6RUV: SCIN stabilized C3bBb convertase

Structure of the SCIN stabilized C3bBb convertase bound to Properdin and a the non-inhibitory nanobody hFPNb1. Determined by X-ray diffraction at 6.15 Å resolution. Released 21 Aug 2019.

Method: X-ray diffraction
Resolution: 6.15 Å
Organisms: Lama glama, Homo sapiens, Staphylococcus aureus
Chains: 14
Atoms: 41,916
Mol. weight: 610.53 kDa
Ligands: MG, MAN
Released: 21 Aug 2019

Explore 6RUV in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6RUV contains 194 α-helices and 362 β-strands across 14 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, 56 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	32
β-strand	11-13	3	33
β-strand	17-25	9	32
β-strand	31-40	10	33
β-strand	47	1	33
β-strand	51-54	4	33
β-strand	55	1	32
α-helix	56-58	3
β-strand	61-67	7	32
β-strand	83-90	8	33
β-strand	93-102	10	33
β-strand	107-112	6	34
β-strand	116-117	2	35
β-strand	122-130	9	34
β-strand	136	1	34
β-strand	140-146	7	35
β-strand	152-159	8	35
β-strand	166-172	7	34
β-strand	180-188	9	35
β-strand	196-202	7	35
β-strand	210-216	7	36
β-strand	221-222	2	37
β-strand	229-237	9	36
β-strand	242	1	36
β-strand	245-255	11	38
β-strand	258-261	4	38
α-helix	263-265	3
β-strand	267-271	5	38
β-strand	272	1	36
β-strand	275-280	6	36
α-helix	282-288	7
β-strand	301-310	10	38
β-strand	316-325	10	38
β-strand	326-327	2	37
β-strand	332-334	3	39
β-strand	341-342	2	40
α-helix	343	1
β-strand	348-355	8	39
α-helix	360	1
β-strand	361	1	39
α-helix	362	1
β-strand	366-369	4	41
β-strand	376-378	3	41
β-strand	384-389	6	39
β-strand	398-404	7	41
β-strand	416-421	6	41
β-strand	422-423	2	40
α-helix	427-429	3
β-strand	433-438	6	42
β-strand	443	1	43
β-strand	448-456	9	42
α-helix	462-464	3
β-strand	467-474	8	44
β-strand	477-485	9	44
β-strand	492-498	7	42
α-helix	501-503	3
β-strand	506-517	12	44
β-strand	521-532	12	44
β-strand	533	1	43
β-strand	542-545	4	45
α-helix	553-554	2
β-strand	558-566	9	45
β-strand	570-577	8	46
α-helix	578-583	6
α-helix	591-600	10
β-strand	608	1	44
α-helix	613-620	8
β-strand	622-626	5	32
β-strand	631	1	32
α-helix	632-634	3
α-helix	640-643	4

