIDSQVLCGAVKWLI
LEKQKPDGVFQEDAPVIHQEMIGGLRNNNEKDMALTAFVLISLQEAKDICEEQVNSLPGS
ITKAGDFLEANYMNLQRSYTVAIAGYALAQMGRLKGPLLNKFLTTAKDKNRWEDPGKQLY
NVEATSYALLALLQLKDFDFVPPVVRWLNEQRYYGGGYGSTQATFMVFQALAQYQKDAPD
HQELNLDVSLQLPSRSSKITHRIHWESASLLRSEETKENEGFTVTAEGKGQGTLSVVTMY
HAKAKDQLTCNKFDLKVTIKPAPETEKRPQDAKNTMILEICTRYRGDQDATMSILDISMM
TGFAPDTDDLKQLANGVDRYISKYELDKAFSDRNTLIIYLDKVSHSEDDCLAFKVHQYFN
VELIQPGAVKVYAYYNLEESCTRFYHPEKEDGKLNKLCRDELCRCAEENCFIQKSDDKVT
LEERLDKACEPGVDYVYKTRLVKVQLSNDFDEYIMAIEQTIKSGSDEVQVGQQRTFISPI
KCREALKLEEKKHYLMWGLSSDFWGEKPNLSYIIGKDTWVEHWPEEDECQDEENQKQCQD
LGAFTESMVVFGCPN

Sequence of entity 3 (D), FASTA

>8EOK_3 Complement factor B (chains D)
GSNLSPQLCLMPFILGLLSGGVTTTPWSLARPQGSCSLEGVEIKGGSFRLLQEGQALEYV
CPSGFYPYPVQTRTCRSTGSWSTLKTQDQKTVRKAECRAIHCPRPHDFENGEYWPRSPYY
NVSDEISFHCYDGYTLRGSANRTCQVNGRWSGQTAICDNGAGYCSNPGIPIGTRKVGSQY
RLEDSVTYHCSRGLTLRGSQRRTCQEGGSWSGTEPSCQDSFMYDTPQEVAEAFLSSLTET
IEGVDAEDGHGPGEQQKRKIVLDPSGSMNIYLVLDGSDSIGASNFTGAKKCLVNLIEKVA
SYGVKPRYGLVTYATYPKIWVKVSEADSSNADWVTKQLNEINYEDHKLKSGTNTKKALQA
VYSMMSWPDDVPPEGWNRTRHVIILMTDGLHNMGGDPITVIDEIRDLLYIGKDRKNPRED
YLDVYVFGVGPLVNQVNINALASKKDNEQHVFKVKDMENLEDVFYQMIDESQSLSLCGMV
WEHRKGTDYHKQPWQAKISVIRPSKGHESCMGAVVSEYFVLTAAHCFTVDDKEHSIKVSV
GGEKRDLEIEVVLFHPNYNINGKKEAGIPEFYDYDVALIKLKNKLKYGQTIRPICLPCTE
GTTRALRLPPTTTCQQQKEELLPAQDIKALFVSEEEKKLTRKEVYIKNGDKKGSCERDAQ
YAPGYDKVKDISEVVTPRFLCTGGVSPYADPNTCRGDSGGPLIVHKRSRFIQVGVISWGV
VDVCKNQKRQKQVPAHARDFHINLFQVLPWLKEKLQDEDLGFL

Sequence of entity 4 (A), FASTA

>8EOK_4 Lufaxin (chains A)
DGDEYFIGKYKEKDETLFFASYGLKRDPCQIVLGYKCSNNQTHFVLNFKTNKKSCISAIK
LTSYPKINQNSDLTRNLYCQTGGIGTDNCKLVFKKRKRQIAANIEIYGIPAKKCSFKDRY
IGADPLHVDSYGLSYQFDQEHGWNLERNNIFKDTRFSTEVFYHKNGLFNTQITYLAEEDS
FSEAREITAKDIKKKFSIILPNEEYKRISFLDVYWFQETMRKKPKYPYIHYNGECSNENK
TCELVFDTDELMTYALVKVFTNPESDGSRLKEEDLGRGHHHHHH

Sequence of entity 5 (L), FASTA

>8EOK_5 Factor X light chain (chains L)
EEMKKGHLERECMEETCSYEEAREVFEDSDKTNEFWNKYKDGDQCETSPCQNQGKCKDGL
GEYTCTCLEGFEGKNCELFTRKLCSLDNGDCDQFCHEEQNSVVCSCARGYTLADNGKACI
PTGPYPCGKQTLER

Sequence of entity 6 (C), FASTA

>8EOK_6 Activated factor Xa heavy chain (chains C)
IVGGQECKDGECPWQALLINEENEGFCGGTILSEFYILTAAHCLYQAKRFKVRVGDRNTE
QEEGGEAVHEVEVVIKHNRFTKETYDFDIAVLRLKTPITFRMNVAPACLPERDWAESTLM
TQKTGIVSGFGRTHEKGRQSTRLKMLEVPYVDRNSCKLSSSFIITQNMFCAGYDTKQEDA
CQGDSGGPHVTRFKDTYFVTGIVSWGEGCARKGKYGIYTKVTAFLKWIDRSMKTRGLPKA
KSHAPEVITSSPLK

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2

Primary citation

A bispecific inhibitor of complement and coagulation blocks activation in complementopathy models via a novel mechanism. Andersen, J.F., Lei, H., Strayer, E.C. et al. Blood (2023) 141:3109-3121. DOI 10.1182/blood.2022019359 · PubMed

Other PDB entries of the same protein (UniProt P01024 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2WY7 1.7 Å, Staphylococcus aureus complement subversion protein Sbi-IV in complex with complement…
2WY8 1.7 Å, Staphylococcus aureus complement subversion protein Sbi-IV in complex with complement…
7UE9 1.75 Å, Structure of anti-C3d Fab(3d8b) in complex with C3d
1C3D 1.8 Å, X-ray crystal structure of C3D: a C3 fragment and ligand for complement receptor 2
6RMT 2.0 Å, Crystal structure of disulphide-linked human C3d dimer
7BAG 2.0 Å, C3b in complex with CP40
1GHQ 2.04 Å, CR2-C3D complex structure
3D5R 2.1 Å, Crystal Structure of Efb-C (N138A) / C3d Complex
3OXU 2.1 Å, Complement components factor H CCP19-20 and C3d in complex
4I6O 2.14 Å, Crystal structure of chemically synthesized human anaphylatoxin C3a
4ONT 2.15 Å, Ternary host recognition complex of complement factor H, C3d, and sialic acid
2GOX 2.2 Å, Crystal structure of Efb-C / C3d Complex

Browse structure collections

About this viewer

MolViewer shows 8EOK 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.