5JTW: Complement C4b re-refined using iMDFF

Crystal structure of complement C4b re-refined using iMDFF. Determined by X-ray diffraction at 3.5 Å resolution. Released 10 Aug 2016.

Method: X-ray diffraction
Resolution: 3.5 Å
Organism: Homo sapiens
Chains: 6
Atoms: 24,312
Mol. weight: 361.66 kDa
Ligands: NAG
Released: 10 Aug 2016

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

Secondary structure: helices and β-sheets

5JTW contains 100 α-helices and 209 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: 23 helices, 52 β-strands

Element	Residues	Length	Sheet
β-strand	22-28	7	1
β-strand	30-32	3	2
α-helix	36	1
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	91-97	7
α-helix	99-101	3
β-strand	107-113	7	2
α-helix	116	1
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
β-strand	197-203	7	3
α-helix	208-209	2
β-strand	211-219	9	4
β-strand	228-233	6	4
β-strand	241-247	7	5
β-strand	251-253	3	6
α-helix	260-261	2
β-strand	262-270	9	5
α-helix	274	1
β-strand	275	1	5
α-helix	276	1
β-strand	278-287	10	6
β-strand	293-295	3	6
β-strand	301-304	4	6
β-strand	306	1	5
β-strand	309-314	6	5
α-helix	316-325	10
α-helix	330-332	3
β-strand	337-346	10	6
β-strand	352-357	6	6
β-strand	361-363	3	6
β-strand	367-370	4	7
α-helix	375	1
β-strand	383-392	10	7
β-strand	397	1	7
α-helix	398	1
β-strand	402-409	8	8
α-helix	415-416	2
β-strand	417-424	8	8
β-strand	427	1	7
β-strand	430-436	7	7
α-helix	437-438	2
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	487	1
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	571-575	5	11
β-strand	581	1	12
α-helix	582	1
β-strand	586-605	20	11
α-helix	607-611	5
α-helix	621-628	8
α-helix	629-631	3
α-helix	643-650	8
β-strand	652-655	4	1
β-strand	660	1	1
α-helix	662-664	3

Chain B: 21 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	766	1	13
β-strand	774-775	2	14
β-strand	781-782	2	11
β-strand	786-798	13	11
β-strand	805-814	10	11
β-strand	818-821	4	11
α-helix	822-824	3
β-strand	825-828	4	11
β-strand	829	1	12
β-strand	833-836	4	15
β-strand	843-844	2	16
β-strand	849-851	3	17
β-strand	854-857	4	15
β-strand	863-869	7	14
α-helix	870-871	2
β-strand	875-877	3	17
α-helix	878-880	3
β-strand	885-889	5	14
β-strand	893-896	4	15
β-strand	899-903	5	17
β-strand	908-917	10	14
β-strand	918	1	13
β-strand	924-932	9	14
β-strand	933-934	2	16
α-helix	935	1
β-strand	938-948	11	4
β-strand	957-961	5	18
β-strand	968	1	4
β-strand	974-982	9	4
α-helix	1000-1002	3
α-helix	1011-1031	21
α-helix	1034-1036	3
α-helix	1041-1056	16
α-helix	1057-1059	3
β-strand	1060-1061	2	19
β-strand	1065-1066	2	19
α-helix	1073-1075	3
α-helix	1076-1092	17
α-helix	1097-1108	12
β-strand	1111	1	20
β-strand	1117	1	20
α-helix	1126-1129	4
α-helix	1137-1153	17
α-helix	1158-1185	28
α-helix	1190-1202	13
α-helix	1207-1220	14
α-helix	1259-1275	17
α-helix	1280-1293	14
α-helix	1295-1297	3
α-helix	1303-1321	19
β-strand	1327-1335	9	18
β-strand	1338-1345	8	18
β-strand	1356-1359	4	4
β-strand	1365-1372	8	18
β-strand	1376-1386	11	4
β-strand	1397-1405	9	21
β-strand	1409	1	22

