5JPM: Complement C4-A

Structure of the complex of human complement C4 with MASP-2 rebuilt using iMDFF. Determined by X-ray diffraction at 3.75 Å resolution. Released 10 Aug 2016.

Method: X-ray diffraction
Resolution: 3.75 Å
Organism: Homo sapiens
Chains: 10
Atoms: 32,214
Mol. weight: 468.73 kDa
Released: 10 Aug 2016

Explore 5JPM in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5JPM contains 151 α-helices and 286 β-strands across 10 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: 19 helices, 53 β-strands

Element	Residues	Length	Sheet
β-strand	22-28	7	1
β-strand	30-32	3	2
β-strand	37-44	8	1
β-strand	51-59	9	2
α-helix	66	1
β-strand	67-77	11	2
β-strand	80	1	2
β-strand	82-87	6	1
α-helix	91-97	7
α-helix	99-101	3
β-strand	107-113	7	2
α-helix	115-116	2
α-helix	117-121	5
β-strand	127-135	9	2
β-strand	140-145	6	3
β-strand	149-150	2	4
β-strand	155-163	9	3
β-strand	169	1	3
β-strand	174-179	6	4
β-strand	185-191	7	4
α-helix	194-196	3
β-strand	197-203	7	3
α-helix	208-209	2
β-strand	211-219	9	4
β-strand	227-233	7	4
β-strand	242-247	6	5
β-strand	252-253	2	6
β-strand	254-255	2	7
β-strand	258-259	2	7
β-strand	263-269	7	5
α-helix	274	1
β-strand	275	1	5
α-helix	276	1
β-strand	278-287	10	8
β-strand	293-295	3	8
β-strand	301-304	4	8
β-strand	306	1	5
β-strand	309-313	5	5
α-helix	316-325	10
α-helix	330-332	3
β-strand	337-346	10	8
β-strand	352-357	6	8
β-strand	361	1	8
β-strand	362-363	2	6
β-strand	368-370	3	9
β-strand	384-391	8	9
β-strand	402-410	9	10
α-helix	415-416	2
β-strand	417-424	8	10
β-strand	426	1	9
β-strand	430-435	6	9
β-strand	443-450	8	10
β-strand	456-463	8	10
α-helix	464-466	3
β-strand	472-476	5	11
α-helix	482-484	3
β-strand	488-496	9	11
β-strand	504-511	8	12
β-strand	514-522	9	12
β-strand	527-532	6	11
α-helix	535-537	3
β-strand	540-548	9	12
β-strand	553-561	9	12
α-helix	562-563	2
β-strand	571-574	4	13
β-strand	580-581	2	14
β-strand	586-605	20	13
α-helix	621-628	8
α-helix	629-631	3
α-helix	646-650	5
β-strand	652-655	4	1
β-strand	660	1	1

Chain B: 33 helices, 37 β-strands

Element	Residues	Length	Sheet
α-helix	682-691	10
α-helix	697-707	11
α-helix	709-710	2
α-helix	716-720	5
α-helix	726-745	20
β-strand	755	1	15
β-strand	758-759	2	16
α-helix	762-766	5
α-helix	771-772	2
β-strand	786-798	13	13
α-helix	799-801	3
β-strand	806-814	9	13
β-strand	818-821	4	13
α-helix	822-824	3
β-strand	825-827	3	13
β-strand	828-829	2	14
β-strand	833-836	4	17
β-strand	843-844	2	18
β-strand	848-851	4	19
β-strand	854-857	4	17
β-strand	863-869	7	20
α-helix	870-871	2
β-strand	875-877	3	19
α-helix	878-880	3
β-strand	885-889	5	20
β-strand	893-896	4	17
β-strand	899-903	5	19
β-strand	908-917	10	20
β-strand	924-932	9	20
β-strand	933-934	2	18
β-strand	938-948	11	21
α-helix	953-955	3
β-strand	957-960	4	22
β-strand	968	1	21
β-strand	975-981	7	21
α-helix	984-989	6
α-helix	999-1004	6
α-helix	1012-1017	6
α-helix	1019-1031	13
α-helix	1041-1056	16
α-helix	1057-1059	3
β-strand	1060	1	23
β-strand	1066-1067	2	23
α-helix	1073	1
β-strand	1074-1075	2	23
α-helix	1076-1093	18
α-helix	1097-1108	12
β-strand	1111	1	24
β-strand	1117	1	24
α-helix	1133-1152	20
α-helix	1153-1155	3
α-helix	1165-1185	21
α-helix	1190-1202	13
α-helix	1207-1218	12
β-strand	1222-1224	3	25
β-strand	1227-1229	3	25
α-helix	1253	1
β-strand	1254	1	21
α-helix	1255	1
α-helix	1259-1275	17
α-helix	1280-1290	11
α-helix	1302-1318	17
β-strand	1326-1335	10	22
β-strand	1338-1347	10	22
α-helix	1354-1356	3
β-strand	1358-1361	4	21
β-strand	1366-1372	7	22
β-strand	1376-1386	11	21
β-strand	1397-1405	9	26
α-helix	1406-1413	8

