5JPN: Human complement C4 rebuilt using iMDFF

Structure of human complement C4 rebuilt using iMDFF. Determined by X-ray diffraction at 3.6 Å resolution. Released 10 Aug 2016.

Method: X-ray diffraction
Resolution: 3.6 Å
Organism: Homo sapiens
Chains: 3
Atoms: 12,891
Mol. weight: 193.08 kDa
Ligands: PBM, A2G
Released: 10 Aug 2016

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

Secondary structure: helices and β-sheets

5JPN contains 52 α-helices and 104 β-strands across 3 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, 49 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
β-strand	67	1	2
β-strand	72-77	6	2
β-strand	80	1	2
β-strand	82-87	6	1
α-helix	91-96	6
β-strand	107-113	7	2
α-helix	116-119	4
β-strand	128-135	8	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
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	241-247	7	5
β-strand	251-253	3	6
β-strand	263-270	8	5
α-helix	274	1
β-strand	275	1	5
α-helix	276-277	2
β-strand	278-288	11	6
β-strand	291-304	14	6
β-strand	306	1	5
β-strand	309-313	5	5
α-helix	316-325	10
β-strand	337-346	10	6
β-strand	352-363	12	6
β-strand	367-370	4	7
β-strand	384-392	9	7
β-strand	396-397	2	7
β-strand	402-410	9	8
β-strand	418-424	7	8
β-strand	426	1	7
β-strand	430-435	6	7
β-strand	443-450	8	8
β-strand	456-463	8	8
α-helix	464-466	3
β-strand	472-476	5	9
α-helix	482-484	3
β-strand	488-496	9	9
β-strand	504-511	8	10
β-strand	514-522	9	10
β-strand	527-532	6	9
β-strand	540-549	10	10
β-strand	552-561	10	10
β-strand	571-579	9	11
β-strand	585-593	9	11
β-strand	597-605	9	12
α-helix	607-610	4
α-helix	617-619	3
α-helix	621-628	8
α-helix	629-631	3
α-helix	643-650	8
β-strand	652-655	4	1
α-helix	662-664	3

Chain B: 28 helices, 37 β-strands

Element	Residues	Length	Sheet
α-helix	699-707	9
α-helix	716-719	4
α-helix	726-737	12
α-helix	738-742	5
β-strand	786-789	4	12
β-strand	792-799	8	11
β-strand	806-814	9	12
β-strand	818-821	4	12
α-helix	822-824	3
β-strand	825-827	3	12
β-strand	833-836	4	13
β-strand	843-844	2	14
β-strand	848-851	4	15
α-helix	853	1
β-strand	854-857	4	13
β-strand	863-869	7	16
β-strand	875-876	2	17
α-helix	878-881	4
β-strand	884-889	6	16
β-strand	893-896	4	13
β-strand	899-901	3	15
β-strand	902-903	2	17
β-strand	908-917	10	16
β-strand	924-932	9	16
β-strand	933-934	2	14
β-strand	938-948	11	18
α-helix	953-955	3
β-strand	957-960	4	19
α-helix	961-963	3
β-strand	968	1	18
β-strand	975-981	7	18
α-helix	984-989	6
α-helix	999-1003	5
α-helix	1012-1017	6
α-helix	1019-1031	13
α-helix	1040-1057	18
β-strand	1060	1	20
β-strand	1066	1	20
β-strand	1067	1	21
α-helix	1072-1073	2
β-strand	1074	1	21
α-helix	1076-1088	13
α-helix	1089-1091	3
α-helix	1097-1108	12
β-strand	1111	1	22
β-strand	1117	1	22
α-helix	1133-1153	21
α-helix	1162-1185	24
α-helix	1190-1202	13
α-helix	1207-1218	12
β-strand	1222-1224	3	23
β-strand	1227-1229	3	23
β-strand	1254	1	18
α-helix	1255-1258	4
α-helix	1259-1275	17
α-helix	1279-1290	12
α-helix	1302-1318	17
β-strand	1326-1335	10	19
β-strand	1338-1347	10	19
α-helix	1354-1356	3
β-strand	1358-1361	4	18
β-strand	1366-1372	7	19
β-strand	1376-1386	11	18
β-strand	1397-1403	7	24
α-helix	1406-1413	8

