6RUR: SCIN stabilized C3bBb convertase

Structure of the SCIN stabilized C3bBb convertase bound to properdin. Determined by X-ray diffraction at 6.0 Å resolution. Released 21 Aug 2019.

Method: X-ray diffraction
Resolution: 6.0 Å
Organisms: Homo sapiens, Staphylococcus aureus
Chains: 12
Atoms: 39,456
Mol. weight: 592.64 kDa
Ligands: MAN, MG
Released: 21 Aug 2019

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

Secondary structure: helices and β-sheets

6RUR contains 181 α-helices and 340 β-strands across 12 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: 14 helices, 57 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	26
β-strand	11-13	3	27
β-strand	14	1	28
β-strand	17-25	9	26
β-strand	31-40	10	27
β-strand	47	1	27
β-strand	51-54	4	27
β-strand	55	1	26
α-helix	56-58	3
β-strand	61-67	7	26
β-strand	68	1	28
β-strand	83-90	8	27
β-strand	93-102	10	27
β-strand	107-112	6	29
β-strand	116-117	2	30
β-strand	122-130	9	29
β-strand	136	1	29
β-strand	140-146	7	30
β-strand	152-159	8	30
β-strand	166-172	7	29
α-helix	173-174	2
β-strand	180-188	9	30
β-strand	196-202	7	30
β-strand	210-216	7	31
β-strand	221-222	2	32
β-strand	229-237	9	31
β-strand	242	1	31
β-strand	245-255	11	33
β-strand	258-271	14	33
β-strand	272	1	31
β-strand	275-280	6	31
α-helix	282-288	7
β-strand	301-310	10	33
β-strand	316-325	10	33
β-strand	326-327	2	32
β-strand	332-334	3	34
β-strand	341-342	2	35
β-strand	348-355	8	34
α-helix	360	1
β-strand	361	1	34
α-helix	362	1
β-strand	366-369	4	36
β-strand	376-378	3	36
β-strand	384-389	6	34
β-strand	398-404	7	36
β-strand	416-421	6	36
β-strand	422-423	2	35
α-helix	427-429	3
β-strand	433-438	6	37
β-strand	443	1	38
β-strand	448-456	9	37
α-helix	462-464	3
β-strand	467-474	8	39
β-strand	477-485	9	39
β-strand	492-498	7	37
α-helix	501-503	3
β-strand	506-517	12	39
β-strand	521-532	12	39
β-strand	533	1	38
β-strand	542-545	4	40
α-helix	553-554	2
β-strand	558-566	9	40
β-strand	570-577	8	41
α-helix	578-583	6
α-helix	591-600	10
β-strand	608	1	39
α-helix	613-620	8
β-strand	622-626	5	26
β-strand	631	1	26
α-helix	632-634	3
α-helix	640-643	4

Chain B: 32 helices, 53 β-strands

Element	Residues	Length	Sheet
α-helix	739-741	3
β-strand	742	1	42
β-strand	748-749	2	41
β-strand	753-755	3	41
α-helix	759	1
β-strand	760-761	2	40
β-strand	764-772	9	40
β-strand	779-788	10	41
β-strand	792-795	4	41
α-helix	796-798	3
β-strand	799-802	4	41
β-strand	807-812	6	43
β-strand	816-818	3	42
β-strand	823-831	9	43
β-strand	838-844	7	42
α-helix	845-846	2
β-strand	850-851	2	44
β-strand	860-866	7	42
β-strand	870-878	9	43
β-strand	879-880	2	44
β-strand	884-894	11	42
β-strand	900-910	11	42
β-strand	914-925	12	45
β-strand	935-940	6	46
α-helix	941-943	3
β-strand	948	1	45
α-helix	949	1
β-strand	954-962	9	45
α-helix	970-973	4
α-helix	979-981	3
α-helix	989-1008	20
α-helix	1012-1015	4
α-helix	1018-1034	17
α-helix	1035-1037	3
β-strand	1038	1	47
β-strand	1044	1	47
α-helix	1051-1053	3
α-helix	1054-1067	14
α-helix	1075-1087	13
β-strand	1090	1	48
β-strand	1096	1	48
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	1182-1191	10
β-strand	1193	1	49
β-strand	1197	1	49
α-helix	1204-1221	18
α-helix	1227-1237	11
α-helix	1247-1260	14
β-strand	1272-1277	6	46
β-strand	1286-1289	4	46
β-strand	1297-1302	6	45
β-strand	1308-1313	6	46
β-strand	1318-1328	11	45
β-strand	1339-1347	9	50
β-strand	1362-1370	9	50
β-strand	1376	1	51
β-strand	1379-1384	6	52
α-helix	1385-1386	2
β-strand	1389-1391	3	50
α-helix	1393-1401	9
β-strand	1405-1406	2	52
α-helix	1409-1412	4
β-strand	1421-1426	6	52
β-strand	1429	1	51
β-strand	1435-1443	9	50
α-helix	1450-1452	3
β-strand	1453-1459	7	52
β-strand	1467-1471	5	52
β-strand	1482-1485	4	53
β-strand	1488-1491	4	53
α-helix	1507-1513	7
β-strand	1521-1532	12	54
β-strand	1536-1549	14	54
β-strand	1559-1565	7	54
α-helix	1566-1568	3
β-strand	1579-1584	6	54
β-strand	1589-1590	2	54
β-strand	1597-1599	3	54
β-strand	1605-1609	5	54
α-helix	1613-1616	4
α-helix	1618-1637	20