Chain C: 12 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	1464-1474	11	26
β-strand	1484-1489	6	27
α-helix	1490-1491	2
β-strand	1494-1496	3	26
α-helix	1498-1506	9
β-strand	1514-1516	3	27
β-strand	1521-1526	6	27
β-strand	1534-1542	9	26
β-strand	1546-1547	2	19
α-helix	1549-1551	3
β-strand	1552-1558	7	27
β-strand	1565-1570	6	27
α-helix	1572-1573	2
α-helix	1577-1579	3
α-helix	1585-1591	7
α-helix	1596-1597	2
α-helix	1603-1605	3
α-helix	1612-1618	7
β-strand	1625-1637	13	28
β-strand	1640-1652	13	28
β-strand	1664-1670	7	28
β-strand	1682-1687	6	28
β-strand	1693	1	29
β-strand	1699	1	29
β-strand	1700-1702	3	28
β-strand	1708-1711	4	28
α-helix	1712-1714	3
α-helix	1715-1718	4
α-helix	1721-1740	20

Chain D: 14 helices, 50 β-strands

Element	Residues	Length	Sheet
β-strand	22-28	7	30
β-strand	30-32	3	31
β-strand	37-44	8	30
β-strand	51-59	9	31
β-strand	67	1	31
β-strand	72-77	6	31
β-strand	80	1	31
β-strand	82-87	6	30
α-helix	91-96	6
β-strand	107-113	7	31
α-helix	115-119	5
β-strand	127-135	9	31
β-strand	140-145	6	32
β-strand	149-150	2	33
β-strand	155-163	9	32
β-strand	169	1	32
β-strand	174-179	6	33
β-strand	185-191	7	33
β-strand	197-203	7	32
α-helix	208-209	2
β-strand	211-219	9	33
β-strand	227-233	7	33
β-strand	242-247	6	34
β-strand	251-253	3	35
β-strand	263-269	7	34
α-helix	274	1
β-strand	275	1	34
α-helix	276	1
β-strand	278-287	10	35
β-strand	293-304	12	35
β-strand	306	1	34
β-strand	309-313	5	34
α-helix	316-325	10
α-helix	330-333	4
β-strand	337-346	10	35
β-strand	352-357	6	35
β-strand	361-363	3	35
β-strand	367-370	4	36
β-strand	383-392	10	36
β-strand	397	1	36
α-helix	398	1
β-strand	402-410	9	37
β-strand	417-424	8	37
β-strand	430-436	7	36
β-strand	443-450	8	37
β-strand	456-463	8	37
α-helix	464-466	3
β-strand	472-476	5	38
α-helix	482-484	3
α-helix	487	1
β-strand	488-496	9	38
β-strand	504-511	8	39
β-strand	514-522	9	39
β-strand	527-532	6	38
β-strand	540-549	10	39
β-strand	552-561	10	39
β-strand	571-574	4	40
β-strand	580-581	2	41
β-strand	586-605	20	40
α-helix	621-628	8
α-helix	629-631	3
β-strand	652-655	4	30
β-strand	660	1	30
α-helix	661-664	4