Chain B: 33 helices, 55 β-strands

Element	Residues	Length	Sheet
α-helix	736-738	3
β-strand	742	1	47
β-strand	748-749	2	46
β-strand	753-755	3	46
β-strand	760-761	2	45
β-strand	764-772	9	45
β-strand	778-788	11	46
β-strand	792-795	4	46
α-helix	796-798	3
β-strand	799-803	5	46
β-strand	807-812	6	48
β-strand	816-818	3	47
β-strand	823-831	9	48
β-strand	838-844	7	47
α-helix	845-846	2
β-strand	850-851	2	49
β-strand	860-866	7	47
β-strand	870-878	9	48
β-strand	879-880	2	49
β-strand	884-894	11	47
β-strand	900-910	11	47
β-strand	914-925	12	50
β-strand	935-940	6	51
α-helix	941-943	3
β-strand	948	1	50
α-helix	949	1
β-strand	954-962	9	50
α-helix	970-973	4
α-helix	977-980	4
α-helix	989-1008	20
α-helix	1012-1015	4
α-helix	1018-1034	17
α-helix	1035-1037	3
β-strand	1038-1039	2	52
β-strand	1043-1044	2	52
α-helix	1051-1053	3
α-helix	1054-1067	14
α-helix	1075-1088	14
β-strand	1090	1	53
β-strand	1096	1	53
α-helix	1109-1112	4
α-helix	1117-1131	15
α-helix	1133-1136	4
α-helix	1143-1156	14
α-helix	1164-1177	14
α-helix	1183-1191	9
β-strand	1193	1	54
β-strand	1197	1	54
α-helix	1204-1221	18
α-helix	1227-1237	11
α-helix	1247-1260	14
β-strand	1272-1277	6	51
β-strand	1286-1289	4	51
β-strand	1297-1301	5	50
β-strand	1308-1313	6	51
β-strand	1318-1328	11	50
β-strand	1339	1	55
β-strand	1342-1347	6	56
β-strand	1362-1368	7	56
β-strand	1370	1	55
β-strand	1376	1	57
β-strand	1379-1384	6	58
α-helix	1385-1386	2
β-strand	1389-1391	3	56
α-helix	1393-1401	9
β-strand	1405-1406	2	58
α-helix	1409-1412	4
α-helix	1416-1418	3
β-strand	1421-1426	6	58
β-strand	1429	1	57
β-strand	1435-1443	9	56
α-helix	1450-1452	3
β-strand	1453-1459	7	58
β-strand	1467-1471	5	58
β-strand	1482-1485	4	59
β-strand	1488-1491	4	59
α-helix	1507-1512	6
α-helix	1513-1515	3
β-strand	1521-1532	12	60
β-strand	1536-1549	14	60
β-strand	1559-1565	7	60
α-helix	1566-1568	3
β-strand	1579-1584	6	60
β-strand	1589-1590	2	60
β-strand	1597-1599	3	60
β-strand	1605-1609	5	60
α-helix	1612-1615	4
α-helix	1619-1634	16

Chain G: 16 helices, 56 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	61
β-strand	11-13	3	62
β-strand	17-25	9	61
β-strand	31-40	10	62
β-strand	47	1	62
β-strand	51-54	4	62
β-strand	55	1	61
α-helix	56-58	3
β-strand	61-67	7	61
β-strand	83-90	8	62
β-strand	93-102	10	62
β-strand	107-112	6	63
β-strand	116-117	2	64
β-strand	122-130	9	63
β-strand	136	1	63
β-strand	140-146	7	64
β-strand	152-159	8	64
β-strand	166-172	7	63
α-helix	173-174	2
β-strand	180-188	9	64
β-strand	196-202	7	64
β-strand	210-216	7	65
β-strand	221-222	2	66
β-strand	229-237	9	65
β-strand	242	1	65
β-strand	245-255	11	67
β-strand	258-261	4	67
α-helix	263-265	3
β-strand	267-271	5	67
β-strand	272	1	65
β-strand	275-280	6	65
α-helix	282-288	7
β-strand	301-310	10	67
β-strand	316-325	10	67
β-strand	326-327	2	66
β-strand	332-334	3	68
β-strand	341-342	2	69
α-helix	343	1
β-strand	348-355	8	68
α-helix	360	1
β-strand	361	1	68
α-helix	362	1
β-strand	366-369	4	70
β-strand	376-378	3	70
β-strand	384-389	6	68
β-strand	398-404	7	70
β-strand	416-421	6	70
β-strand	422-423	2	69
α-helix	427-429	3
β-strand	433-438	6	71
β-strand	443	1	72
β-strand	448-456	9	71
α-helix	462-464	3
β-strand	467-474	8	73
β-strand	477-485	9	73
β-strand	492-498	7	71
α-helix	501-503	3
β-strand	506-517	12	73
β-strand	521-532	12	73
β-strand	533	1	72
β-strand	542-545	4	74
α-helix	553-554	2
β-strand	558-566	9	74
β-strand	570-577	8	75
α-helix	578-583	6
α-helix	591-600	10
β-strand	608	1	73
α-helix	613-620	8
β-strand	622-626	5	61
β-strand	631	1	61
α-helix	632-634	3
α-helix	640-643	4