Chain G: 17 helices, 57 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	55
β-strand	11-13	3	56
β-strand	14	1	57
β-strand	18-25	8	55
β-strand	31-40	10	56
β-strand	47	1	56
β-strand	51-54	4	56
α-helix	56-58	3
β-strand	61-66	6	55
β-strand	68	1	57
β-strand	83-90	8	56
β-strand	93-102	10	56
β-strand	107-112	6	58
β-strand	116-117	2	59
β-strand	122-130	9	58
β-strand	136	1	58
β-strand	140-146	7	59
β-strand	152-159	8	59
β-strand	166-172	7	58
α-helix	173-174	2
β-strand	180-188	9	59
β-strand	195-202	8	59
β-strand	210-216	7	60
β-strand	221-222	2	61
β-strand	229-237	9	60
β-strand	242	1	60
β-strand	245-255	11	62
β-strand	258-261	4	62
α-helix	263-265	3
β-strand	267-271	5	62
β-strand	272	1	60
β-strand	275-280	6	60
α-helix	282-288	7
α-helix	295-297	3
β-strand	301-310	10	62
β-strand	316-325	10	62
β-strand	326-327	2	61
β-strand	332-334	3	63
β-strand	341-342	2	64
β-strand	347-355	9	63
α-helix	360	1
β-strand	361	1	63
α-helix	362	1
β-strand	366-369	4	65
β-strand	376-378	3	65
β-strand	384-390	7	63
β-strand	398-404	7	65
α-helix	411-413	3
β-strand	416-421	6	65
β-strand	422-423	2	64
β-strand	425	1	66
α-helix	427-429	3
β-strand	433-437	5	67
β-strand	448-456	9	67
α-helix	462-464	3
β-strand	467-474	8	68
β-strand	477-485	9	68
β-strand	492-498	7	67
α-helix	501-503	3
β-strand	506-517	12	68
β-strand	521-532	12	68
β-strand	541-545	5	69
α-helix	552-554	3
β-strand	558-566	9	69
β-strand	570-577	8	70
α-helix	578-583	6
α-helix	591-600	10
β-strand	608	1	68
β-strand	612	1	66
α-helix	613-620	8
β-strand	622-626	5	55
β-strand	631	1	55
α-helix	632-634	3
α-helix	640	1