Chain C: 10 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	1465-1474	10	24
β-strand	1484-1489	6	25
α-helix	1490-1491	2
β-strand	1494-1496	3	24
α-helix	1498-1506	9
β-strand	1514-1518	5	25
β-strand	1521-1526	6	25
β-strand	1534-1542	9	24
β-strand	1546-1547	2	15
α-helix	1549-1551	3
β-strand	1552-1558	7	25
β-strand	1565-1570	6	25
α-helix	1572-1573	2
α-helix	1585-1591	7
β-strand	1597-1599	3	26
α-helix	1612-1618	7
β-strand	1626-1637	12	26
β-strand	1640-1652	13	26
β-strand	1664-1670	7	26
α-helix	1677-1678	2
β-strand	1682-1686	5	26
β-strand	1693	1	27
β-strand	1699	1	27
β-strand	1700-1702	3	26
β-strand	1708-1711	4	26
α-helix	1712-1714	3
α-helix	1715-1719	5
α-helix	1724-1739	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Complement C4-A	A	protein	656	Homo sapiens	P0C0L4 (AlphaFold model)
Complement C4-A	B	protein	767	Homo sapiens	P0C0L4 (AlphaFold model)
Complement C4-A	C	protein	290	Homo sapiens	P0C0L4 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5JPN_1 Complement C4-A (chains A)
KPRLLLFSPSVVHLGVPLSVGVQLQDVPRGQVVKGSVFLRNPSRNNVPCSPKVDFTLSSE
RDFALLSLQVPLKDAKSCGLHQLLRGPEVQLVAHSPWLKDSLSRTTNIQGINLLFSSRRG
HLFLQTDQPIYNPGQRVRYRVFALDQKMRPSTDTITVMVENSHGLRVRKKEVYMPSSIFQ
DDFVIPDISEPGTWKISARFSDGLESNSSTQFEVKKYVLPNFEVKITPGKPYILTVPGHL
DEMQLDIQARYIYGKPVQGVAYVRFGLLDEDGKKTFFRGLESQTKLVNGQSHISLSKAEF
QDALEKLNMGITDLQGLRLYVAAAIIESPGGEMEEAELTSWYFVSSPFSLDLSKTKRHLV
PGAPFLLQALVREMSGSPASGIPVKVSATVSSPGSVPEVQDIQQNTDGSGQVSIPIIIPQ
TISELQLSVSAGSPHPAIARLTVAAPPSGGPGFLSIERPDSRPPRVGDTLNLNLRAVGSG
ATFSHYYYMILSRGQIVFMNREPKRTLTSVSVFVDHHLAPSFYFVAFYYHGDHPVANSLR
VDVQAGACEGKLELSVDGAKQYRNGESVKLHLETDSLALVALGALDTALYAAGSKSHKPL
NMGKVFEAMNSYDLGCGPGGGDSALQVFQAAGLAFSDGDQWTLSRKRLSCPKEKTT

Sequence of entity 2 (B), FASTA

>5JPN_2 Complement C4-A (chains B)
NVNFQKAINEKLGQYASPTAKRCCQDGVTRLPMMRSCEQRAARVQQPDCREPFLSCCQFA
ESLRKKSRDKGQAGLQRALEILQEEDLIDEDDIPVRSFFPENWLWRVETVDRFQILTLWL
PDSLTTWEIHGLSLSKTKGLCVATPVQLRVFREFHLHLRLPMSVRRFEQLELRPVLYNYL
DKNLTVSVHVSPVEGLCLAGGGGLAQQVLVPAGSARPVAFSVVPTAAAAVSLKVVARGSF
EFPVGDAVSKVLQIEKEGAIHREELVYELNPLDHRGRTLEIPGNSDPNMIPDGDFNSYVR
VTASDPLDTLGSEGALSPGGVASLLRLPRGCGEQTMIYLAPTLAASRYLDKTEQWSTLPP
ETKDHAVDLIQKGYMRIQQFRKADGSYAAWLSRDSSTWLTAFVLKVLSLAQEQVGGSPEK
LQETSNWLLSQQQADGSFQDPCPVLDRSMQGGLVGNDETVALTAFVTIALHHGLAVFQDE
GAEPLKQRVEASISKANSFLGEKASAGLLGAHAAAITAYALSLTKAPVDLLGVAHNNLMA
MAQETGDNLYWGSVTGSQSNAVSPTPAPRNPSDPMPQAPALWIETTAYALLHLLLHEGKA
EMADQASAWLTRQGSFQGGFRSTQDTVIALDALSAYWIASHTTEERGLNVTLSSTGRNGF
KSHALQLNNRQIRGLEEELQFSLGSKINVKVGGNSKGTLKVLRTYNVLDMKNTTCQDLQI
EVTVKGHVEYTMEANEDYEDYEYDELPAKDDPDAPLQPVTPLQLFEG

Sequence of entity 3 (C), FASTA

>5JPN_3 Complement C4-A (chains C)
APKVVEEQESRVHYTVCIWRNGKVGLSGMAIADVTLLSGFHALRADLEKLTSLSDRYVSH
FETEGPHVLLYFDSVPTSRECVGFEAVQEVPVGLVQPASATLYDYYNPERRCSVFYGAPS
KSRLLATLCSAEVCQCAEGKCPRQRRALERGLQDEDGYRMKFACYYPRVEYGFQVKVLRE
DSRAAFRLFETKITQVLHFTKDVKAAANQMRNFLVRASCRLRLEPGKEYLIMGLDGATYD
LEGHPQYLLDSNSWIEEMPSERLCRSTRQRAACAQLNDFLQEYGTQGCQV

Ligands and cofactors

ID	Name	Formula	Copies
PBM	Trimethyl lead ion	C3 H9 Pb	4
A2G	2-acetamido-2-deoxy-alpha-D-galactopyranose	C8 H15 N O6	1

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…
5JPM 3.75 Å, Structure of the complex of human complement C4 with MASP-2 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

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