Chain H: 33 helices, 55 β-strands

Element	Residues	Length	Sheet
α-helix	736-738	3
β-strand	742	1	76
β-strand	748-749	2	75
β-strand	753-755	3	75
β-strand	760-761	2	74
β-strand	764-772	9	74
β-strand	779-788	10	75
β-strand	792-795	4	75
α-helix	796-798	3
β-strand	799-802	4	75
β-strand	807-812	6	77
β-strand	816-818	3	76
β-strand	823-831	9	77
β-strand	838-844	7	76
α-helix	845-846	2
β-strand	850-851	2	78
β-strand	860-866	7	76
β-strand	870-878	9	77
β-strand	879-880	2	78
β-strand	884-894	11	76
β-strand	900-910	11	76
β-strand	914-925	12	79
β-strand	935-940	6	80
α-helix	941-943	3
β-strand	948	1	79
α-helix	949	1
β-strand	954-962	9	79
α-helix	970-973	4
α-helix	977-980	4
α-helix	989-1008	20
α-helix	1012-1015	4
α-helix	1018-1034	17
α-helix	1035-1037	3
β-strand	1038-1039	2	81
β-strand	1043-1044	2	81
α-helix	1051-1053	3
α-helix	1054-1067	14
α-helix	1075-1089	15
β-strand	1090	1	82
β-strand	1096	1	82
α-helix	1109-1112	4
α-helix	1117-1131	15
α-helix	1133-1136	4
α-helix	1143-1156	14
α-helix	1164-1177	14
α-helix	1183-1191	9
β-strand	1193	1	83
β-strand	1197	1	83
α-helix	1204-1221	18
α-helix	1227-1237	11
α-helix	1247-1260	14
β-strand	1272-1277	6	80
β-strand	1286-1289	4	80
β-strand	1297-1301	5	79
β-strand	1308-1313	6	80
β-strand	1318-1328	11	79
β-strand	1339	1	84
β-strand	1342-1347	6	85
β-strand	1361-1368	8	85
β-strand	1370	1	84
β-strand	1376	1	86
β-strand	1379-1384	6	87
α-helix	1385-1386	2
β-strand	1389-1391	3	85
α-helix	1393-1401	9
β-strand	1405-1406	2	87
α-helix	1409-1412	4
α-helix	1416-1418	3
β-strand	1421-1426	6	87
β-strand	1429	1	86
β-strand	1435-1443	9	85
α-helix	1450-1452	3
β-strand	1453-1459	7	87
β-strand	1462-1471	10	87
β-strand	1482-1485	4	88
β-strand	1488-1491	4	88
α-helix	1507-1512	6
α-helix	1513-1515	3
β-strand	1521-1532	12	89
β-strand	1536-1549	14	89
β-strand	1559-1565	7	89
α-helix	1566-1568	3
β-strand	1579-1584	6	89
β-strand	1589-1590	2	89
β-strand	1597-1599	3	89
β-strand	1605-1609	5	89
α-helix	1612-1615	4
α-helix	1619-1634	16

Chain J: 27 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	237	1	90
β-strand	244-251	8	91
α-helix	258-276	19
α-helix	282	1
β-strand	283-289	7	91
β-strand	293-297	5	91
α-helix	302-305	4
α-helix	307-316	10
α-helix	319-321	3
α-helix	323-325	3
α-helix	330-341	12
α-helix	342-343	2
α-helix	348-349	2
β-strand	356-363	8	91
α-helix	374-383	10
α-helix	395-397	3
β-strand	398-404	7	91
α-helix	411-417	7
β-strand	427-428	2	91
α-helix	431-433	3
α-helix	436-443	8
β-strand	445	1	90
α-helix	464-467	4
β-strand	471-478	8	92
β-strand	482-490	9	92
β-strand	495-498	4	92
α-helix	509-511	3
β-strand	512-515	4	92
α-helix	522	1
β-strand	523	1	92
α-helix	524	1
β-strand	525-530	6	92
β-strand	553-557	5	92
α-helix	569-570	2
β-strand	571	1	93
β-strand	575	1	94
α-helix	576-581	6
α-helix	590-597	8
β-strand	602-610	9	93
β-strand	615-623	9	93
α-helix	628-633	6
α-helix	634-637	4
α-helix	647-650	4
β-strand	655-659	5	93
β-strand	660	1	95
β-strand	666	1	95
α-helix	671-673	3
α-helix	676	1
β-strand	677-682	6	93
β-strand	685-695	11	93
β-strand	714-719	6	93
α-helix	724-731	8
β-strand	738	1	94