Chain H: 34 helices, 57 β-strands

Element	Residues	Length	Sheet
β-strand	733	1	71
α-helix	739-741	3
β-strand	742	1	72
β-strand	748-749	2	70
β-strand	753-755	3	70
β-strand	761	1	69
β-strand	764-772	9	69
β-strand	779-788	10	70
β-strand	792-795	4	70
α-helix	796-798	3
β-strand	799-802	4	70
β-strand	807-812	6	73
β-strand	816-818	3	72
β-strand	823-831	9	73
β-strand	838-844	7	72
α-helix	845-846	2
β-strand	847	1	74
β-strand	850-851	2	74
β-strand	860-866	7	72
β-strand	870-878	9	73
β-strand	879-880	2	74
β-strand	884-894	11	72
β-strand	895	1	71
β-strand	900-910	11	72
β-strand	914-925	12	75
β-strand	935-940	6	76
α-helix	941-943	3
β-strand	948	1	75
α-helix	949	1
β-strand	954-963	10	75
α-helix	970-973	4
α-helix	979-981	3
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	77
β-strand	1043-1044	2	77
α-helix	1051-1052	2
β-strand	1053	1	77
α-helix	1054-1066	13
α-helix	1067-1069	3
α-helix	1075-1087	13
β-strand	1090	1	78
β-strand	1096	1	78
α-helix	1109-1112	4
α-helix	1117-1131	15
α-helix	1143-1156	14
α-helix	1164-1177	14
α-helix	1183-1190	8
β-strand	1193	1	79
β-strand	1197	1	79
α-helix	1204-1221	18
α-helix	1227-1237	11
α-helix	1247-1262	16
β-strand	1272-1277	6	76
β-strand	1285-1289	5	76
β-strand	1298-1302	5	75
β-strand	1308-1313	6	76
β-strand	1317-1328	12	75
β-strand	1339-1347	9	80
α-helix	1350-1353	4
β-strand	1361-1370	10	80
β-strand	1376	1	81
β-strand	1379-1384	6	82
α-helix	1385-1386	2
β-strand	1389-1391	3	80
α-helix	1393-1400	8
β-strand	1405-1406	2	82
α-helix	1409-1412	4
α-helix	1415-1417	3
β-strand	1421-1426	6	82
β-strand	1429	1	81
β-strand	1435-1443	9	80
α-helix	1450-1452	3
β-strand	1453-1459	7	82
β-strand	1466-1471	6	82
β-strand	1483-1485	3	83
β-strand	1488-1490	3	83
α-helix	1508-1514	7
β-strand	1521-1532	12	84
β-strand	1536-1548	13	84
β-strand	1559-1565	7	84
α-helix	1566-1569	4
β-strand	1579-1584	6	84
β-strand	1589-1590	2	84
β-strand	1597-1599	3	84
α-helix	1600	1
β-strand	1605-1609	5	84
α-helix	1613-1616	4
α-helix	1618-1637	20

Chain J: 25 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	236-237	2	85
β-strand	244-251	8	86
α-helix	258-277	20
β-strand	283-289	7	86
β-strand	293-297	5	86
α-helix	302-305	4
α-helix	307-316	10
α-helix	319-325	7
α-helix	330-341	12
α-helix	342-343	2
α-helix	348-349	2
β-strand	356-363	8	86
α-helix	374-383	10
α-helix	395-397	3
β-strand	398-404	7	86
α-helix	411-417	7
β-strand	427-428	2	86
α-helix	431-433	3
α-helix	436-443	8
β-strand	444-445	2	85
α-helix	464-467	4
β-strand	471-478	8	87
β-strand	482-490	9	87
β-strand	495-498	4	87
α-helix	509-511	3
β-strand	512-516	5	87
α-helix	522	1
β-strand	523	1	87
α-helix	524	1
β-strand	525-530	6	87
β-strand	553-557	5	87
α-helix	569-570	2
β-strand	571	1	88
β-strand	575	1	89
α-helix	576-581	6
α-helix	590-597	8
β-strand	602-610	9	88
β-strand	615-623	9	88
α-helix	628-633	6
α-helix	634-637	4
α-helix	647-650	4
β-strand	655-659	5	88
β-strand	660	1	90
β-strand	666	1	90
α-helix	676	1
β-strand	677-682	6	88
β-strand	685-695	11	88
α-helix	708-710	3
β-strand	714-719	6	88
α-helix	724-730	7
β-strand	738	1	89