Chain E: 31 helices, 37 β-strands

Element	Residues	Length	Sheet
α-helix	682-691	10
α-helix	697-707	11
α-helix	709-710	2
α-helix	716-720	5
α-helix	726-749	24
β-strand	755	1	42
β-strand	758-759	2	43
α-helix	766-768	3
α-helix	771-772	2
β-strand	786-798	13	40
β-strand	806-814	9	40
β-strand	818-821	4	40
α-helix	822-824	3
β-strand	825-827	3	40
β-strand	828-829	2	41
β-strand	833-836	4	44
β-strand	843-844	2	45
β-strand	848-851	4	46
β-strand	854-857	4	44
β-strand	863-869	7	47
α-helix	870-871	2
β-strand	875-877	3	46
α-helix	878-880	3
β-strand	885-889	5	47
β-strand	893-896	4	44
β-strand	899-903	5	46
β-strand	909-918	10	47
β-strand	921-931	11	47
β-strand	933-934	2	45
β-strand	938-948	11	48
β-strand	957-960	4	49
β-strand	968	1	48
β-strand	976-981	6	48
α-helix	984-989	6
α-helix	1000-1003	4
α-helix	1012-1017	6
α-helix	1019-1031	13
α-helix	1040-1056	17
α-helix	1057-1059	3
β-strand	1060	1	50
β-strand	1066-1067	2	50
α-helix	1073	1
β-strand	1074-1075	2	50
α-helix	1076-1093	18
α-helix	1097-1108	12
β-strand	1111	1	51
β-strand	1117	1	51
α-helix	1133-1152	20
α-helix	1162-1185	24
α-helix	1190-1202	13
α-helix	1207-1219	13
β-strand	1221-1224	4	52
β-strand	1227-1230	4	52
α-helix	1242-1244	3
α-helix	1253	1
β-strand	1254	1	48
α-helix	1255-1258	4
α-helix	1259-1275	17
α-helix	1280-1290	11
α-helix	1302-1318	17
β-strand	1326-1333	8	49
β-strand	1340-1347	8	49
α-helix	1354-1356	3
β-strand	1358-1360	3	48
β-strand	1366-1372	7	49
β-strand	1376-1386	11	48
β-strand	1397-1405	9	53
α-helix	1406-1414	9

Chain F: 13 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	1465-1474	10	53
β-strand	1484-1489	6	54
α-helix	1490-1491	2
β-strand	1494-1496	3	53
α-helix	1498-1505	8
β-strand	1514-1516	3	54
β-strand	1521-1526	6	54
β-strand	1534-1542	9	53
β-strand	1546-1547	2	46
α-helix	1549-1551	3
β-strand	1552-1558	7	54
β-strand	1565-1570	6	54
α-helix	1572-1573	2
α-helix	1577-1579	3
α-helix	1585-1591	7
α-helix	1596-1598	3
α-helix	1603-1605	3
α-helix	1612-1618	7
β-strand	1625-1637	13	55
β-strand	1640-1652	13	55
β-strand	1664-1670	7	55
α-helix	1671-1673	3
β-strand	1682-1687	6	55
β-strand	1693	1	56
β-strand	1699	1	56
β-strand	1700-1702	3	55
β-strand	1708-1711	4	55
α-helix	1712-1714	3
α-helix	1715-1718	4
α-helix	1724-1740	17

Chain G: 6 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	299-302	4
α-helix	304-306	3
β-strand	309-312	4	57
β-strand	323-328	6	57
α-helix	329	1
β-strand	332-336	5	58
β-strand	339-340	2	58
β-strand	344-347	4	57
β-strand	348	1	59
β-strand	354	1	59
β-strand	360-363	4	58
β-strand	365	1	60
α-helix	369-372	4
β-strand	375-379	5	61
β-strand	387	1	60
β-strand	391-396	6	61
α-helix	397	1
β-strand	401-402	2	62
β-strand	409-412	4	61
β-strand	418-420	3	61
α-helix	427-428	2
β-strand	431-432	2	62