Chain L: 28 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	237	1	96
β-strand	244-251	8	97
α-helix	258-276	19
α-helix	282	1
β-strand	283-289	7	97
β-strand	293-297	5	97
α-helix	302-305	4
α-helix	307-316	10
α-helix	319-321	3
α-helix	323-325	3
α-helix	330-341	12
α-helix	342-343	2
α-helix	348-349	2
β-strand	356-363	8	97
α-helix	374-383	10
α-helix	395-397	3
β-strand	398-404	7	97
α-helix	411-417	7
β-strand	427-428	2	97
α-helix	431-433	3
α-helix	436-443	8
β-strand	445	1	96
α-helix	464-467	4
β-strand	471-478	8	98
β-strand	482-490	9	98
β-strand	495-498	4	98
α-helix	509-511	3
β-strand	512-515	4	98
α-helix	522	1
β-strand	523	1	98
α-helix	524	1
β-strand	525-530	6	98
β-strand	553-557	5	98
α-helix	569-570	2
β-strand	571	1	99
β-strand	575	1	100
α-helix	576-581	6
α-helix	590-597	8
β-strand	602-611	10	99
β-strand	614-623	10	99
α-helix	628-633	6
α-helix	634-637	4
α-helix	647-650	4
β-strand	655-659	5	99
β-strand	660	1	101
β-strand	666	1	101
α-helix	671-673	3
α-helix	676	1
β-strand	677-682	6	99
β-strand	685-695	11	99
β-strand	714-719	6	99
α-helix	724-731	8
α-helix	732-734	3
β-strand	738	1	100

Chains N and Q: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	3-6	4
α-helix	8-24	17
α-helix	26-32	7
α-helix	33-35	3
α-helix	38-57	20
α-helix	60-84	25

Chains R and S: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	1
β-strand	11-14	4	2
β-strand	19-25	7	1
α-helix	30-32	3
β-strand	33-40	8	2
β-strand	46-52	7	2
β-strand	59-61	3	2
β-strand	66	1	1
β-strand	69-74	6	1
β-strand	79-84	6	1
α-helix	89-91	3
β-strand	93-101	9	2
β-strand	114-115	2	2
β-strand	119-124	6	2

4 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Nanobody hFPNb1	R, S	protein	131	Lama glama
Properdin	U, X	protein	170	Homo sapiens	P27918 (AlphaFold model)
Properdin	V, Y	protein	221	Homo sapiens	P27918 (AlphaFold model)
Complement C3	A, G	protein	645	Homo sapiens	P01024 (AlphaFold model)
Complement C3	B, H	protein	915	Homo sapiens	P01024 (AlphaFold model)
Complement factor B	J, L	protein	505	Homo sapiens	P00751 (AlphaFold model)
Inhibitor	N, Q	protein	86	Staphylococcus aureus	Q931M7 (AlphaFold model)

Sequence of entity 1 (R, S), FASTA

>6RUV_1 Nanobody hFPNb1 (chains R, S)
MQVQLVESGGGLVQAGGSLRLSCAASERTFTIYAMGWFRQAPGKEREFVAAISRSGENTD
YADSVKGRFTISRDNNKNTISLQMNSLKPEDTAVYYCAAGRAILVHTTKKEYDHWGQGTQ
VTVSSHHHHHH

Sequence of entity 2 (U, X), FASTA

>6RUV_2 Properdin (chains U, X)
DPVLCFTQYEESSGKCKGLLGGGVSVEDCCLNTAFAYQKRSGGLCQPCRSPRWSLWSTWA
PCSVTCSEGSQLRYRRCVGWNGQCSGKVAPGTLEWQLQACEDQQCCPEMGGWSGWGPWEP
CSVTCSKGTRTRRRACNHPAPKCGGHCPGQAQESEACDTQQVCPENLYFQ