Chain L: 27 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	236-237	2	91
β-strand	244-251	8	92
α-helix	258-277	20
β-strand	283-289	7	92
β-strand	293-297	5	92
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	92
α-helix	374-383	10
α-helix	395-397	3
β-strand	398-404	7	92
α-helix	411-417	7
β-strand	421	1	93
β-strand	424	1	93
β-strand	427-428	2	92
α-helix	431-433	3
α-helix	436-443	8
β-strand	444-445	2	91
α-helix	464-467	4
β-strand	471-478	8	94
β-strand	482-490	9	94
β-strand	495-498	4	94
α-helix	509-511	3
β-strand	512-515	4	94
α-helix	522	1
β-strand	523	1	94
α-helix	524	1
β-strand	525-530	6	94
β-strand	553-557	5	94
α-helix	569-570	2
β-strand	571	1	95
β-strand	575	1	96
α-helix	576-581	6
α-helix	590-597	8
β-strand	602-611	10	95
β-strand	614-623	10	95
α-helix	628-633	6
α-helix	634-637	4
α-helix	647-650	4
β-strand	655-659	5	95
β-strand	660	1	97
β-strand	666	1	97
α-helix	671-673	3
α-helix	676	1
β-strand	677-682	6	95
β-strand	685-695	11	95
β-strand	714-719	6	95
α-helix	724-730	7
α-helix	731-734	4
β-strand	738	1	96

Chain N: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	3-5	3
α-helix	7-24	18
α-helix	26-32	7
α-helix	33-35	3
α-helix	38-57	20
α-helix	60-84	25

Chain Q: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	5-6	2
α-helix	9-24	16
α-helix	26-32	7
α-helix	33-35	3
α-helix	38-57	20
α-helix	60-84	25

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
Properdin	U, X	protein	234	Homo sapiens	P27918 (AlphaFold model)
Properdin	V, Y	protein	215	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	85	Staphylococcus aureus	Q931M7 (AlphaFold model)

Sequence of entity 1 (U, X), FASTA

>6RUR_1 Properdin (chains U, X)
DPVLCFTQYEESSGKCKGLLGGGVSVEDCCLNTAFAYQKRSGGLCQPCRSPRWSLWSTWA
PCSVTCSEGSQLRYRRCVGWNGQCSGKVAPGTLEWQLQACEDQQCCPEMGGWSGWGPWEP
CSVTCSKGTRTRRRACNHPAPKCGGHCPGQAQESEACDTQQVCPTHGAWATWGPWTPCSA
SCHGGPHEPKETRSRKCSAPEPSQKPPGKPCPGLAYEQRRCTGLPPCPENLYFQ

Sequence of entity 2 (V, Y), FASTA

>6RUR_2 Properdin (chains V, Y)
GVAGGWGPWGPVSPCPVTCGLGQTMEQRTCNHPVPQHGGPFCAGDATRTHICNTAVPCPV
DGEWDSWGEWSPCIRRNMKSISCQEIPGQQSRGRTCRGRKFDGHRCAGQQQDIRHCYSIQ
HCPLKGSWSEWSTWGLCMPPCGPNPTRARQRLCTPLLPKYPPTVSMVEGQGEKNVTFWGR
PLPRCEELQGQKLVVEEKRPCLHVPACKDPEEEEL

Sequence of entity 3 (A, G), FASTA

>6RUR_3 Complement C3 (chains A, G)
SPMYSIITPNILRLESEETMVLEAHDAQGDVPVTVTVHDFPGKKLVLSSEKTVLTPATNH
MGNVTFTIPANREFKSEKGRNKFVTVQATFGTQVVEKVVLVSLQSGYLFIQTDKTIYTPG
STVLYRIFTVNHKLLPVGRTVMVNIENPEGIPVKQDSLSSQNQLGVLPLSWDIPELVNMG
QWKIRAYYENSPQQVFSTEFEVKEYVLPSFEVIVEPTEKFYYIYNEKGLEVTITARFLYG
KKVEGTAFVIFGIQDGEQRISLPESLKRIPIEDGSGEVVLSRKVLLDGVQNPRAEDLVGK
SLYVSATVILHSGSDMVQAERSGIPIVTSPYQIHFTKTPKYFKPGMPFDLMVFVTNPDGS
PAYRVPVAVQGEDTVQSLTQGDGVAKLSINTHPSQKPLSITVRTKKQELSEAEQATRTMQ
ALPYSTVGNSNNYLHLSVLRTELRPGETLNVNFLLRMDRAHEAKIRYYTYLIMNKGRLLK
AGRQVREPGQDLVVLPLSITTDFIPSFRLVAYYTLIGASGQREVVADSVWVDVKDSCVGS
LVVKSGQSEDRQPVPGQQMTLKIEGDHGARVVLVAVDKGVFVLNKKNKLTQSKIWDVVEK
ADIGCTPGSGKDYAGVFSDAGLTFTSSSGQQTAQRAELQCPQPAA