Chain C: 6 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	1465-1474	10	21
β-strand	1484-1489	6	23
β-strand	1494-1496	3	21
α-helix	1498-1506	9
β-strand	1512-1518	7	23
β-strand	1521-1526	6	23
β-strand	1534-1542	9	21
β-strand	1546	1	22
β-strand	1552-1558	7	23
β-strand	1565-1570	6	23
β-strand	1581-1584	4	24
β-strand	1587-1590	4	24
α-helix	1613-1618	6
β-strand	1625-1637	13	25
β-strand	1640-1652	13	25
β-strand	1664-1670	7	25
β-strand	1682-1687	6	25
β-strand	1701-1702	2	25
β-strand	1708-1711	4	25
α-helix	1712-1713	2
α-helix	1716-1719	4
α-helix	1721-1723	3
α-helix	1726-1740	15

Chain D: 20 helices, 50 β-strands

Element	Residues	Length	Sheet
β-strand	22-28	7	26
β-strand	30-32	3	27
α-helix	36	1
β-strand	37-44	8	26
β-strand	52-60	9	27
β-strand	66-67	2	27
β-strand	72-76	5	27
β-strand	82-87	6	26
α-helix	91-96	6
β-strand	107-113	7	27
α-helix	116-119	4
β-strand	127-135	9	27
β-strand	140-145	6	28
β-strand	149-150	2	29
β-strand	155-163	9	28
β-strand	169	1	28
β-strand	174-179	6	29
β-strand	185-191	7	29
β-strand	197-203	7	28
β-strand	211-219	9	29
β-strand	227-233	7	29
β-strand	241-247	7	30
β-strand	252-253	2	31
α-helix	260-261	2
β-strand	262-270	9	30
α-helix	274	1
β-strand	275	1	30
α-helix	276-277	2
β-strand	278-287	10	32
β-strand	293-295	3	32
β-strand	301-304	4	32
β-strand	306	1	30
β-strand	309-314	6	30
α-helix	316-326	11
α-helix	330-332	3
β-strand	337-346	10	32
β-strand	352-357	6	32
α-helix	360	1
β-strand	361	1	32
β-strand	362-363	2	31
β-strand	367-370	4	33
α-helix	378-379	2
β-strand	384-392	9	33
α-helix	396	1
β-strand	397	1	33
α-helix	398	1
β-strand	402-411	10	34
β-strand	414-424	11	34
β-strand	430-435	6	33
β-strand	443-450	8	34
β-strand	456-463	8	34
α-helix	464-465	2
β-strand	472-476	5	35
α-helix	483-484	2
β-strand	488-496	9	35
β-strand	504-511	8	36
β-strand	514-522	9	36
β-strand	527-532	6	35
α-helix	535-537	3
β-strand	540-549	10	36
β-strand	552-561	10	36
β-strand	571-575	5	37
β-strand	586-605	20	37
α-helix	607-611	5
α-helix	621-628	8
α-helix	629-631	3
α-helix	643-650	8
β-strand	652-655	4	26
β-strand	660	1	26
α-helix	661-664	4

Chain E: 22 helices, 35 β-strands

Element	Residues	Length	Sheet
α-helix	773	1
β-strand	774-775	2	38
β-strand	781	1	37
β-strand	786-798	13	37
β-strand	805-814	10	37
β-strand	818-821	4	37
α-helix	822-824	3
β-strand	825-828	4	37
β-strand	833-836	4	39
β-strand	843-844	2	40
β-strand	849-851	3	41
β-strand	854-857	4	39
β-strand	863-869	7	38
α-helix	870-871	2
β-strand	875-877	3	41
β-strand	885-889	5	38
β-strand	893-896	4	39
β-strand	899-903	5	41
β-strand	908-917	10	38
β-strand	924-932	9	38
β-strand	933-934	2	40
α-helix	935	1
β-strand	938-948	11	29
β-strand	959-961	3	42
β-strand	968	1	29
β-strand	974-982	9	29
α-helix	994-996	3
α-helix	997-1001	5
α-helix	1006-1008	3
α-helix	1011-1031	21
α-helix	1034-1036	3
α-helix	1040-1057	18
β-strand	1060-1061	2	43
β-strand	1065-1066	2	43
α-helix	1073-1074	2
α-helix	1076-1092	17
α-helix	1097-1108	12
β-strand	1111	1	44
β-strand	1117	1	44
α-helix	1126-1129	4
α-helix	1137-1155	19
α-helix	1162-1185	24
α-helix	1190-1202	13
α-helix	1207-1218	12
β-strand	1223-1224	2	45
β-strand	1228-1229	2	45
α-helix	1259-1275	17
α-helix	1280-1294	15
α-helix	1302-1320	19
β-strand	1327-1334	8	42
β-strand	1340-1346	7	42
α-helix	1348-1351	4
β-strand	1355-1360	6	29
β-strand	1365-1370	6	42
β-strand	1376-1386	11	29
β-strand	1397-1405	9	46
β-strand	1409	1	47