Sequence of entity 3 (V, Y), FASTA

>6RUV_3 Properdin (chains V, Y)
GVAGGWGPWGPVSPCPVTCGLGQTMEQRTCNHPVPQHGGPFCAGDATRTHICNTAVPCPV
DGEWDSWGEWSPCIRRNMKSISCQEIPGQQSRGRTCRGRKFDGHRCAGQQQDIRHCYSIQ
HCPLKGSWSEWSTWGLCMPPCGPNPTRARQRLCTPLLPKYPPTVSMVEGQGEKNVTFWGR
PLPRCEELQGQKLVVEEKRPCLHVPACKDPEEEELENLYFQ

Sequence of entity 4 (A, G), FASTA

>6RUV_4 Complement C3 (chains A, G)
SPMYSIITPNILRLESEETMVLEAHDAQGDVPVTVTVHDFPGKKLVLSSEKTVLTPATNH
MGNVTFTIPANREFKSEKGRNKFVTVQATFGTQVVEKVVLVSLQSGYLFIQTDKTIYTPG
STVLYRIFTVNHKLLPVGRTVMVNIENPEGIPVKQDSLSSQNQLGVLPLSWDIPELVNMG
QWKIRAYYENSPQQVFSTEFEVKEYVLPSFEVIVEPTEKFYYIYNEKGLEVTITARFLYG
KKVEGTAFVIFGIQDGEQRISLPESLKRIPIEDGSGEVVLSRKVLLDGVQNPRAEDLVGK
SLYVSATVILHSGSDMVQAERSGIPIVTSPYQIHFTKTPKYFKPGMPFDLMVFVTNPDGS
PAYRVPVAVQGEDTVQSLTQGDGVAKLSINTHPSQKPLSITVRTKKQELSEAEQATRTMQ
ALPYSTVGNSNNYLHLSVLRTELRPGETLNVNFLLRMDRAHEAKIRYYTYLIMNKGRLLK
AGRQVREPGQDLVVLPLSITTDFIPSFRLVAYYTLIGASGQREVVADSVWVDVKDSCVGS
LVVKSGQSEDRQPVPGQQMTLKIEGDHGARVVLVAVDKGVFVLNKKNKLTQSKIWDVVEK
ADIGCTPGSGKDYAGVFSDAGLTFTSSSGQQTAQRAELQCPQPAA

Sequence of entity 5 (B, H), FASTA

>6RUV_5 Complement C3 (chains B, H)
SNLDEDIIAEENIVSRSEFPESWLWNVEDLKEPPKNGISTKLMNIFLKDSITTWEILAVS
MSDKKGICVADPFEVTVMQDFFIDLRLPYSVVRNEQVEIRAVLYNYRQNQELKVRVELLH
NPAFCSLATTKRRHQQTVTIPPKSSLSVPYVIVPLKTGLQEVEVKAAVYHHFISDGVRKS
LKVVPEGIRMNKTVAVRTLDPERLGREGVQKEDIPPADLSDQVPDTESETRILLQGTPVA
QMTEDAVDAERLKHLIVTPSGCGEQNMIGMTPTVIAVHYLDETEQWEKFGLEKRQGALEL
IKKGYTQQLAFRQPSSAFAAFVKRAPSTWLTAYVVKVFSLAVNLIAIDSQVLCGAVKWLI
LEKQKPDGVFQEDAPVIHQEMIGGLRNNNEKDMALTAFVLISLQEAKDICEEQVNSLPGS
ITKAGDFLEANYMNLQRSYTVAIAGYALAQMGRLKGPLLNKFLTTAKDKNRWEDPGKQLY
NVEATSYALLALLQLKDFDFVPPVVRWLNEQRYYGGGYGSTQATFMVFQALAQYQKDAPD
HQELNLDVSLQLPSRSSKITHRIHWESASLLRSEETKENEGFTVTAEGKGQGTLSVVTMY
HAKAKDQLTCNKFDLKVTIKPAPETEKRPQDAKNTMILEICTRYRGDQDATMSILDISMM
TGFAPDTDDLKQLANGVDRYISKYELDKAFSDRNTLIIYLDKVSHSEDDCLAFKVHQYFN
VELIQPGAVKVYAYYNLEESCTRFYHPEKEDGKLNKLCRDELCRCAEENCFIQKSDDKVT
LEERLDKACEPGVDYVYKTRLVKVQLSNDFDEYIMAIEQTIKSGSDEVQVGQQRTFISPI
KCREALKLEEKKHYLMWGLSSDFWGEKPNLSYIIGKDTWVEHWPEEDECQDEENQKQCQD
LGAFTESMVVFGCPN