Chain H: 8 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	446	1	63
β-strand	449-450	2	42
α-helix	451-452	2
β-strand	459-463	5	43
β-strand	466-473	8	43
β-strand	477-480	4	43
α-helix	482-485	4
β-strand	496-499	4	43
β-strand	503	1	64
β-strand	510-519	10	43
β-strand	534-538	5	43
α-helix	550-551	2
β-strand	552	1	42
α-helix	553-554	2
α-helix	558-560	3
β-strand	567-572	6	42
β-strand	575	1	65
β-strand	581	1	65
β-strand	584	1	64
β-strand	586-593	8	42
α-helix	595-600	6
β-strand	616-619	4	42
β-strand	627	1	63
β-strand	636-641	6	42
β-strand	646-655	10	42
β-strand	667-671	5	42
α-helix	673-675	3
α-helix	676-684	9

2 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
Complement C4-A	A, D	protein	656	Homo sapiens	P0C0L4 (AlphaFold model)
Complement C4-A	B, E	protein	767	Homo sapiens	P0C0L4 (AlphaFold model)
Complement C4-A	C, F	protein	291	Homo sapiens	P0C0L4 (AlphaFold model)
Mannan-binding lectin serine protease 2	G, I	protein	154	Homo sapiens	O00187 (AlphaFold model)
Mannan-binding lectin serine protease 2	H, J	protein	242	Homo sapiens	O00187 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>5JPM_1 Complement C4-A (chains A, D)
KPRLLLFSPSVVHLGVPLSVGVQLQDVPRGQVVKGSVFLRNPSRNNVPCSPKVDFTLSSE
RDFALLSLQVPLKDAKSCGLHQLLRGPEVQLVAHSPWLKDSLSRTTNIQGINLLFSSRRG
HLFLQTDQPIYNPGQRVRYRVFALDQKMRPSTDTITVMVENSHGLRVRKKEVYMPSSIFQ
DDFVIPDISEPGTWKISARFSDGLESNSSTQFEVKKYVLPNFEVKITPGKPYILTVPGHL
DEMQLDIQARYIYGKPVQGVAYVRFGLLDEDGKKTFFRGLESQTKLVNGQSHISLSKAEF
QDALEKLNMGITDLQGLRLYVAAAIIESPGGEMEEAELTSWYFVSSPFSLDLSKTKRHLV
PGAPFLLQALVREMSGSPASGIPVKVSATVSSPGSVPEVQDIQQNTDGSGQVSIPIIIPQ
TISELQLSVSAGSPHPAIARLTVAAPPSGGPGFLSIERPDSRPPRVGDTLNLNLRAVGSG
ATFSHYYYMILSRGQIVFMNREPKRTLTSVSVFVDHHLAPSFYFVAFYYHGDHPVANSLR
VDVQAGACEGKLELSVDGAKQYRNGESVKLHLETDSLALVALGALDTALYAAGSKSHKPL
NMGKVFEAMNSYDLGCGPGGGDSALQVFQAAGLAFSDGDQWTLSRKRLSCPKEKTT

Sequence of entity 2 (B, E), FASTA

>5JPM_2 Complement C4-A (chains B, E)
NVNFQKAINEKLGQYASPTAKRCCQDGVTRLPMMRSCEQRAARVQQPDCREPFLSCCQFA
ESLRKKSRDKGQAGLQRALEILQEEDLIDEDDIPVRSFFPENWLWRVETVDRFQILTLWL
PDSLTTWEIHGLSLSKTKGLCVATPVQLRVFREFHLHLRLPMSVRRFEQLELRPVLYNYL
DKNLTVSVHVSPVEGLCLAGGGGLAQQVLVPAGSARPVAFSVVPTAAAAVSLKVVARGSF
EFPVGDAVSKVLQIEKEGAIHREELVYELNPLDHRGRTLEIPGNSDPNMIPDGDFNSYVR
VTASDPLDTLGSEGALSPGGVASLLRLPRGCGEQTMIYLAPTLAASRYLDKTEQWSTLPP
ETKDHAVDLIQKGYMRIQQFRKADGSYAAWLSRDSSTWLTAFVLKVLSLAQEQVGGSPEK
LQETSNWLLSQQQADGSFQDPCPVLDRSMQGGLVGNDETVALTAFVTIALHHGLAVFQDE
GAEPLKQRVEASISKANSFLGEKASAGLLGAHAAAITAYALSLTKAPVDLLGVAHNNLMA
MAQETGDNLYWGSVTGSQSNAVSPTPAPRNPSDPMPQAPALWIETTAYALLHLLLHEGKA
EMADQASAWLTRQGSFQGGFRSTQDTVIALDALSAYWIASHTTEERGLNVTLSSTGRNGF
KSHALQLNNRQIRGLEEELQFSLGSKINVKVGGNSKGTLKVLRTYNVLDMKNTTCQDLQI
EVTVKGHVEYTMEANEDYEDYEYDELPAKDDPDAPLQPVTPLQLFEG