Sequence of entity 4 (B, H), FASTA

>6RUR_4 Complement C3 (chains B, H)
SNLDEDIIAEENIVSRSEFPESWLWNVEDLKEPPKNGISTKLMNIFLKDSITTWEILAVS
MSDKKGICVADPFEVTVMQDFFIDLRLPYSVVRNEQVEIRAVLYNYRQNQELKVRVELLH
NPAFCSLATTKRRHQQTVTIPPKSSLSVPYVIVPLKTGLQEVEVKAAVYHHFISDGVRKS
LKVVPEGIRMNKTVAVRTLDPERLGREGVQKEDIPPADLSDQVPDTESETRILLQGTPVA
QMTEDAVDAERLKHLIVTPSGCGEQNMIGMTPTVIAVHYLDETEQWEKFGLEKRQGALEL
IKKGYTQQLAFRQPSSAFAAFVKRAPSTWLTAYVVKVFSLAVNLIAIDSQVLCGAVKWLI
LEKQKPDGVFQEDAPVIHQEMIGGLRNNNEKDMALTAFVLISLQEAKDICEEQVNSLPGS
ITKAGDFLEANYMNLQRSYTVAIAGYALAQMGRLKGPLLNKFLTTAKDKNRWEDPGKQLY
NVEATSYALLALLQLKDFDFVPPVVRWLNEQRYYGGGYGSTQATFMVFQALAQYQKDAPD
HQELNLDVSLQLPSRSSKITHRIHWESASLLRSEETKENEGFTVTAEGKGQGTLSVVTMY
HAKAKDQLTCNKFDLKVTIKPAPETEKRPQDAKNTMILEICTRYRGDQDATMSILDISMM
TGFAPDTDDLKQLANGVDRYISKYELDKAFSDRNTLIIYLDKVSHSEDDCLAFKVHQYFN
VELIQPGAVKVYAYYNLEESCTRFYHPEKEDGKLNKLCRDELCRCAEENCFIQKSDDKVT
LEERLDKACEPGVDYVYKTRLVKVQLSNDFDEYIMAIEQTIKSGSDEVQVGQQRTFISPI
KCREALKLEEKKHYLMWGLSSDFWGEKPNLSYIIGKDTWVEHWPEEDECQDEENQKQCQD
LGAFTESMVVFGCPN

Sequence of entity 5 (J, L), FASTA

>6RUR_5 Complement factor B (chains J, L)
KIVLDPSGSMNIYLVLDGSGSIGASNFTGAKKCLVNLIEKVASYGVKPRYGLVTYATYPK
IWVKVSEADSSNADWVTKQLNEINYEDHKLKSGTNTKKALQAVYSMMSWPDDVPPEGWNR
TRHVIILMTDGLHNMGGDPITVIDEIRDLLYIGKDRKNPREDYLDVYVFGVGPLVNQVNI
NALASKKDNEQHVFKVKDMENLEDVFYQMIDESQSLSLCGMVWEHRKGTDYHKQPWQAKI
SVIRPSKGHESCMGAVVSEYFVLTAAHCFTVDDKEHSIKVSVGGEKRDLEIEVVLFHPNY
NINGKKEAGIPEFYDYDVALIKLKNKLKYGQTIRPICLPCTEGTTRALRLPPTTTCQQQK
EELLPAQDIKALFVSEEEKKLTRKEVYIKNGDKKGSCERDAQYAPGYDKVKDISEVVTPR
FLCTGGVSPYADPNTCRGDAGGPLIVHKRSRFIQVGVISWGVVDVCKNQKRQKQVPAHAR
DFHINLFQVLPWLKEKLQDEDLGFL

Sequence of entity 6 (N, Q), FASTA

>6RUR_6 Inhibitor (chains N, Q)
STSLPTSNEYQNEKLANELKSLLDELNVNELATGSLNTYYKRTIKISGQKAMYALKSKDF
KKMSEAKYQLQKIYNEIDEALKSKY

Ligands and cofactors

ID	Name	Formula	Copies
MAN	alpha-D-mannopyranose	C6 H12 O6	18
MG	Magnesium ion	Mg	2

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…
6RUV 6.15 Å, Structure of the SCIN stabilized C3bBb convertase bound to Properdin and a the…
1W0R Solution structure of dimeric form of properdin by X-ray solution scattering and…

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