Sequence of entity 6 (J, L), FASTA

>6RUV_6 Complement factor B (chains J, L)
KIVLDPSGSMNIYLVLDGSGSIGASNFTGAKKCLVNLIEKVASYGVKPRYGLVTYATYPK
IWVKVSEADSSNADWVTKQLNEINYEDHKLKSGTNTKKALQAVYSMMSWPDDVPPEGWNR
TRHVIILMTDGLHNMGGDPITVIDEIRDLLYIGKDRKNPREDYLDVYVFGVGPLVNQVNI
NALASKKDNEQHVFKVKDMENLEDVFYQMIDESQSLSLCGMVWEHRKGTDYHKQPWQAKI
SVIRPSKGHESCMGAVVSEYFVLTAAHCFTVDDKEHSIKVSVGGEKRDLEIEVVLFHPNY
NINGKKEAGIPEFYDYDVALIKLKNKLKYGQTIRPICLPCTEGTTRALRLPPTTTCQQQK
EELLPAQDIKALFVSEEEKKLTRKEVYIKNGDKKGSCERDAQYAPGYDKVKDISEVVTPR
FLCTGGVSPYADPNTCRGDAGGPLIVHKRSRFIQVGVISWGVVDVCKNQKRQKQVPAHAR
DFHINLFQVLPWLKEKLQDEDLGFL

Sequence of entity 7 (N, Q), FASTA

>6RUV_7 Inhibitor (chains N, Q)
GSTSLPTSNEYQNEKLANELKSLLDELNVNELATGSLNTYYKRTIKISGQKAMYALKSKD
FKKMSEAKYQLQKIYNEIDEALKSKY

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2
MAN	alpha-D-mannopyranose	C6 H12 O6	21

Primary citation

Structural Basis for Properdin Oligomerization and Convertase Stimulation in the Human Complement System. Pedersen, D.V., Gadeberg, T.A.F., Thomas, C. et al. Front Immunol (2019) 10:2007-2007. DOI 10.3389/fimmu.2019.02007 · PubMed

Other PDB entries of the same protein (UniProt P27918 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8Q6R 1.9 Å, Structure of complement FP in complex with the TPP-3077 VHH
6S08 2.03 Å, Crystal Structure of Properdin (TSR domains N1 & 456)
6S0B 2.31 Å, Crystal Structure of Properdin in complex with the CTC domain of C3/C3b
6S0A 2.52 Å, Crystal Structure of Properdin (TSR domains N12 & 456)
9U62 2.7 Å, AP pathways C3 convertase C3bBbP and C3 complex
6RUS 2.8 Å, Structure of a functional properdin monomer
7B26 3.4 Å, CirpA1 in complex with pseudo-monomeric Properdin lacking TSR2-3
6SEJ 3.5 Å, Structure of a functional monomeric properdin lacking TSR3
6RV6 3.51 Å, Structure of properdin lacking TSR3 based on anomalous data
7NOZ 3.9 Å, Structure of the nanobody stablized properdin bound alternative pathway proconvertase…
6RUR 6.0 Å, Structure of the SCIN stabilized C3bBb convertase bound to properdin
1W0R Solution structure of dimeric form of properdin by X-ray solution scattering and…

Browse structure collections

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