Sequence of entity 3 (C, F), FASTA

>5JPM_3 Complement C4-A (chains C, F)
EAPKVVEEQESRVHYTVCIWRNGKVGLSGMAIADVTLLSGFHALRADLEKLTSLSDRYVS
HFETEGPHVLLYFDSVPTSRECVGFEAVQEVPVGLVQPASATLYDYYNPERRCSVFYGAP
SKSRLLATLCSAEVCQCAEGKCPRQRRALERGLQDEDGYRMKFACYYPRVEYGFQVKVLR
EDSRAAFRLFETKITQVLHFTKDVKAAANQMRNFLVRASCRLRLEPGKEYLIMGLDGATY
DLEGHPQYLLDSNSWIEEMPSERLCRSTRQRAACAQLNDFLQEYGTQGCQV

Sequence of entity 4 (G, I), FASTA

>5JPM_4 Mannan-binding lectin serine protease 2 (chains G, I)
IHYTSTAHACPYPMAPPNGHVSPVQAKYILKDSFSIFCETGYELLQGHLPLKSFTAVCQK
DGSWDRPMPACSIVDCGPPDDLPSGRVEYITGPGVTTYKAVIQYSCEETFYTMKVNDGKY
VCEADGFWTSSKGEKSLPVCEPVCGLSARTTGGR

Sequence of entity 5 (H, J), FASTA

>5JPM_5 Mannan-binding lectin serine protease 2 (chains H, J)
IYGGQKAKPGDFPWQVLILGGTTAAGALLYDNWVLTAAHAVYEQKHDASALDIRMGTLKR
LSPHYTQAWSEAVFIHEGYTHDAGFDNDIALIKLNNKVVINSNITPICLPRKEAESFMRT
DDIGTASGWGLTQRGFLARNLMYVDIPIVDHQKCTAAYEKPPYPRGSVTANMLCAGLESG
GKDSCRGDAGGALVFLDSETERWFVGGIVSWGSMNCGEAGQYGVYTKVINYIPWIENIIS
DF

Primary citation

Re-evaluation of low-resolution crystal structures via interactive molecular-dynamics flexible fitting (iMDFF): a case study in complement C4. Croll, T.I., Andersen, G.R. Acta Crystallogr D Struct Biol (2016) 72:1006-1016. DOI 10.1107/S2059798316012201 · PubMed

Other PDB entries of the same protein (UniProt P0C0L4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1HZF 2.3 Å, C4ADG fragment of human complement factor C4A
6YSQ 3.3 Å, The hC4Nb8 complement inhibitory nanobody in complex with C4b
7B2M 3.39 Å, Cryo-EM structure of complement C4b in complex with nanobody E3
7B2P 3.43 Å, Cryo-EM structure of complement C4b in complex with nanobody B5
5JTW 3.5 Å, Crystal structure of complement C4b re-refined using iMDFF
9QJ5 3.5 Å, Structure of the Complement classical and lectin pathway proconvertase, C4b2
9QK2 3.5 Å, Structure of the Complement classical and lectin pathway C3 convertase in complex with…
5JPN 3.6 Å, Structure of human complement C4 rebuilt using iMDFF
7B2Q 3.76 Å, Cryo-EM structure of complement C4b in complex with nanobody B12
9QJ4 3.9 Å, Structure of the Complement classical and lectin pathway proconvertase, C4b2
9QPY 4.3 Å, Structure of the Complement classical and lectin pathway C3 convertase

Browse structure collections

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