Chain F: 8 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	1465-1474	10	46
β-strand	1484-1489	6	48
β-strand	1494-1496	3	46
α-helix	1498-1505	8
β-strand	1514-1518	5	48
β-strand	1521-1526	6	48
β-strand	1535-1542	8	46
β-strand	1546	1	47
β-strand	1552-1558	7	48
β-strand	1561-1570	10	48
β-strand	1581-1584	4	49
β-strand	1587-1590	4	49
α-helix	1595-1598	4
α-helix	1612-1618	7
α-helix	1622-1623	2
β-strand	1625-1637	13	50
β-strand	1640-1652	13	50
β-strand	1664-1670	7	50
β-strand	1682-1687	6	50
β-strand	1693	1	51
β-strand	1699	1	51
α-helix	1700	1
β-strand	1701-1702	2	50
β-strand	1708-1711	4	50
α-helix	1712-1713	2
α-helix	1715-1717	3
α-helix	1726-1740	15

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	690	Homo sapiens	P0C0L4 (AlphaFold model)
Complement C4-A	C, F	protein	291	Homo sapiens	P0C0L4 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>5JTW_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

>5JTW_2 Complement C4-A (chains B, E)
ALEILQEEDLIDEDDIPVRSFFPENWLWRVETVDRFQILTLWLPDSLTTWEIHGLSLSKT
KGLCVATPVQLRVFREFHLHLRLPMSVRRFEQLELRPVLYNYLDKNLTVSVHVSPVEGLC
LAGGGGLAQQVLVPAGSARPVAFSVVPTAAAAVSLKVVARGSFEFPVGDAVSKVLQIEKE
GAIHREELVYELNPLDHRGRTLEIPGNSDPNMIPDGDFNSYVRVTASDPLDTLGSEGALS
PGGVASLLRLPRGCGEQTMIYLAPTLAASRYLDKTEQWSTLPPETKDHAVDLIQKGYMRI
QQFRKADGSYAAWLSRDSSTWLTAFVLKVLSLAQEQVGGSPEKLQETSNWLLSQQQADGS
FQDPCPVLDRSMQGGLVGNDETVALTAFVTIALHHGLAVFQDEGAEPLKQRVEASISKAN
SFLGEKASAGLLGAHAAAITAYALSLTKAPVDLLGVAHNNLMAMAQETGDNLYWGSVTGS
QSNAVSPTPAPRNPSDPMPQAPALWIETTAYALLHLLLHEGKAEMADQASAWLTRQGSFQ
GGFRSTQDTVIALDALSAYWIASHTTEERGLNVTLSSTGRNGFKSHALQLNNRQIRGLEE
ELQFSLGSKINVKVGGNSKGTLKVLRTYNVLDMKNTTCQDLQIEVTVKGHVEYTMEANED
YEDYEYDELPAKDDPDAPLQPVTPLQLFEG

Sequence of entity 3 (C, F), FASTA

>5JTW_3 Complement C4-A (chains C, F)
EAPKVVEEQESRVHYTVCIWRNGKVGLSGMAIADVTLLSGFHALRADLEKLTSLSDRYVS
HFETEGPHVLLYFDSVPTSRECVGFEAVQEVPVGLVQPASATLYDYYNPERRCSVFYGAP
SKSRLLATLCSAEVCQCAEGKCPRQRRALERGLQDEDGYRMKFACYYPRVEYGFQVKVLR
EDSRAAFRLFETKITQVLHFTKDVKAAANQMRNFLVRASCRLRLEPGKEYLIMGLDGATY
DLEGHPQYLLDSNSWIEEMPSERLCRSTRQRAACAQLNDFLQEYGTQGCQV

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	4

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
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
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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